Mercurial > repos > jbrayet > annotatepeaks
changeset 21:6f794643f7cd draft default tip
planemo upload
| author | oinizan |
|---|---|
| date | Wed, 25 May 2016 09:43:12 -0400 |
| parents | f4c30d97d804 |
| children | |
| files | annotatePeaks_wrapper.xml test-data/Probesets_FC1.5_10022011.txt test-data/annotatePeaks_wrapper.xml test-data/peaks_control.bed test-data/peaks_test.bed test-data/test_annotatePeaks_1.dat test-data/test_annotatePeaks_2.dat test-data/test_annotatePeaks_3.dat test-data/test_annotatePeaks_4.dat |
| diffstat | 9 files changed, 17284 insertions(+), 2 deletions(-) [+] |
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--- a/annotatePeaks_wrapper.xml Mon Sep 28 11:05:52 2015 -0400 +++ b/annotatePeaks_wrapper.xml Wed May 25 09:43:12 2016 -0400 @@ -122,8 +122,8 @@ <param name="version" value="mm9"/> <param name="use_reg_selector" value="yes"/> <param name="regfile" value="Probesets_FC1.5_10022011.txt"/> - <param name="if_PDF" value="1"/> - <output name="outputPDF" file="test_annotatePeaks_1.dat" ftype="pdf"/> + <param name="if_PDF" value="0"/> + <output name="outputPNG" file="test_annotatePeaks_1.dat" ftype="png"/> <output name="stats" file="test_annotatePeaks_2.dat" ftype="tabular"/> <output name="log" file="test_annotatePeaks_3.dat" ftype="log"/> <output name="statsControl" file="test_annotatePeaks_4.dat" ftype="tabular"/>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Probesets_FC1.5_10022011.txt Wed May 25 09:43:12 2016 -0400 @@ -0,0 +1,16142 @@ + gene Fold.Change pvalue.adjust FC=1.5 +A 0610010O12Rik 2.54 down-regulated down-regulated 474 +A 0910001A06Rik 0.556666667 up-regulated no-response 14871 +A 1110002B05Rik 0.51 up-regulated up-regulated 796 +A 1110003E01Rik 1.575 down-regulated +A 1110006G14Rik 1.68 down-regulated +A 1110007A13Rik 0.66 up-regulated +A 1110013L07Rik 0.26 up-regulated +A 1110031I02Rik 1.73 down-regulated +A 1110032A03Rik 0.42 up-regulated +A 1110032E23Rik 0.18 up-regulated +A 1110054O05Rik 0.63 up-regulated +A 1110059E24Rik 0.47 up-regulated +A 1110067D22Rik 1.81 down-regulated +A 1190002F15Rik 1.88 down-regulated +A 1190002N15Rik 1.69 down-regulated +A 1200016E24Rik 0.6375 up-regulated +A 1300002E11Rik 1.99 down-regulated +A 1600012F09Rik 1.88 down-regulated +A 1600014C10Rik 0.66 up-regulated +A 1700019H03Rik 0.46 up-regulated +A 1700020I14Rik 1.94 down-regulated +A 1700065O13Rik 2.33 down-regulated +A 1700097N02Rik 0.31 up-regulated +A 1810007M14Rik 0.67 up-regulated +A 1810007P19Rik 1.78 down-regulated +A 1810014F10Rik 1.77 down-regulated +A 1810034K20Rik 1.89 down-regulated +A 1810063B05Rik 1.54 down-regulated +A 2010002N04Rik 0.43 up-regulated +A 2010004M13Rik 0.51 up-regulated +A 2010011I20Rik 2.026666667 down-regulated +A 2010305C02Rik 1.92 down-regulated +A 2210010N04Rik 0.61 up-regulated +A 2210020M01Rik 0.54 up-regulated +A 2210408K08Rik 1.5 down-regulated +A 2310002J21Rik 1.51 down-regulated +A 2310005E10Rik 0.485 up-regulated +A 2310007F21Rik 0.64 up-regulated +A 2310008H04Rik 1.62 down-regulated +A 2310010J17Rik 1.86 down-regulated +A 2310015A05Rik 1.53 down-regulated +A 2310022B05Rik 2.58 down-regulated +A 2310022M17Rik 1.57 down-regulated +A 2310040C09Rik 1.57 down-regulated +A 2310061C15Rik 0.67 up-regulated +A 2310066E14Rik 0.62 up-regulated +A 2410014A08Rik 0.59 up-regulated +A 2410187C16Rik 0.31 up-regulated +A 2610020H08Rik 1.595 down-regulated +A 2610030H06Rik 0.45 up-regulated +A 2610201A13Rik 0.37 up-regulated +A 2610207I05Rik 1.69 down-regulated +A 2610528G24Rik 1.8 down-regulated +A 2810001G20Rik 1.53 down-regulated +A 2810002O09Rik 0.625 up-regulated +A 2810013P06Rik 0.515 up-regulated +A 2810021B07Rik 0.57 up-regulated +A 2810432L12Rik 1.9 down-regulated +A 2810482I07Rik 0.5 up-regulated +A 2900006A08Rik 0.63 up-regulated +A 2900006K08Rik 1.93 down-regulated +A 2900034E22Rik 0.58 up-regulated +A 3110003A17Rik 0.67 up-regulated +A 3110003A22Rik 1.63 down-regulated +A 3110043O21Rik 2.45 down-regulated +A 3200002M19Rik 0.6 up-regulated +A 3830406C13Rik 0.66 up-regulated +A 3830612M24 0.23 up-regulated +A 3930401K13Rik 0.44 up-regulated +A 4432416J03Rik 4.56 down-regulated +A 4632404H22Rik 0.45 up-regulated +A 4732418C07Rik 0.595 up-regulated +A 4833428C12Rik 0.46 up-regulated +A 4922501C03Rik 1.87 down-regulated +A 4922503N01Rik 3.06 down-regulated +A 4930414L22Rik 1.68 down-regulated +A 4930420K17Rik 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up-regulated +A 9630025I21Rik 0.67 up-regulated +A A030001D16Rik 0.3 up-regulated +A A030009H04Rik 0.67 up-regulated +A A230067G21Rik 0.58 up-regulated +A A430107D22Rik 0.265 up-regulated +A A730089K16Rik 0.56 up-regulated +A A930026I22Rik 0.43 up-regulated +A A930037G23Rik 0.36 up-regulated +A AB124611 0.14 up-regulated +A Abca1 0.45 up-regulated +A Abcb10 1.54 down-regulated +A Abcc1 0.265 up-regulated +A Abcd1 0.65 up-regulated +A Abcg4 3.445 down-regulated +A Abhd10 1.58 down-regulated +A Abhd13 0.645 up-regulated +A Abhd5 1.54 down-regulated +A Abhd8 1.52 down-regulated +A Acadl 1.54 down-regulated +A Acbd5 0.56 up-regulated +A Acot1 2.71 down-regulated +A Acot2 2.493333333 down-regulated +A Acot7 0.63 up-regulated +A Acp5 1.83 down-regulated +A Acsl4 1.88 down-regulated +A Acss1 1.54 down-regulated +A Acvr1b 0.13 up-regulated +A Acyp2 1.5 down-regulated +A Adam9 0.16 up-regulated +A Adcy7 0.546666667 up-regulated +A Adcy9 2.485 down-regulated +A Add2 3.196666667 down-regulated +A Adh5 0.45 up-regulated +A Adipor1 0.66 up-regulated +A Adm2 1.59 down-regulated +A Aff3 0.29 up-regulated +A Agpat3 1.83 down-regulated +A Agpat5 0.535 up-regulated +A Ahcyl2 0.53 up-regulated +A Ahi1 2.355 down-regulated +A AI413582 0.65 up-regulated +A AI452195 0.66 up-regulated +A Ak3l1 0.49 up-regulated +A Akt3 1.74 down-regulated +A Aktip 0.47 up-regulated +A Aldh1l2 2.13 down-regulated +A Aldh3a2 0.61 up-regulated +A Aldh4a1 0.55 up-regulated +A Aldoc 0.25 up-regulated +A Alox5 0.43 up-regulated +A Alox5ap 0.11 up-regulated +A Als2cr2 1.72 down-regulated +A Angpt1 0.14 up-regulated +A Angptl6 1.65 down-regulated +A Ank1 1.65 down-regulated +A Ankra2 0.43 up-regulated +A Ankrd10 0.65 up-regulated +A Ankrd12 0.55 up-regulated +A Ankrd28 0.63 up-regulated +A Ankrd43 1.87 down-regulated +A Anp32a 0.65 up-regulated +A Anxa2 0.1 up-regulated +A Anxa5 0.51 up-regulated +A Anxa7 0.67 up-regulated +A Ap1g1 0.6 up-regulated +A Ap1s2 0.37 up-regulated +A Apaf1 0.655 up-regulated +A Apc 1.543333333 down-regulated +A Aph1a 0.65 up-regulated +A Aqp1 3.48 down-regulated +A Aqp9 0.58 up-regulated +A Arhgap12 0.45 up-regulated +A Arhgap19 1.88 down-regulated +A Arhgap29 2.26 down-regulated +A Arhgap30 0.405 up-regulated +A Arhgap9 0.61 up-regulated +A Arhgdib 0.55 up-regulated +A Arhgdig 3.71 down-regulated +A Arhgef1 0.64 up-regulated +A Arhgef2 0.53 up-regulated +A Arl2 0.67 up-regulated +A Arl6 1.56 down-regulated +A Arl6ip1 0.635 up-regulated +A Arl8a 0.6 up-regulated +A Armc3 0.5 up-regulated +A Armc8 0.55 up-regulated +A Armc9 1.755 down-regulated +A Arnt 1.63 down-regulated +A Arpc1b 0.275 up-regulated +A Arpc4 0.565 up-regulated +A Arpp19 0.06 up-regulated +A Arrb2 0.42 up-regulated +A Arrdc3 1.66 down-regulated +A Art4 1.65 down-regulated +A Ash2l 0.52 up-regulated +A Asrgl1 1.54 down-regulated +A Atf2 0.41 up-regulated +A Atf5 1.57 down-regulated +A Atp10d 0.63 up-regulated +A Atp13a2 0.46 up-regulated +A Atp1b2 0.63 up-regulated +A Atp2a3 0.51 up-regulated +A Atp2c1 0.67 up-regulated +A Atp6v0a1 0.615 up-regulated +A Atp6v0d1 0.33 up-regulated +A Atp7a 0.65 up-regulated +A Atp8a1 0.51 up-regulated +A Avil 10.12 down-regulated +A B230112C05Rik 1.81 down-regulated +A B230217C12Rik 0.32 up-regulated +A B4galnt1 0.6 up-regulated +A B4galt3 1.54 down-regulated +A B630005N14Rik 0.65 up-regulated +A B9d1 1.63 down-regulated +A Bard1 2.23 down-regulated +A BB125219 1.72 down-regulated +A Bbs5 1.69 down-regulated +A BC004728 0.13 up-regulated +A BC005537 0.475 up-regulated +A BC010981 0.6 up-regulated +A BC013712 0.61 up-regulated +A BC021614 3.46 down-regulated +A BC022687 1.54 down-regulated +A BC023202 0.58 up-regulated +A BC023892 0.34 up-regulated +A BC025546 0.64 up-regulated +A BC028528 0.16 up-regulated +A BC037034 0.65 up-regulated +A BC046331 1.64 down-regulated +A BC063749 0.63 up-regulated +A BC072620 1.55 down-regulated +A Bcdin3d 1.75 down-regulated +A Bckdhb 0.62 up-regulated +A Bcl2l1 0.653333333 up-regulated +A Bcl2l11 3.476 down-regulated +A Bcl7a 1.57 down-regulated +A Bcl7c 1.58 down-regulated +A Bclaf1 0.44 up-regulated +A Bhlhb2 0.26 up-regulated +A Bin1 0.64 up-regulated +A Birc3 0.62 up-regulated +A Bmpr2 0.35 up-regulated +A Bnip2 0.4125 up-regulated +A Bpgm 1.555 down-regulated +A Braf 1.69 down-regulated +A Brd8 1.505 down-regulated +A Bri3bp 0.523333333 up-regulated +A Brwd1 0.426666667 up-regulated +A Brwd2 0.62 up-regulated +A Brwd3 0.51 up-regulated +A Btbd7 0.46 up-regulated +A Btk 0.58 up-regulated +A Butr1 4.19 down-regulated +A Bzrpl1 1.89 down-regulated +A C130071C03Rik 2.27 down-regulated +A C1d 0.47 up-regulated +A C1qtnf4 2.19 down-regulated +A C330006P03Rik 0.45 up-regulated +A C87436 0.65 up-regulated +A Cab39l 0.65 up-regulated +A Calm1 0.63 up-regulated +A Camsap1l1 2.145 down-regulated +A Canx 0.67 up-regulated +A Cap1 0.635 up-regulated +A Capg 0.16 up-regulated +A Caprin2 1.69 down-regulated +A Car13 1.53 down-regulated +A Carhsp1 1.985 down-regulated +A Casp2 1.53 down-regulated +A Casp3 0.46 up-regulated +A Casp6 0.46 up-regulated +A Cast 0.51 up-regulated +A Cat 0.215 up-regulated +A Cbfa2t3 0.53 up-regulated +A Cbfb 0.41 up-regulated +A Cbl 0.403333333 up-regulated +A Ccbl2 0.43 up-regulated +A Ccdc123 1.605 down-regulated +A Ccdc28b 0.605 up-regulated +A Ccdc34 1.53 down-regulated +A Ccdc88b 0.04 up-regulated +A Ccdc88c 1.53 down-regulated +A Ccne1 1.75 down-regulated +A Ccng2 0.54 up-regulated +A Ccnh 0.39 up-regulated +A Ccny 1.55 down-regulated +A Ccnyl1 1.69 down-regulated +A Cct4 0.54 up-regulated +A Cd200r1 0.595 up-regulated +A Cd274 0.33 up-regulated +A Cd37 0.415 up-regulated +A Cd48 0.05 up-regulated +A Cd84 0.45 up-regulated +A Cd99l2 1.52 down-regulated +A Cdc14a 0.49 up-regulated +A Cdc25b 1.99 down-regulated +A Cdc42 0.65 up-regulated +A Cdc42bpa 1.63 down-regulated +A Cdc42ep4 1.68 down-regulated +A Cdc42se2 0.61 up-regulated +A Cdc6 1.54 down-regulated +A Cdkn2b 0.49 up-regulated +A Cdkn2c 1.59 down-regulated +A Cdr2 1.98 down-regulated +A Cebpg 1.555 down-regulated +A Cenpk 1.58 down-regulated +A Centb1 0.265 up-regulated +A Centd3 0.67 up-regulated +A Centg2 1.89 down-regulated +A Cep250 0.64 up-regulated +A Cep290 1.5 down-regulated +A Cep55 0.285 up-regulated +A Cep72 1.86 down-regulated +A Cfl2 1.51 down-regulated +A Cflar 0.41 up-regulated +A Chac2 2.02 down-regulated +A Chfr 0.54 up-regulated +A Chst10 3.09 down-regulated +A Chst11 0.52 up-regulated +A Chst12 0.65 up-regulated +A Chsy1 1.78 down-regulated +A Cish 0.67 up-regulated +A Cited2 0.34 up-regulated +A Cited4 2.4 down-regulated +A Clcn2 3.59 down-regulated +A Cldn13 2.08 down-regulated +A Cldnd1 0.575 up-regulated +A Clec4d 0.12 up-regulated +A Clic1 0.67 up-regulated +A Clip1 1.606666667 down-regulated +A Cln3 0.64 up-regulated +A Cln8 1.905 down-regulated +A Cmtm3 0.22 up-regulated +A Cmtm6 0.6 up-regulated +A Cmtm7 0.285 up-regulated +A Cnih4 0.615 up-regulated +A Cnn2 0.66 up-regulated +A Cnnm1 1.95 down-regulated +A Cnot6l 0.56 up-regulated +A Cnr2 0.49 up-regulated +A Col4a3bp 0.62 up-regulated +A Col5a1 0.55 up-regulated +A Commd8 0.62 up-regulated +A Coro1a 0.273333333 up-regulated +A Coro2a 0.373333333 up-regulated +A Coro7 0.63 up-regulated +A Cotl1 0.46 up-regulated +A Cox6a2 7.17 down-regulated +A Cox6b2 2.19 down-regulated +A Cpne3 0.47 up-regulated +A Cpne9 2.18 down-regulated +A Cpox 1.696666667 down-regulated +A Cpsf6 0.453333333 up-regulated +A Creb1 1.516666667 down-regulated +A Crebzf 0.6 up-regulated +A Crip2 1.9 down-regulated +A Cryl1 0.58 up-regulated +A Csf2rb 0.24 up-regulated +A Csnk2a1 0.62 up-regulated +A Cst7 0.09 up-regulated +A Ctdspl2 0.51 up-regulated +A Cth 2.77 down-regulated +A Ctnnal1 3.57 down-regulated +A Ctps2 0.56 up-regulated +A Ctsa 0.44 up-regulated +A Ctsb 1.52 down-regulated +A Ctso 0.53 up-regulated +A Cugbp2 0.185 up-regulated +A Cul2 0.67 up-regulated +A Cwf19l2 0.61 up-regulated +A Cyb561 0.38 up-regulated +A Cyb561d2 0.64 up-regulated +A Cyba 0.19 up-regulated +A D030022P07Rik 0.56 up-regulated +A D030063E12 0.36 up-regulated +A D10627 1.68 down-regulated +A D16Ertd472e 0.523333333 up-regulated +A D16Wsu65e 2.33 down-regulated +A D17H6S56E-5 0.635 up-regulated +A D19Bwg1357e 0.45 up-regulated +A D2Ertd750e 0.615 up-regulated +A D4Wsu53e 0.61 up-regulated +A D5Ertd579e 1.63 down-regulated +A D6Wsu176e 0.355 up-regulated +A D930028F11Rik 2.32 down-regulated +A D9Ertd402e 1.65 down-regulated +A Daam1 1.72 down-regulated +A Dapp1 0.573333333 up-regulated +A Darc 2.27 down-regulated +A Dbndd2 0.58 up-regulated +A Dcbld2 1.51 down-regulated +A Dclre1a 1.87 down-regulated +A Dclre1b 1.575 down-regulated +A Dcp2 0.64 up-regulated +A Dcxr 0.5 up-regulated +A Ddah2 0.44 up-regulated +A Ddef2 0.62 up-regulated +A Ddhd1 1.64 down-regulated +A Ddx19b 0.6 up-regulated +A Ddx25 0.59 up-regulated +A Ddx46 0.615 up-regulated +A Ddx5 0.63 up-regulated +A Dedd 0.65 up-regulated +A Dennd4b 0.62 up-regulated +A Depdc7 0.67 up-regulated +A Derl2 0.67 up-regulated +A Dgka 0.23 up-regulated +A Dhx32 1.68 down-regulated +A Diap1 0.5375 up-regulated +A Disp1 1.61 down-regulated +A Dkkl1 0.51 up-regulated +A Dmwd 2.67 down-regulated +A Dnajb10 1.51 down-regulated +A Dnajc10 0.545 up-regulated +A Dnajc16 1.52 down-regulated +A Dnase2a 1.66 down-regulated +A Dock10 0.21 up-regulated +A Dok2 0.29 up-regulated +A Dph3 0.63 up-regulated +A Drg1 0.43 up-regulated +A Dsg2 1.61 down-regulated +A Dtl 1.565 down-regulated +A Dtwd2 0.625 up-regulated +A Dusp3 0.313333333 up-regulated +A Dync1li2 0.615 up-regulated +A E130120F12Rik 0.64 up-regulated +A E130303B06Rik 1.61 down-regulated +A E130308A19Rik 1.545 down-regulated +A E230008J23Rik 0.41 up-regulated +A E430016P22Rik 1.56 down-regulated +A Eea1 0.51 up-regulated +A EG433637 0.63 up-regulated +A EG545989 1.64 down-regulated +A EG626571 0.36 up-regulated +A EG627232 0.64 up-regulated +A Ehd4 0.66 up-regulated +A Eif1ay 0.45 up-regulated +A Eif2b2 0.59 up-regulated +A Eif2c1 0.48 up-regulated +A Eif2s1 0.655 up-regulated +A Eif4e 0.67 up-regulated +A Eif4ebp2 0.4 up-regulated +A Eif5b 0.67 up-regulated +A Elf1 0.615 up-regulated +A Emilin2 0.52 up-regulated +A Eml3 2.07 down-regulated +A Eml4 0.51 up-regulated +A Emp3 0.4 up-regulated +A Endod1 1.645 down-regulated +A Enoph1 0.55 up-regulated +A Enpp1 4.77 down-regulated +A Enpp3 1.79 down-regulated +A Enpp5 0.66 up-regulated +A ENSMUSG00000071543 0.67 up-regulated +A Epb4.2 1.99 down-regulated +A Epm2aip1 1.54 down-regulated +A Erbb2ip 0.666666667 up-regulated +A Ero1l 0.605 up-regulated +A Ero1lb 0.66 up-regulated +A Ets1 0.35 up-regulated +A Etv6 0.615 up-regulated +A Evi2a 0.18 up-regulated +A Exoc3 0.54 up-regulated +A Extl2 0.61 up-regulated +A F2r 0.66 up-regulated +A Fads2 2.045 down-regulated +A Fads3 4.836666667 down-regulated +A Fancd2 1.54 down-regulated +A Fanci 1.61 down-regulated +A Fbxw4 1.9 down-regulated +A Fech 1.5 down-regulated +A Fez2 1.6 down-regulated +A Fgd3 0.51 up-regulated +A Fgd6 1.94 down-regulated +A Fgfrl1 2.16 down-regulated +A Fhdc1 4.59 down-regulated +A Fhod1 0.56 up-regulated +A Fig4 0.46 up-regulated +A Fkbp1b 0.53 up-regulated +A Fli1 0.44 up-regulated +A Flot1 0.53 up-regulated +A Fnbp1 0.49 up-regulated +A Foxc1 3.015 down-regulated +A Foxj2 1.85 down-regulated +A Frrs1 0.54 up-regulated +A Fry 0.66 up-regulated +A Fut8 0.58 up-regulated +A G3bp1 0.47 up-regulated +A G6pc3 0.63 up-regulated +A Gab2 0.61 up-regulated +A Gabpa 0.57 up-regulated +A Gabpb1 1.52 down-regulated +A Gadd45a 2.09 down-regulated +A Gadd45b 0.65 up-regulated +A Gadd45gip1 1.65 down-regulated +A Galc 1.59 down-regulated +A Galk1 0.51 up-regulated +A Galk2 0.43 up-regulated +A Galnt4 0.5 up-regulated +A Galnt6 0.465 up-regulated +A Galnt7 0.595 up-regulated +A Garnl4 0.46 up-regulated +A Gas2 1.91 down-regulated +A Gatad2a 0.55 up-regulated +A Gba2 0.67 up-regulated +A Gcat 0.67 up-regulated +A Gcc1 1.56 down-regulated +A Gch1 2.07 down-regulated +A Gcnt2 0.33 up-regulated +A Gfm1 0.57 up-regulated +A Ggps1 0.62 up-regulated +A Gimap9 0.4 up-regulated +A Gins2 1.51 down-regulated +A Git2 0.67 up-regulated +A Glo1 0.67 up-regulated +A Gls2 1.6 down-regulated +A Glud1 0.585 up-regulated +A Gm1964 1.67 down-regulated +A Gmcl1 0.666666667 up-regulated +A Gmip 0.12 up-regulated +A Gmps 0.42 up-regulated +A Gna14 0.285 up-regulated +A Gna15 0.55 up-regulated +A Gnb4 0.46 up-regulated +A Gnpda2 0.645 up-regulated +A Gnpnat1 0.6 up-regulated +A Golm1 0.66 up-regulated +A Gpatch8 0.38 up-regulated +A Gpr155 2.45 down-regulated +A Gpsm3 0.28 up-regulated +A Gpt2 1.595 down-regulated +A Gramd1a 0.63 up-regulated +A Gsdmd 0.48 up-regulated +A Gsn 0.22 up-regulated +A Gspt1 0.486666667 up-regulated +A Gss 1.52 down-regulated +A Gypa 2.92 down-regulated +A Gzf1 1.59 down-regulated +A H13 0.545 up-regulated +A H1f0 0.465 up-regulated +A H2afj 0.66 up-regulated +A H2-DMa 0.44 up-regulated +A H2-T23 0.67 up-regulated +A H47 0.67 up-regulated +A Habp4 1.545 down-regulated +A Hace1 1.55 down-regulated +A Hagh 1.61 down-regulated +A Havcr2 0.14 up-regulated +A Hdac7 0.49 up-regulated +A Hdhd2 0.21 up-regulated +A Hebp1 4.22 down-regulated +A Hemgn 1.75 down-regulated +A Hexa 0.57 up-regulated +A Hexdc 1.53 down-regulated +A Hexim1 0.67 up-regulated +A Hgs 0.56 up-regulated +A Hhex 0.5 up-regulated +A Hipk1 1.6 down-regulated +A Hipk2 1.86 down-regulated +A Hipk3 0.65 up-regulated +A Hivep1 0.45 up-regulated +A Hltf 0.62 up-regulated +A Hmbs 1.56 down-regulated +A Hmga2-ps1 0.26 up-regulated +A Hmx2 1.87 down-regulated +A Hnrpa3 0.65 up-regulated +A Hnrpdl 0.62 up-regulated +A Hook3 0.46 up-regulated +A Hopx 2.63 down-regulated +A Hpcal1 0.42 up-regulated +A Hps1 0.66 up-regulated +A Hrasls3 1.63 down-regulated +A Hs1bp3 0.47 up-regulated +A Hsd17b11 0.49 up-regulated +A Hsd3b7 0.26 up-regulated +A Hspa1b 0.67 up-regulated +A Hspa4 0.625 up-regulated +A Hspb6 2.97 down-regulated +A Icam1 0.34 up-regulated +A Icam2 0.36 up-regulated +A Id1 0.14 up-regulated +A Id2 0.39 up-regulated +A Idh1 0.52 up-regulated +A Idi1 0.435 up-regulated +A Ier3 0.46 up-regulated +A Ifi30 2.81 down-regulated +A Ifi47 0.58 up-regulated +A Ifih1 1.67 down-regulated +A Ift80 1.855 down-regulated +A Ikzf2 0.3 up-regulated +A Ikzf3 0.51 up-regulated +A Il1b 4.49 down-regulated +A Il27ra 0.59 up-regulated +A Impact 0.49 up-regulated +A Ing5 1.61 down-regulated +A Inpp4b 0.31 up-regulated +A Inpp5d 0.54 up-regulated +A Insig2 0.65 up-regulated +A Insl6 0.42 up-regulated +A Ipmk 1.603333333 down-regulated +A Ipo11 0.26 up-regulated +A Ipo13 0.67 up-regulated +A Iqcb1 1.69 down-regulated +A Iqgap1 0.41 up-regulated +A Irak1 0.575 up-regulated +A Irak1bp1 2 down-regulated +A Irak2 2.41 down-regulated +A Irak4 0.58 up-regulated +A Irf5 0.45 up-regulated +A Itfg1 0.6 up-regulated +A Itga6 0.415 up-regulated +A Itgal 0.29 up-regulated +A Itgb1 1.5 down-regulated +A Itgb2 0.21 up-regulated +A Itpr1 0.63 up-regulated +A Itsn1 0.64 up-regulated +A Ivns1abp 1.56 down-regulated +A Jhdm1d 1.713333333 down-regulated +A Jmy 1.525 down-regulated +A Kalrn 0.57 up-regulated +A Kcnk6 0.06 up-regulated +A Kctd10 0.64 up-regulated +A Kctd6 1.58 down-regulated +A Kel 2.33 down-regulated +A Khk 0.4 up-regulated +A Kif1c 1.92 down-regulated +A Kif3a 1.525 down-regulated +A Kifap3 0.65 up-regulated +A Klf10 2.12 down-regulated +A Klf5 2 down-regulated +A Klf7 0.59 up-regulated +A Klhdc2 1.55 down-regulated +A Klhl2 0.47 up-regulated +A Klhl6 0.27 up-regulated +A Klhl7 1.56 down-regulated +A Lactb 0.62 up-regulated +A Lair1 0.39 up-regulated +A Lama5 1.74 down-regulated +A Larp2 1.53 down-regulated +A Larp4 0.543333333 up-regulated +A Lasp1 0.445 up-regulated +A Lats1 0.645 up-regulated +A Lcp1 0.225 up-regulated +A Lcp2 0.04 up-regulated +A Ldlrap1 0.61 up-regulated +A Lfng 0.64 up-regulated +A Lgals1 0.125 up-regulated +A Lgtn 1.51 down-regulated +A Limd2 0.11 up-regulated +A Lims1 0.635 up-regulated +A Lin7c 1.56 down-regulated +A Lin9 1.51 down-regulated +A Lipa 0.41 up-regulated +A Lipt1 1.55 down-regulated +A LOC632329 0.12 up-regulated +A LOC641050 0.31 up-regulated +A LOC677213 0.27 up-regulated +A Loh11cr2a 0.42 up-regulated +A Lpcat1 1.995 down-regulated +A Lpcat2 0.1 up-regulated +A Lrch1 1.92 down-regulated +A Lrch4 0.63 up-regulated +A Lrmp 0.6 up-regulated +A Lrp8 0.61 up-regulated +A Lrrc57 0.5 up-regulated +A Lrrcc1 0.52 up-regulated +A Lss 0.55 up-regulated +A Lst1 0.18 up-regulated +A Lta4h 0.62 up-regulated +A Ltbr 0.44 up-regulated +A Lxn 0.2 up-regulated +A Ly96 0.2 up-regulated +A Lyl1 0.57 up-regulated +A Lyn 0.46 up-regulated +A Lztfl1 1.64 down-regulated +A Magt1 0.5 up-regulated +A Man2a2 0.58 up-regulated +A Man2b1 0.38 up-regulated +A Map3k2 0.65 up-regulated +A Map3k3 0.6 up-regulated +A Map4k5 1.673333333 down-regulated +A Mapk8 0.5 up-regulated +A Mapkap1 0.46 up-regulated +A Mapkapk3 0.505 up-regulated +A March2 1.68 down-regulated +A March8 0.63 up-regulated +A Marcksl1 1.5725 down-regulated +A Marveld1 1.61 down-regulated +A Mast3 0.64 up-regulated +A Mast4 0.6 up-regulated +A Mbd2 0.58 up-regulated +A Mbnl2 0.54 up-regulated +A Mbnl3 1.66 down-regulated +A Mboat2 1.57 down-regulated +A Mboat7 0.61 up-regulated +A Mcart1 1.62 down-regulated +A Mcl1 0.56 up-regulated +A Mcpt2 0.12 up-regulated +A Mdm1 1.56 down-regulated +A Med13l 1.61 down-regulated +A Med19 0.635 up-regulated +A Med31 1.55 down-regulated +A Megf9 1.71 down-regulated +A Meis1 0.56 up-regulated +A Metap1 0.535 up-regulated +A Mex3d 1.57 down-regulated +A Mfhas1 2.79 down-regulated +A Mgat4a 0.51 up-regulated +A Mier1 0.475 up-regulated +A Mier3 2.16 down-regulated +A Mkx 0.5 up-regulated +A Mlkl 0.54 up-regulated +A Mllt3 1.61 down-regulated +A Mmp14 0.51 up-regulated +A Mobkl1b 0.37 up-regulated +A Mobkl2a 0.34 up-regulated +A Mospd2 0.665 up-regulated +A Mphosph6 0.64 up-regulated +A Mpnd 1.5 down-regulated +A Mpp6 1.58 down-regulated +A Mppe1 0.29 up-regulated +A Mpst 1.53 down-regulated +A Mrpl1 0.38 up-regulated +A Mrps33 0.61 up-regulated +A Msh5 0.43 up-regulated +A Msn 0.575 up-regulated +A Mtap4 0.4 up-regulated +A Mtap7d1 2.28 down-regulated +A Mtbp 1.51 down-regulated +A Mtcp1 1.665 down-regulated +A Mtfr1 1.705 down-regulated +A Mtm1 1.88 down-regulated +A Mtmr9 0.405 up-regulated +A Mtpn 0.386 up-regulated +A Muc13 0.18 up-regulated +A Mum1 1.94 down-regulated +A Mvk 0.62 up-regulated +A Mvp 0.52 up-regulated +A Mxd4 0.5 up-regulated +A Mybl2 0.56 up-regulated +A Mycn 0.49 up-regulated +A Mylk3 0.54 up-regulated +A Mylpf 2.05 down-regulated +A Myo18a 1.6 down-regulated +A Naga 0.64 up-regulated +A Nagk 0.36 up-regulated +A Naip2 0.26 up-regulated +A Nanos1 1.88 down-regulated +A Narf 1.69 down-regulated +A Nars2 0.63 up-regulated +A Nav1 0.49 up-regulated +A Nbeal2 0.32 up-regulated +A Ncf2 0.26 up-regulated +A Nck1 0.67 up-regulated +A Nckap1 1.77 down-regulated +A Nckap1l 0.44 up-regulated +A Ncoa1 1.745 down-regulated +A Ncoa2 1.645 down-regulated +A Ncoa7 2.14 down-regulated +A Ncor1 0.6 up-regulated +A Ndrg1 0.48 up-regulated +A Ndrg2 3.91 down-regulated +A Nek8 1.72 down-regulated +A Nenf 1.75 down-regulated +A Net1 0.59 up-regulated +A Nf1 0.435 up-regulated +A Nfatc1 0.616666667 up-regulated +A Nfix 1.54 down-regulated +A Nfkb1 0.65 up-regulated +A Ng23 0.66 up-regulated +A Nhlrc2 1.55 down-regulated +A Niban 2.175 down-regulated +A Nipa1 1.735 down-regulated +A Nipa2 0.46 up-regulated +A Nipsnap3a 0.34 up-regulated +A Nln 0.64 up-regulated +A Nlrx1 0.63 up-regulated +A Nmt2 1.93 down-regulated +A Nnt 0.49 up-regulated +A Nolc1 0.64 up-regulated +A Notch2 0.64 up-regulated +A Nphp1 2.01 down-regulated +A Nptn 0.53 up-regulated +A Nptxr 1.55 down-regulated +A Nrip3 1.983333333 down-regulated +A Nsmaf 3.04 down-regulated +A Nudt14 0.62 up-regulated +A Nufip2 0.65 up-regulated +A Nupr1 2.05 down-regulated +A Oaf 1.73 down-regulated +A Oas1g 0.53 up-regulated +A Ocrl 0.31 up-regulated +A Ogfrl1 0.66 up-regulated +A Oma1 0.66 up-regulated +A Orai2 0.405 up-regulated +A Orai3 0.45 up-regulated +A Osbpl8 0.6 up-regulated +A Osgin1 1.9 down-regulated +A Osm 0.55 up-regulated +A Osr2 2.25 down-regulated +A Osta 2.56 down-regulated +A Ostf1 0.61 up-regulated +A Ostm1 0.5 up-regulated +A Otub2 3.29 down-regulated +A Otud5 0.57 up-regulated +A P4ha1 2.16 down-regulated +A Pa2g4 0.64 up-regulated +A Pacs2 1.74 down-regulated +A Pafah2 0.57 up-regulated +A Paip1 0.54 up-regulated +A Pank1 0.4525 up-regulated +A Paox 1.87 down-regulated +A Papd4 0.52 up-regulated +A Papss2 0.235 up-regulated +A Parp14 0.64 up-regulated +A Parp16 1.66 down-regulated +A Parvg 0.585 up-regulated +A Patl1 0.55 up-regulated +A Pcnp 0.63 up-regulated +A Pcnx 2.98 down-regulated +A Pctp 0.47 up-regulated +A Pdcd1lg2 0.29 up-regulated +A Pdcd6ip 0.42 up-regulated +A Pde3b 1.65 down-regulated +A Pde7a 1.5625 down-regulated +A Pdia2 8.76 down-regulated +A Pdk1 0.553333333 up-regulated +A Pdlim7 0.57 up-regulated +A Pds5b 1.54 down-regulated +A Pdxk 0.49 up-regulated +A Pex11a 0.38 up-regulated +A Pex2 0.62 up-regulated +A Pfdn2 0.48 up-regulated +A Pgam1 0.67 up-regulated +A Pgd 0.63 up-regulated +A Phca 0.585 up-regulated +A Phf10 1.59 down-regulated +A Phf2 1.54 down-regulated +A Phf3 0.65 up-regulated +A Phlda1 1.92 down-regulated +A Phlda2 0.55 up-regulated +A Phlda3 2.26 down-regulated +A Phlpp 1.76 down-regulated +A Piga 1.64 down-regulated +A Pik3cd 0.465 up-regulated +A Pik3cg 0.18 up-regulated +A Pik3r1 0.535 up-regulated +A Pik3r3 0.56 up-regulated +A Pim1 0.62 up-regulated +A Pip5k1c 0.63 up-regulated +A Pitpna 0.4 up-regulated +A Pitpnc1 0.64 up-regulated +A Pklr 2.27 down-regulated +A Pkm2 0.58 up-regulated +A Plaa 0.52 up-regulated +A Plcg2 0.66 up-regulated +A Plcl2 1.54 down-regulated +A Plek 0.536666667 up-regulated +A Plek2 2.42 down-regulated +A Plekha2 0.495 up-regulated +A Plk3 0.66 up-regulated +A Plk4 1.57 down-regulated +A Plscr1 0.63 up-regulated +A Plscr3 1.615 down-regulated +A Plvap 0.51 up-regulated +A Plxnc1 0.443333333 up-regulated +A Pml 0.66 up-regulated +A Pnpla8 1.79 down-regulated +A Pnrc1 0.64 up-regulated +A Pnrc2 0.64 up-regulated +A Pole3 0.31 up-regulated +A Por 0.64 up-regulated +A Ppap2a 5.8 down-regulated +A Ppard 1.6 down-regulated +A Ppm1a 0.51 up-regulated +A Ppm1l 1.57 down-regulated +A Ppox 1.84 down-regulated +A Ppp2cb 0.66 up-regulated +A Prkacb 0.485 up-regulated +A Prkca 0.523333333 up-regulated +A Prkcd 0.59 up-regulated +A Prnp 2.32 down-regulated +A Prokr1 2.76 down-regulated +A Pros1 0.13 up-regulated +A Prpf31 0.67 up-regulated +A Prpf40a 0.61 up-regulated +A Prr11 1.54 down-regulated +A Prr13 0.67 up-regulated +A Prrc1 0.55 up-regulated +A Prune 0.67 up-regulated +A Psen2 0.64 up-regulated +A Psmb8 0.5 up-regulated +A Psmb9 0.555 up-regulated +A Psph 0.36 up-regulated +A Pstpip2 0.166666667 up-regulated +A Ptar1 1.57 down-regulated +A Ptdss2 2.165 down-regulated +A Ptger1 0.65 up-regulated +A Ptk2b 0.63 up-regulated +A Ptp4a1 0.425 up-regulated +A Ptpn13 0.61 up-regulated +A Ptpn18 0.22 up-regulated +A Ptpn4 1.58 down-regulated +A Ptpn6 0.45 up-regulated +A Ptpn9 0.62 up-regulated +A Ptprcap 0.19 up-regulated +A Ptpre 0.175 up-regulated +A Ptrh2 0.6 up-regulated +A Purg 1.82 down-regulated +A Pus10 0.33 up-regulated +A Pvt1 0.57 up-regulated +A Pxn 0.655 up-regulated +A Pycr1 1.94 down-regulated +A Pycrl 0.39 up-regulated +A Pygl 0.37 up-regulated +A Rab11a 0.35 up-regulated +A Rab18 0.24 up-regulated +A Rab27a 0.46 up-regulated +A Rab3gap2 0.45 up-regulated +A Rab7l1 0.63 up-regulated +A Rab8b 0.65 up-regulated +A Rabgap1l 0.473333333 up-regulated +A Rac2 0.53 up-regulated +A Rad23a 1.64 down-regulated +A Rad23b 0.37 up-regulated +A Rala 1.68 down-regulated +A Ralb 0.62 up-regulated +A Ramp1 0.11 up-regulated +A Ran 0.67 up-regulated +A Rap1gap 3.71 down-regulated +A Rap2c 0.51 up-regulated +A Rasa2 0.54 up-regulated +A Rassf3 0.57 up-regulated +A Rbm11 1.75 down-regulated +A Rbm28 0.65 up-regulated +A Rdh10 0.52 up-regulated +A Reep3 2.066666667 down-regulated +A Reep5 0.36 up-regulated +A Reep6 2.39 down-regulated +A Rell1 1.84 down-regulated +A Relt 0.46 up-regulated +A Renbp 0.58 up-regulated +A Reps2 0.16 up-regulated +A Retsat 0.52 up-regulated +A Rex2 0.64 up-regulated +A Rfc2 0.66 up-regulated +A Rffl 0.6 up-regulated +A Rftn1 0.66 up-regulated +A Rfx2 2.39 down-regulated +A Rfx5 0.58 up-regulated +A Rgs1 0.49 up-regulated +A Rgs12 2.54 down-regulated +A Rgs14 0.47 up-regulated +A Rgs18 0.25 up-regulated +A Rgs19 0.23 up-regulated +A Rgs9bp 2.95 down-regulated +A Rhd 2.21 down-regulated +A Rhob 1.75 down-regulated +A Rhobtb3 3.44 down-regulated +A Rhof 0.6 up-regulated +A Rhog 0.44 up-regulated +A Rhoh 0.37 up-regulated +A Ribc1 1.55 down-regulated +A Rilpl1 1.76 down-regulated +A Ripk3 0.64 up-regulated +A Ripply3 2.25 down-regulated +A Rlf 1.645 down-regulated +A Rnase6 0.14 up-regulated +A Rnasel 0.51 up-regulated +A Rnd2 0.48 up-regulated +A Rnf135 0.56 up-regulated +A Rnf144b 0.62 up-regulated +A Rnf157 1.72 down-regulated +A Rnf170 0.615 up-regulated +A Rnft1 0.57 up-regulated +A Rnmt 0.55 up-regulated +A Rnpepl1 0.67 up-regulated +A Rp2h 0.56 up-regulated +A Rpl15 0.46 up-regulated +A Rpl5 0.55 up-regulated +A Rps20 0.36 up-regulated +A Rps6ka1 0.4 up-regulated +A Rps6ka4 1.59 down-regulated +A Rrad 0.57 up-regulated +A Rsu1 0.51 up-regulated +A Rwdd4a 0.27 up-regulated +A S100a10 0.45 up-regulated +A S100a13 0.63 up-regulated +A Samd14 1.72 down-regulated +A Samd9l 0.5 up-regulated +A Samsn1 0.45 up-regulated +A Sap18 0.58 up-regulated +A Saps2 1.64 down-regulated +A Sbk1 1.685 down-regulated +A Scamp2 0.66 up-regulated +A Scamp3 0.58 up-regulated +A Scarb2 1.6 down-regulated +A Scin 0.09 up-regulated +A Scmh1 2.26 down-regulated +A Sco1 0.66 up-regulated +A Scoc 2.83 down-regulated +A Scpep1 1.655 down-regulated +A Sdc1 2.51 down-regulated +A Sdf4 0.55 up-regulated +A Sec13 0.57 up-regulated +A Sec61b 0.59 up-regulated +A Sema4a 0.15 up-regulated +A Sepsecs 0.63 up-regulated +A sept-01 0.59 up-regulated +A sept-04 1.9 down-regulated +A sept-06 1.55 down-regulated +A sept-09 0.46 up-regulated +A Serf1 0.37 up-regulated +A Serpinb9 0.46 up-regulated +A Sf3b1 0.47 up-regulated +A Sfmbt1 1.87 down-regulated +A Sfpi1 0.21 up-regulated +A Sfrp4 1.97 down-regulated +A Sfrs3 0.61 up-regulated +A Sfrs6 0.66 up-regulated +A Sft2d2 0.603333333 up-regulated +A Sfxn2 0.54 up-regulated +A Sgk3 1.526666667 down-regulated +A Sh3bgrl3 0.42 up-regulated +A Sh3yl1 1.84 down-regulated +A Shank3 0.18 up-regulated +A Shoc2 0.54 up-regulated +A Siah1b 1.54 down-regulated +A Siah2 1.6 down-regulated +A Sirpa 0.51 up-regulated +A Skap2 0.385 up-regulated +A Sla 0.06 up-regulated +A Slc10a7 0.32 up-regulated +A Slc12a6 0.59 up-regulated +A Slc16a10 1.623333333 down-regulated +A Slc16a6 1.56 down-regulated +A Slc1a4 1.536666667 down-regulated +A Slc25a10 0.5 up-regulated +A Slc25a12 0.54 up-regulated +A Slc25a32 0.62 up-regulated +A Slc25a36 0.485 up-regulated +A Slc25a37 1.64 down-regulated +A Slc25a45 0.15 up-regulated +A Slc29a1 2.04 down-regulated +A Slc2a3 0.31 up-regulated +A Slc30a10 3.65 down-regulated +A Slc35a3 0.573333333 up-regulated +A Slc37a3 1.88 down-regulated +A Slc38a5 2.58 down-regulated +A Slc39a11 0.54 up-regulated +A Slc39a6 0.64 up-regulated +A Slc39a8 1.84 down-regulated +A Slc43a1 0.51 up-regulated +A Slc45a3 0.095 up-regulated +A Slc46a3 1.74 down-regulated +A Slc6a13 0.09 up-regulated +A Slc7a11 2.2 down-regulated +A Slc7a3 2.59 down-regulated +A Slc7a4 0.49 up-regulated +A Slc7a7 1.76 down-regulated +A Slc9a3r1 0.48 up-regulated +A Slc9a6 0.52 up-regulated +A Slco3a1 0.503333333 up-regulated +A Slfn10 0.54 up-regulated +A Slmo1 1.97 down-regulated +A Smtnl2 0.52 up-regulated +A Snapc3 1.545 down-regulated +A Snapin 0.63 up-regulated +A Snca 0.4 up-regulated +A Soat2 1.64 down-regulated +A Socs4 1.8 down-regulated +A Socs6 1.57 down-regulated +A Sorbs1 4.166666667 down-regulated +A Sox6 2.956666667 down-regulated +A Spa17 1.5 down-regulated +A Spast 0.67 up-regulated +A Spef1 1.82 down-regulated +A Spn 0.57 up-regulated +A Spna2 0.395 up-regulated +A Spnb1 1.91 down-regulated +A Spns3 0.39 up-regulated +A Spopl 1.82 down-regulated +A Spry1 2.13 down-regulated +A Srgn 0.63 up-regulated +A Sri 0.51 up-regulated +A Srprb 0.6 up-regulated +A Srr 1.57 down-regulated +A Ssbp2 1.99 down-regulated +A Ssbp3 1.79 down-regulated +A St3gal1 1.9 down-regulated +A St3gal5 1.575 down-regulated +A St3gal6 3.393333333 down-regulated +A St5 1.93 down-regulated +A Stard10 4.06 down-regulated +A Stim1 0.64 up-regulated +A Stk10 0.25 up-regulated +A Stk32a 1.71 down-regulated +A Strbp 1.6 down-regulated +A Stt3a 0.67 up-regulated +A Stx17 1.59 down-regulated +A Stxbp2 0.66 up-regulated +A Sulf2 0.44 up-regulated +A Suv39h2 1.595 down-regulated +A Suv420h1 0.65 up-regulated +A Svil 1.64 down-regulated +A Taf1c 1.73 down-regulated +A Taok3 0.606666667 up-regulated +A Tapt1 1.53 down-regulated +A Tarsl2 1.81 down-regulated +A Tax1bp1 0.66 up-regulated +A Tbc1d10c 0.25 up-regulated +A Tbc1d12 1.53 down-regulated +A Tbc1d8b 0.63 up-regulated +A Tbpl1 1.59 down-regulated +A Tceb1 0.54 up-regulated +A Tcf15 1.53 down-regulated +A Tcfe3 0.65 up-regulated +A Tcirg1 0.41 up-regulated +A Tcn2 0.43 up-regulated +A Tcte3 2.14 down-regulated +A Tec 0.17 up-regulated +A Tep1 0.41 up-regulated +A Tfdp2 1.5 down-regulated +A Tgfb1 0.55 up-regulated +A Tgm2 2.175 down-regulated +A Tgs1 0.6525 up-regulated +A Thra 1.553333333 down-regulated +A Tial1 0.24 up-regulated +A Ticam1 0.66 up-regulated +A Tifa 2.13 down-regulated +A Tigd2 1.55 down-regulated +A Tinagl 3.15 down-regulated +A Tjp1 1.74 down-regulated +A Tk1 1.68 down-regulated +A Tlcd1 1.885 down-regulated +A Tle1 1.78 down-regulated +A Tlk2 1.503333333 down-regulated +A Tm9sf3 0.47 up-regulated +A Tmcc3 5.706666667 down-regulated +A Tmem106b 0.64 up-regulated +A Tmem107 1.625 down-regulated +A Tmem109 1.55 down-regulated +A Tmem120b 1.85 down-regulated +A Tmem134 1.53 down-regulated +A Tmem144 0.545 up-regulated +A Tmem16f 0.583333333 up-regulated +A Tmem176b 0.11 up-regulated +A Tmem184b 0.66 up-regulated +A Tmem189 0.55 up-regulated +A Tmem194 1.82 down-regulated +A Tmem40 0.39 up-regulated +A Tmem48 0.63 up-regulated +A Tmem50b 0.66 up-regulated +A Tmem56 2.47 down-regulated +A Tmem65 1.88 down-regulated +A Tmem8 1.91 down-regulated +A Tmem9 2.73 down-regulated +A Tmem9b 0.61 up-regulated +A Tmod1 1.96 down-regulated +A Tnfaip1 0.53 up-regulated +A Tnfaip8 0.58 up-regulated +A Tnfaip8l1 0.49 up-regulated +A Tnfaip8l2 0.64 up-regulated +A Tnfrsf13b 0.1 up-regulated +A Tnk2 1.605 down-regulated +A Tnnt2 1.93 down-regulated +A Tomm20 0.665 up-regulated +A Tor3a 0.41 up-regulated +A Tpm1 1.5 down-regulated +A Tpp1 0.57 up-regulated +A Tpst2 0.56 up-regulated +A Tpx2 0.46 up-regulated +A Traf3 0.64 up-regulated +A Traf4 1.82 down-regulated +A Trappc2 0.58 up-regulated +A Treml2 0.423333333 up-regulated +A Trib3 1.93 down-regulated +A Trim10 1.96 down-regulated +A Trim12 0.64 up-regulated +A Trim30 0.62 up-regulated +A Trim44 1.63 down-regulated +A Trpv2 0.58 up-regulated +A Tspan15 1.55 down-regulated +A Tspan33 1.54 down-regulated +A Ttc14 1.6375 down-regulated +A Ttc32 0.64 up-regulated +A Ttc7b 0.55 up-regulated +A Ttll1 1.69 down-regulated +A Tuba8 0.2 up-regulated +A Tulp2 0.39 up-regulated +A Twf2 0.29 up-regulated +A Twsg1 1.8 down-regulated +A Txnip 0.505 up-regulated +A Uap1l1 0.57 up-regulated +A Ubac1 1.73 down-regulated +A Ubash3b 0.555 up-regulated +A Ube2a 0.67 up-regulated +A Ube2i 0.58 up-regulated +A Ube2j1 1.515 down-regulated +A Ube2n 0.44 up-regulated +A Ube2q1 0.635 up-regulated +A Ube2v2 0.235 up-regulated +A Ubfd1 0.305 up-regulated +A Uhmk1 0.61 up-regulated +A Ulk2 1.57 down-regulated +A Unc119 0.31 up-regulated +A Uros 3.04 down-regulated +A Usp14 0.63 up-regulated +A Usp18 0.63 up-regulated +A Usp40 0.595 up-regulated +A Usp45 2.285 down-regulated +A Usp9x 0.655 up-regulated +A Vamp3 0.3 up-regulated +A Vasp 0.47 up-regulated +A 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1.000310478 no-response +ABC Hdgfrp2 0.94610034 no-response +ABC Hdgfrp3 1.000477464 no-response +ABC Hdhd1a 0.998971392 no-response +ABC Hdhd3 1.005645872 no-response +ABC Hdlbp 1.062855194 no-response +ABC Heatr3 0.977155504 no-response +ABC Heatr5a 0.9255844 no-response +ABC Heatr5b 0.963561467 no-response +ABC Hebp2 0.999848169 no-response +ABC Hectd1 0.945274775 no-response +ABC Hectd2 0.999404793 no-response +ABC Hecw1 1.000260672 no-response +ABC Hecw2 1.00005491 no-response +ABC Helz 0.907608562 no-response +ABC Hemk1 0.83623225 no-response +ABC Hepacam 1.000116185 no-response +ABC Heph 0.993223889 no-response +ABC Herc2 0.994039889 no-response +ABC Herc3 0.996633584 no-response +ABC Herc4 0.996873762 no-response +ABC Herc5 1.036842902 no-response +ABC Hes2 1.00002649 no-response +ABC Hes3 1.00056434 no-response +ABC Hes5 1.003860693 no-response +ABC Hes7 1.003895607 no-response +ABC Hesx1 1.120904288 no-response +ABC Hexb 0.824769823 no-response +ABC Hey1 0.99677159 no-response +ABC Hey2 0.966157618 no-response +ABC Heyl 0.989626118 no-response +ABC Hfe 0.937499245 no-response +ABC Hfe2 0.998866248 no-response +ABC Hgd 1.000374522 no-response +ABC Hgf 0.994725263 no-response +ABC Hgfac 1.012268266 no-response +ABC Hgsnat 1.031540454 no-response +ABC Hhat 0.997515906 no-response +ABC Hhatl 0.997873603 no-response +ABC Hhip 1.001879552 no-response +ABC Hhipl1 0.999942429 no-response +ABC Hhipl2 0.999082025 no-response +ABC Hiatl1 0.920951608 no-response +ABC Hibch 0.931134511 no-response +ABC Hic1 1.001271471 no-response +ABC Higd1b 0.998698207 no-response +ABC Higd2a 0.980560742 no-response +ABC Hils1 0.994507945 no-response +ABC Hint1 1.028934234 no-response +ABC Hint3 1.140497865 no-response +ABC Hip1 1.003204009 no-response +ABC Hip1r 1.009010653 no-response +ABC Hisppd2a 0.959894504 no-response +ABC Hist1h1c 0.97629614 no-response +ABC Hist1h1t 1.00944004 no-response +ABC Hist1h2ae 1.025796208 no-response +ABC Hist1h2be 0.996903696 no-response 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0.996098099 no-response +ABC Hmgn1 1.012322988 no-response +ABC Hmgn3 1.000447855 no-response +ABC Hmox2 0.912486475 no-response +ABC Hmx1 0.99922589 no-response +ABC Hmx3 1.001520642 no-response +ABC Hn1l 1.089905346 no-response +ABC Hnf1a 0.99954004 no-response +ABC Hnf1b 0.999746231 no-response +ABC Hnf4a 0.98890801 no-response +ABC Hnf4g 1.006280674 no-response +ABC Hnmt 0.998645744 no-response +ABC Hnrnpa2b1 1.076672184 no-response +ABC Hnrnpl 1.086815562 no-response +ABC Hnrnpr 1.044575697 no-response +ABC Hnrpf 1.00288619 no-response +ABC Hnrph1 1.066026616 no-response +ABC Hnrph2 0.984034844 no-response +ABC Hnrpk 1.02270135 no-response +ABC Hnrpm 1.06644518 no-response +ABC Hnrpul1 0.953224886 no-response +ABC Hnt 1.001171148 no-response +ABC Homer2 0.998283466 no-response +ABC Homer3 0.9779599 no-response +ABC Homez 0.910728982 no-response +ABC Hook1 0.999861299 no-response +ABC Hook2 1.057611119 no-response +ABC Hormad1 1.014702391 no-response +ABC Hormad2 0.950583691 no-response +ABC Hoxa1 0.998407282 no-response +ABC Hoxa10 1.002074468 no-response +ABC Hoxa11 0.998423344 no-response +ABC Hoxa11os 0.99914029 no-response +ABC Hoxa13 1.001205795 no-response +ABC Hoxa2 1.013440174 no-response +ABC Hoxa3 1.008516224 no-response +ABC Hoxa4 1.000040731 no-response +ABC Hoxa5 0.997583673 no-response +ABC Hoxa7 1.006214668 no-response +ABC Hoxa9 1.000370751 no-response +ABC Hoxb1 1.001671866 no-response +ABC Hoxb13 1.143923674 no-response +ABC Hoxb2 0.999329986 no-response +ABC Hoxb3 0.999907949 no-response +ABC Hoxb4 0.967076124 no-response +ABC Hoxb5 1.002755706 no-response +ABC Hoxb6 0.999686868 no-response +ABC Hoxb7 1.001524557 no-response +ABC Hoxb9 0.998507096 no-response +ABC Hoxc10 0.998814343 no-response +ABC Hoxc13 1.00510024 no-response +ABC Hoxc4 1.015164252 no-response +ABC Hoxc5 1.005582787 no-response +ABC Hoxc6 0.995678114 no-response +ABC Hoxc8 1.018881903 no-response +ABC Hoxc9 0.892810088 no-response +ABC Hoxd1 0.999042583 no-response 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no-response +ABC Hs3st2 0.999676842 no-response +ABC Hs3st3a1 1.001334512 no-response +ABC Hs3st3b1 1.010660929 no-response +ABC Hs3st5 1.003260942 no-response +ABC Hs3st6 1.024402206 no-response +ABC Hs6st1 1.145451072 no-response +ABC Hs6st2 1.000411378 no-response +ABC Hs6st3 1.001995073 no-response +ABC Hsd11b1 1.004765858 no-response +ABC Hsd11b2 0.999370465 no-response +ABC Hsd17b1 1.085361258 no-response +ABC Hsd17b13 0.996210416 no-response +ABC Hsd17b14 0.798032899 no-response +ABC Hsd17b2 1.000325111 no-response +ABC Hsd17b3 0.997819264 no-response +ABC Hsd17b4 0.953482583 no-response +ABC Hsd17b6 1.000643871 no-response +ABC Hsd3b2 1.000656164 no-response +ABC Hsd3b3 0.99984807 no-response +ABC Hsd3b4 1.000937887 no-response +ABC Hsd3b5 0.999701316 no-response +ABC Hsf1 1.077126445 no-response +ABC Hsf2 0.998748906 no-response +ABC Hsf2bp 0.999799254 no-response +ABC Hsf4 0.9835638 no-response +ABC Hsf5 0.999099839 no-response +ABC Hsfy2 0.999541713 no-response +ABC Hsp25-ps1 0.997488486 no-response +ABC Hspa12b 1.000395884 no-response +ABC Hspa1a 1.000317393 no-response +ABC Hspa1l 0.993411416 no-response +ABC Hspa2 1.028776306 no-response +ABC Hspa5 0.906410348 no-response +ABC Hspa8 0.961130217 no-response +ABC Hspb1 0.99869488 no-response +ABC Hspb2 1.000252953 no-response +ABC Hspb3 0.999541472 no-response +ABC Hspb7 0.998595457 no-response +ABC Hspb8 0.995574169 no-response +ABC Hspb9 0.999605278 no-response +ABC Hspd1 1.010215819 no-response +ABC Hspe1 1.044647717 no-response +ABC Hspg2 1.172862834 no-response +ABC Htatip 0.976160299 no-response +ABC Htr1a 0.997354055 no-response +ABC Htr1b 0.993308359 no-response +ABC Htr1d 0.990631998 no-response +ABC Htr1f 0.99873304 no-response +ABC Htr2b 0.999408197 no-response +ABC Htr2c 0.999608859 no-response +ABC Htr3a 1.001218014 no-response +ABC Htr3b 0.998970721 no-response +ABC Htr4 1.001406811 no-response +ABC Htr5a 1.000080794 no-response +ABC Htr5b 1.00034679 no-response +ABC Htr6 0.999183392 no-response +ABC Htr7 1.006624177 no-response +ABC Htra1 0.998266658 no-response +ABC Htra3 0.99985926 no-response +ABC Htra4 1.030006081 no-response +ABC Hunk 0.999564428 no-response +ABC Hus1 1.034880523 no-response +ABC Huwe1 0.997812799 no-response +ABC Hvcn1 0.998264444 no-response +ABC Hyal3 0.875704163 no-response +ABC Hyal4 0.993760563 no-response +ABC Hyal5 0.998287439 no-response +ABC Hyal6 0.995555347 no-response +ABC Hydin 0.989801662 no-response +ABC Hyi 1.122807765 no-response +ABC Hyou1 0.881604268 no-response +ABC Iapp 0.996255983 no-response +ABC Iars2 1.039243129 no-response +ABC Ibtk 1.110614544 no-response +ABC Ica1 0.938429142 no-response +ABC Ica1l 0.955993942 no-response +ABC Icam5 1.000713159 no-response +ABC Icos 1.000868471 no-response +ABC Icosl 0.996015946 no-response +ABC Id3 1.22764861 no-response +ABC Id4 0.998989631 no-response +ABC Idh2 1.034917339 no-response +ABC Idh3b 1.047412914 no-response +ABC Idh3g 0.986150125 no-response +ABC Idi2 0.998795215 no-response +ABC Ids 1.09530557 no-response +ABC Idua 1.007250232 no-response +ABC Ier2 1.037940252 no-response +ABC Ier5l 1.00099741 no-response +ABC Ifi203 1.002287827 no-response +ABC Ifi204 0.996734691 no-response +ABC Ifi205 0.999513843 no-response +ABC Ifi27 0.82429144 no-response +ABC Ifi44 0.99914947 no-response +ABC Ifit2 0.966677371 no-response +ABC Ifit3 1.073903221 no-response +ABC Ifitm1 0.998241507 no-response +ABC Ifitm2 0.867670037 no-response +ABC Ifitm3 1.000595962 no-response +ABC Ifitm5 1.000211079 no-response +ABC Ifitm6 0.998181948 no-response +ABC Ifitm7 1.000083365 no-response +ABC Ifltd1 1.001950995 no-response +ABC Ifna11 0.999585993 no-response +ABC Ifna2 0.999795136 no-response +ABC Ifna4 0.998984945 no-response +ABC Ifna6 0.996668366 no-response +ABC Ifna7 1.000180982 no-response +ABC Ifna9 0.96358677 no-response +ABC Ifnb1 1.007317741 no-response +ABC Ifng 0.999834273 no-response +ABC Ifngr1 1.068101138 no-response +ABC Ifnz 1.039836227 no-response +ABC Ift122 1.067806837 no-response +ABC Ift172 1.143570109 no-response +ABC Ift20 0.949312936 no-response +ABC Ift52 1.151459634 no-response +ABC Ift74 0.890365608 no-response +ABC Ift81 1.000759522 no-response +ABC Ift88 1.016723731 no-response +ABC Igbp1 0.990211973 no-response +ABC Igbp1b 0.999371018 no-response +ABC Igf1 1.000457137 no-response +ABC Igf1r 0.975588524 no-response +ABC Igf2 1.000306238 no-response +ABC Igf2as 1.012521217 no-response +ABC Igf2bp1 1.006147192 no-response +ABC Igf2bp2 0.996521812 no-response +ABC Igf2bp3 1.153031567 no-response +ABC Igf2r 1.167501575 no-response +ABC Igfals 0.997857612 no-response +ABC Igfbp1 0.999880153 no-response +ABC Igfbp2 1.001147867 no-response +ABC Igfbp3 0.991413878 no-response +ABC Igfbp4 0.984189184 no-response +ABC Igfbp5 1.032930892 no-response +ABC Igfbp6 1.001545598 no-response +ABC Igfbpl1 0.99987937 no-response +ABC Igh 0.99896333 no-response +ABC Igh-6 0.996222177 no-response +ABC Ighg 1.007152792 no-response +ABC Ighmbp2 1.030053744 no-response +ABC Ighv6-6 1.001042105 no-response +ABC Igh-V7183 0.999036584 no-response +ABC Igh-VJ558 1.00037874 no-response +ABC Igj 0.999530963 no-response +ABC Igk-V1 0.990811692 no-response +ABC Igkv1-117 0.998911689 no-response +ABC Igkv14-111 0.999614087 no-response +ABC Igk-V19-14 0.995864566 no-response +ABC Igk-V21 0.999733543 no-response +ABC Igk-V32 0.999010727 no-response +ABC Igk-V38 1.005230252 no-response +ABC Igl-V1 0.970965246 no-response +ABC Igsf1 1.008993423 no-response +ABC Igsf11 0.99925864 no-response +ABC Igsf21 0.999319019 no-response +ABC Igsf3 0.999980692 no-response +ABC Igsf5 0.999944819 no-response +ABC Igsf6 0.999253961 no-response +ABC Igsf9 1.002663001 no-response +ABC Ihh 0.999161787 no-response +ABC Ihpk2 1.075189735 no-response +ABC Ihpk3 1.003934185 no-response +ABC Iigp1 1.00299011 no-response +ABC Ik 1.005769463 no-response +ABC Ikbke 1.001211968 no-response +ABC Ikzf4 0.999609948 no-response +ABC Il10 1.000643535 no-response +ABC Il10ra 1.001768865 no-response +ABC Il11 0.935675986 no-response +ABC Il12a 1.000305201 no-response +ABC Il12b 0.999284196 no-response +ABC Il12rb1 1.07017715 no-response +ABC Il12rb2 0.998579868 no-response +ABC Il13 1.01167374 no-response +ABC Il13ra1 0.999738012 no-response +ABC Il13ra2 0.993232507 no-response +ABC Il15 1.000738784 no-response +ABC Il15ra 1.253437665 no-response +ABC Il16 1.014950211 no-response +ABC Il17a 1.000272178 no-response +ABC Il17b 0.998593273 no-response +ABC Il17rb 0.99941375 no-response +ABC Il17rc 1.000229082 no-response +ABC Il17rd 1.002271597 no-response +ABC Il17re 0.998455828 no-response +ABC Il18 1.00163356 no-response +ABC Il18bp 0.996736517 no-response +ABC Il18r1 0.999003422 no-response +ABC Il18rap 0.999830113 no-response +ABC Il1a 1.001790698 no-response +ABC Il1f5 0.993562162 no-response +ABC Il1f6 1.00116725 no-response +ABC Il1f8 1.000055968 no-response +ABC Il1f9 0.9995659 no-response +ABC Il1r1 1.167634604 no-response +ABC Il1r2 1.005150127 no-response +ABC Il1rap 1.11881357 no-response +ABC Il1rapl2 0.999567872 no-response +ABC Il1rl2 0.999245773 no-response +ABC Il1rn 0.998474268 no-response +ABC Il2 0.998880681 no-response +ABC Il20 0.998663008 no-response +ABC Il20ra 0.997564651 no-response +ABC Il20rb 1.008265708 no-response +ABC Il21 0.999228309 no-response +ABC Il21r 1.000889189 no-response +ABC Il22ra2 1.000490671 no-response +ABC Il23a 1.004707425 no-response +ABC Il24 1.000495685 no-response +ABC Il25 1.000710453 no-response +ABC Il28ra 0.999396802 no-response +ABC Il2ra 0.998070858 no-response +ABC Il2rb 1.000370588 no-response +ABC Il2rg 0.614567533 no-response +ABC Il3 0.999453448 no-response +ABC Il31 0.998113786 no-response +ABC Il31ra 0.858112454 no-response +ABC Il33 1.000138955 no-response +ABC Il3ra 1.043564715 no-response +ABC Il4 0.870553465 no-response +ABC Il4i1 1.003124979 no-response +ABC Il4ra 0.951370567 no-response +ABC Il5 0.999824823 no-response +ABC Il5ra 0.996434624 no-response +ABC Il6ra 1.002173641 no-response +ABC Il7 1.000158908 no-response +ABC Il7r 0.998955425 no-response +ABC Il8rb 0.999226169 no-response +ABC Il9 0.999397175 no-response +ABC Il9r 0.999197341 no-response +ABC Ildr1 1.000629512 no-response +ABC Ilf2 1.005399614 no-response +ABC Ilk 0.936893822 no-response +ABC Immp1l 0.959140538 no-response +ABC Immp2l 0.971356323 no-response +ABC Imp3 1.015814868 no-response +ABC Imp4 0.920768399 no-response +ABC Impa1 0.968936414 no-response +ABC Impa2 1.028271733 no-response +ABC Impad1 1.108860383 no-response +ABC Impdh1 1.048856058 no-response +ABC Impg1 1.000575452 no-response +ABC Ina 0.999429938 no-response +ABC Inadl 0.998065602 no-response +ABC Incenp 1.002070233 no-response +ABC Indo 0.999986222 no-response +ABC Indol1 0.999127484 no-response +ABC Ing1 1.023825139 no-response +ABC Ing3 1.11271637 no-response +ABC Ing4 0.998966872 no-response +ABC Inha 0.999678007 no-response +ABC Inhba 0.999052736 no-response +ABC Inhbb 1.000858851 no-response +ABC Inhbc 1.048332679 no-response +ABC Inhbe 0.999275071 no-response +ABC Inmt 0.999185419 no-response +ABC Inpp1 0.991219506 no-response +ABC Inpp4a 1.003973904 no-response +ABC Inpp5a 0.992102752 no-response +ABC Inpp5e 1.110127321 no-response +ABC Inppl1 1.211570056 no-response +ABC Ins1 0.99703094 no-response +ABC Insc 0.999406916 no-response +ABC Insig1 1.120635823 no-response +ABC Insl5 0.999902526 no-response +ABC Insm1 0.976859588 no-response +ABC Insm2 0.999846686 no-response +ABC Insr 1.000131936 no-response +ABC Insrr 0.963154277 no-response +ABC Ints1 1.116367309 no-response +ABC Ints2 0.953777566 no-response +ABC Ints3 1.11951073 no-response +ABC Ints4 0.904605019 no-response +ABC Ints8 1.044811718 no-response +ABC Ints9 1.050233633 no-response +ABC Invs 1.002852684 no-response +ABC Ipo4 0.920261789 no-response +ABC Ippk 1.02963059 no-response +ABC Ipw 1.000298378 no-response +ABC Iqca 1.007605992 no-response +ABC Iqcd 0.987325283 no-response 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotatePeaks_wrapper.xml Wed May 25 09:43:12 2016 -0400 @@ -0,0 +1,152 @@ +<!--annotatePeaks - developed by Jocelyn Brayet <jocelyn.brayet@curie.fr> +Copyright (C) 2015 Institut Curie + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see <http://www.gnu.org/licenses/>.--> +<tool id="annotatePeaks" name="AnnotatePeaks" version="1.0"> + <description>Genomic annotation of Chip-Seq peaks</description> + <requirements> + <requirement type="package" version="2.11.1">fontconfig</requirement> + <requirement type="package" version="3.1.2">R</requirement> + </requirements> + <command interpreter="bash"> +#if str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "no" #annotatePeaks_wrapper.sh -f $inputfile -y $log -m $minScore -l $left -o $outputPNG -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 0 #elif str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "yes" # annotatePeaks_wrapper.sh -f $inputfile -y $log -c $controlfile -x $statsControl -o $outputPNG -m $minScore -l $left -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 0 #elif str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "no" # annotatePeaks_wrapper.sh -y $log -f $inputfile -e $regfile -m $minScore -l $left -o $outputPNG -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 0 #elif str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "yes" # annotatePeaks_wrapper.sh -f $inputfile -c $controlfile -x $statsControl -l $left -y $log -o $outputPNG -m $minScore -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -e $regfile -p 0 #elif str( $if_PDF ) == '1' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "no" #annotatePeaks_wrapper.sh -f $inputfile -y $log -m $minScore -l $left -o $outputPDF -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 1 #elif str( $if_PDF ) == '1' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "yes" # annotatePeaks_wrapper.sh -f $inputfile -y $log -c $controlfile -x $statsControl -o $outputPDF -m $minScore -l $left -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 1 #elif str( $if_PDF ) == '1' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "no" # annotatePeaks_wrapper.sh -y $log -f $inputfile -e $regfile -m $minScore -l $left -o $outputPDF -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 1 #elif str( $if_PDF ) == '1' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "yes" # annotatePeaks_wrapper.sh -f $inputfile -c $controlfile -x $statsControl -l $left -y $log -o $outputPDF -m $minScore -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -e $regfile -p 1#end if + </command> + <inputs> + + <param name="inputfile" type="data" label="ChIP peaks" value="ChIP peaks File" format="bed"/> + <param name="minScore" type="float" label="MinimalScore" value="0" help="Set to 0 if you don't want to filter your .BED file with peaks"/> + + <conditional name="use_control"> + <param name="use_control_selector" type="select" label="Use control data"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="yes"> + <param name="controlfile" type="data" label="Control peaks" value="Control peaks File" format="bed"/> + </when> + </conditional> + + <param name="left" type="integer" label="Define Promoter is a region up to X bp upstream gene TSS" value="-2000"/> + <param name="right" type="integer" label="Define Immediate Downstream is a region up to X bp downstream gene TSS" value="2000"/> + <param name="EnhLeft" type="integer" label="Define Enhancer is a region up to X bp upstream gene TSS" value="-30000"/> + <param name="DownGene" type="integer" label="Define Gene Downstream is a region up to X bp downstream transcription end" value="5000"/> + + +<conditional name="input_organism"> + <param name="input_organism_selector" type="select" label="Select organism"> + <option value="Human" selected="true">Homo sapiens</option> + <option value="Mouse">Mus musculus</option> + <option value="Zebrafish">Zebrafish (Danio rerio)</option> + <option value="XTropicalis">X.Tropicalis</option> + <option value="Bacteria/MycoTube">M. tuberculosis</option> + </param> + <when value="Human"> + <param name="version" type="select" label="Select genome vesion"> + <option value="hg19" selected="true">hg19</option> + <option value="hg18">hg18</option> + </param> + </when> + <when value="Mouse"> + <param name="version" type="select" label="Select genome vesion"> + <option value="mm8" >mm8</option> + <option value="mm9" selected="true">mm9</option> + <option value="mm10" >mm10</option> + </param> + </when> + <when value="Zebrafish"> + <param name="version" type="select" label="Select genome vesion"> + <option value="zv9" selected="true">zv9</option> + </param> + </when> + <when value="XTropicalis"> + <param name="version" type="select" label="Select genome vesion"> + <option value="xenTro2" >xenTro2</option> + <option value="xenTro3" selected="true">xenTro3</option> + </param> + </when> + <when value="Bacteria/MycoTube"> + <param name="version" type="select" label="Select genome vesion"> + <option value="H37Rv" selected="true">H37Rv</option> + </param> + </when> +</conditional> + +<conditional name="use_reg"> + <param name="use_reg_selector" type="select" label="Use transcriptomic data (up- and down- regulated genes)"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="yes"> + <param name="regfile" type="data" label="File with information about gene regulation" value="Regulation data" format="txt"/> + </when> + </conditional> + + <param name="if_PDF" type="boolean" label="Do you want to have a PDF image (default PNG)?" truevalue="1" falsevalue="0" checked="False"/> + </inputs> + <outputs> + <data name="outputPNG" format="png" label="Peaks Stats (png)"> + <filter>(if_PDF == 0)</filter> + </data> + <data name="outputPDF" format="pdf" label="Peaks Stats (pdf)"> + <filter>(if_PDF == True)</filter> + </data> + + <data name="stats" format="tabular" label="Annotated Peaks (ChIP)"/> + <data name="log" format="log" label=".LOG for Annotated Peaks"/> + <data name="statsControl" format="tabular" label="Annotated Peaks (Control)"> + <filter>(use_control['use_control_selector'] == 'yes')</filter> + </data> + </outputs> + <tests> + <test> + <param name="inputfile" value="peaks_test.bed"/> + <param name="minScore" value="0.0"/> + <param name="use_control_selector" value="yes"/> + <param name="controlfile" value="peaks_control.bed"/> + <param name="left" value="-2000"/> + <param name="right" value="2000"/> + <param name="EnhLeft" value="-30000"/> + <param name="DownGene" value="5000"/> + <param name="input_organism_selector" value="Mouse"/> + <param name="version" value="mm9"/> + <param name="use_reg_selector" value="yes"/> + <param name="regfile" value="Probesets_FC1.5_10022011.txt"/> + <param name="if_PDF" value="0"/> + <output name="outputPNG" file="test_annotatePeaks_1.dat" ftype="png"/> + <output name="stats" file="test_annotatePeaks_2.dat" ftype="tabular"/> + <output name="log" file="test_annotatePeaks_3.dat" ftype="log"/> + <output name="statsControl" file="test_annotatePeaks_4.dat" ftype="tabular"/> + </test> + </tests> + <help> +**What it does** + +This tool annotates peaks with genomic feature (promoter, enhancer, exon, intron, etc.) and creates a .png file with distribution + + </help> + <citations> + <citation type="bibtex">@article{Boeva01102012, + author = {Boeva, Valentina and Lermine, Alban and Barette, Camille and Guillouf, Christel and Barillot, Emmanuel}, + title = {Nebula—a web-server for advanced ChIP-seq data analysis}, + volume = {28}, + number = {19}, + pages = {2517-2519}, + year = {2012}, + doi = {10.1093/bioinformatics/bts463}, + URL = {http://bioinformatics.oxfordjournals.org/content/28/19/2517.abstract}, + eprint = {http://bioinformatics.oxfordjournals.org/content/28/19/2517.full.pdf+html}, + journal = {Bioinformatics} + }</citation> + </citations> +</tool>
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183467012 183469366 183468086 25.558 + 183467012 183469366 255,120,11 1 2354 0 +chr1 183789933 183791449 183790892 26.353 + 183789933 183791449 255,120,11 1 1516 0 +chr1 184174646 184177272 184175307 23.618 + 184174646 184177272 255,120,11 1 2626 0 +chr1 184183197 184187309 184185406 19.718 + 184183197 184187309 255,120,11 1 4112 0 +chr1 184271354 184272113 184271852 16.483 + 184271354 184272113 255,120,11 1 759 0 +chr1 184287360 184290486 184288441 22.542 + 184287360 184290486 255,120,11 1 3126 0 +chr1 184330274 184333645 184332447 15.043 + 184330274 184333645 255,120,11 1 3371 0 +chr1 184434000 184435322 184434443 17.394 + 184434000 184435322 255,120,11 1 1322 0 +chr1 184857681 184859946 184858836 40.630 + 184857681 184859946 255,120,11 1 2265 0 +chr1 186168611 186169426 186169091 31.688 + 186168611 186169426 255,120,11 1 815 0 +chr1 186676509 186678645 186677353 23.983 + 186676509 186678645 255,120,11 1 2136 0 +chr1 186786807 186788445 186787356 38.701 + 186786807 186788445 255,120,11 1 1638 0 +chr1 187292371 187295833 187293754 34.926 + 187292371 187295833 255,120,11 1 3462 0 +chr1 187297265 187298979 187297837 17.624 + 187297265 187298979 255,120,11 1 1714 0 +chr1 188981843 188984332 188982985 39.932 + 188981843 188984332 255,120,11 1 2489 0 +chr1 189076902 189079238 189078472 17.800 + 189076902 189079238 255,120,11 1 2336 0 +chr1 190660946 190663842 190661923 19.813 + 190660946 190663842 255,120,11 1 2896 0 +chr1 190908684 190910801 190909362 18.217 + 190908684 190910801 255,120,11 1 2117 0 +chr1 191743560 191747573 191745411 15.543 + 191743560 191747573 255,120,11 1 4013 0 +chr1 191756537 191758282 191757576 45.918 + 191756537 191758282 255,120,11 1 1745 0 +chr1 192663449 192665927 192665196 15.149 + 192663449 192665927 255,120,11 1 2478 0 +chr1 192751984 192753614 192752374 28.623 + 192751984 192753614 255,120,11 1 1630 0 +chr1 192795085 192799106 192798318 16.157 + 192795085 192799106 255,120,11 1 4021 0 +chr1 192877253 192879807 192879235 14.524 + 192877253 192879807 255,120,11 1 2554 0 +chr1 192910609 192911926 192910987 30.443 + 192910609 192911926 255,120,11 1 1317 0 +chr1 192937804 192939516 192938912 25.093 + 192937804 192939516 255,120,11 1 1712 0 +chr1 192956181 192958637 192956859 14.645 + 192956181 192958637 255,120,11 1 2456 0 +chr1 192961824 192963730 192962512 17.926 + 192961824 192963730 255,120,11 1 1906 0 +chr1 193073417 193075666 193073983 44.110 + 193073417 193075666 255,120,11 1 2249 0 +chr1 193090098 193092023 193090833 14.577 + 193090098 193092023 255,120,11 1 1925 0 +chr1 193136010 193137719 193136667 52.718 + 193136010 193137719 255,120,11 1 1709 0 +chr1 193146718 193150678 193149744 94.908 + 193146718 193150678 255,120,11 1 3960 0 +chr1 193198447 193200447 193199761 22.740 + 193198447 193200447 255,120,11 1 2000 0 +chr1 193220599 193222535 193221290 25.244 + 193220599 193222535 255,120,11 1 1936 0 +chr1 193243881 193246848 193245119 53.118 + 193243881 193246848 255,120,11 1 2967 0 +chr1 193274298 193275606 193274628 19.345 + 193274298 193275606 255,120,11 1 1308 0 +chr1 193357528 193358638 193358158 14.826 + 193357528 193358638 255,120,11 1 1110 0 +chr1 193397840 193400580 193399573 36.214 + 193397840 193400580 255,120,11 1 2740 0 +chr1 193579631 193581813 193580601 15.117 + 193579631 193581813 255,120,11 1 2182 0 +chr1 193673809 193677186 193676028 26.539 + 193673809 193677186 255,120,11 1 3377 0 +chr1 193678745 193680293 193679584 20.146 + 193678745 193680293 255,120,11 1 1548 0 +chr1 193697427 193701297 193699744 50.673 + 193697427 193701297 255,120,11 1 3870 0 +chr1 193739853 193742679 193741009 62.815 + 193739853 193742679 255,120,11 1 2826 0 +chr1 193813273 193814594 193813883 15.771 + 193813273 193814594 255,120,11 1 1321 0 +chr1 193894134 193895937 193895049 14.635 + 193894134 193895937 255,120,11 1 1803 0 +chr1 193902015 193903929 193902594 16.281 + 193902015 193903929 255,120,11 1 1914 0 +chr1 194885738 194887518 194886612 14.544 + 194885738 194887518 255,120,11 1 1780 0 +chr1 194998924 195000733 194999992 21.493 + 194998924 195000733 255,120,11 1 1809 0 +chr1 195026428 195029033 195027864 22.410 + 195026428 195029033 255,120,11 1 2605 0 +chr1 195229820 195230657 195230341 15.737 + 195229820 195230657 255,120,11 1 837 0 +chr1 195234215 195235310 195234523 27.787 + 195234215 195235310 255,120,11 1 1095 0 +chr1 195541028 195542548 195541891 14.913 + 195541028 195542548 255,120,11 1 1520 0 +chr1 196006842 196007962 196007511 15.796 + 196006842 196007962 255,120,11 1 1120 0 +chr1 196670238 196671698 196670835 22.287 + 196670238 196671698 255,120,11 1 1460 0 +chr1 196810899 196813250 196812184 24.401 + 196810899 196813250 255,120,11 1 2351 0 +chr1 197067024 197068314 197067920 53.613 + 197067024 197068314 255,120,11 1 1290 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peaks_test.bed Wed May 25 09:43:12 2016 -0400 @@ -0,0 +1,52 @@ +track name='Control' description='Control' +chr1 5098753 5100098 5099525 30.340 + 5098753 5100098 255,120,11 1 1345 0 +chr1 24740336 24742942 24741035 14.761 + 24740336 24742942 255,120,11 1 2606 0 +chr1 26742253 26745384 26743917 35.652 + 26742253 26745384 255,120,11 1 3131 0 +chr1 85080880 85082307 85081583 16.460 + 85080880 85082307 255,120,11 1 1427 0 +chr1 85082307 85083866 85082969 17.508 + 85082307 85083866 255,120,11 1 1559 0 +chr1 85083866 85085683 85084958 18.151 + 85083866 85085683 255,120,11 1 1817 0 +chr1 85086721 85088276 85087510 20.363 + 85086721 85088276 255,120,11 1 1555 0 +chr1 85093203 85094671 85093546 16.670 + 85093203 85094671 255,120,11 1 1468 0 +chr1 85240563 85242641 85241538 17.296 + 85240563 85242641 255,120,11 1 2078 0 +chr1 85246352 85247580 85247301 16.999 + 85246352 85247580 255,120,11 1 1228 0 +chr1 85253320 85257213 85254272 16.447 + 85253320 85257213 255,120,11 1 3893 0 +chr1 85257621 85259101 85258529 21.444 + 85257621 85259101 255,120,11 1 1480 0 +chr1 85259545 85260323 85259967 15.712 + 85259545 85260323 255,120,11 1 778 0 +chr1 85270080 85271421 85271052 19.694 + 85270080 85271421 255,120,11 1 1341 0 +chr1 85272884 85274153 85273226 22.711 + 85272884 85274153 255,120,11 1 1269 0 +chr1 85274153 85275922 85274451 28.374 + 85274153 85275922 255,120,11 1 1769 0 +chr1 85275922 85278661 85277009 21.258 + 85275922 85278661 255,120,11 1 2739 0 +chr1 85280947 85281918 85281246 15.619 + 85280947 85281918 255,120,11 1 971 0 +chr1 85305760 85306442 85306162 16.120 + 85305760 85306442 255,120,11 1 682 0 +chr1 87377795 87378470 87378067 18.535 + 87377795 87378470 255,120,11 1 675 0 +chr1 87484790 87486388 87485192 14.833 + 87484790 87486388 255,120,11 1 1598 0 +chr1 87487300 87490747 87487765 39.111 + 87487300 87490747 255,120,11 1 3447 0 +chr1 87517743 87519910 87518396 16.896 + 87517743 87519910 255,120,11 1 2167 0 +chr1 87519910 87523146 87521627 21.372 + 87519910 87523146 255,120,11 1 3236 0 +chr1 90112957 90116251 90114826 17.112 + 90112957 90116251 255,120,11 1 3294 0 +chr1 90129280 90131003 90129865 18.014 + 90129280 90131003 255,120,11 1 1723 0 +chr1 90149913 90155167 90154240 15.666 + 90149913 90155167 255,120,11 1 5254 0 +chr1 90161629 90167024 90164681 15.647 + 90161629 90167024 255,120,11 1 5395 0 +chr1 90196885 90200154 90198304 17.008 + 90196885 90200154 255,120,11 1 3269 0 +chr1 90200154 90202008 90201761 15.754 + 90200154 90202008 255,120,11 1 1854 0 +chr1 90622832 90623575 90623101 18.059 + 90622832 90623575 255,120,11 1 743 0 +chr1 104524314 104525195 104524820 18.655 + 104524314 104525195 255,120,11 1 881 0 +chr1 124253099 124254836 124253796 26.800 + 124253099 124254836 255,120,11 1 1737 0 +chr1 128925924 128926872 128926604 23.313 + 128925924 128926872 255,120,11 1 948 0 +chr1 172999429 173000226 172999818 20.122 + 172999429 173000226 255,120,11 1 797 0 +chr1 173004303 173004972 173004678 20.0 + 173004303 173004972 255,120,11 1 669 0 +chr1 173445362 173446039 173445660 15.539 + 173445362 173446039 255,120,11 1 677 0 +chr1 173446039 173448068 173447027 15.857 + 173446039 173448068 255,120,11 1 2029 0 +chr1 173448068 173448969 173448585 15.122 + 173448068 173448969 255,120,11 1 901 0 +chr1 173459672 173460984 173460431 17.304 + 173459672 173460984 255,120,11 1 1312 0 +chr1 173460984 173462519 173461358 16.876 + 173460984 173462519 255,120,11 1 1535 0 +chr1 173463168 173465077 173463594 20.211 + 173463168 173465077 255,120,11 1 1909 0 +chr1 173469908 173472042 173471498 20.587 + 173469908 173472042 255,120,11 1 2134 0 +chr1 173480851 173483155 173481939 16.263 + 173480851 173483155 255,120,11 1 2304 0 +chr1 173485968 173487517 173486922 16.472 + 173485968 173487517 255,120,11 1 1549 0 +chr1 173488643 173490235 173489318 15.417 + 173488643 173490235 255,120,11 1 1592 0 +chr1 173494034 173495040 173494357 17.452 + 173494034 173495040 255,120,11 1 1006 0 +chr1 173495040 173496926 173495733 14.890 + 173495040 173496926 255,120,11 1 1886 0 +chr1 173509347 173510690 173509867 16.537 + 173509347 173510690 255,120,11 1 1343 0 +chr1 180991269 180993616 180993114 14.523 + 180991269 180993616 255,120,11 1 2347 0 +chr1 197067549 197068732 197067936 28.745 + 197067549 197068732 255,120,11 1 1183 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_annotatePeaks_2.dat Wed May 25 09:43:12 2016 -0400 @@ -0,0 +1,66 @@ +Chromosome Start End Max Score DistTSS Type TypeIntra Reg FoldChange DistTE GeneName GeneCoordinates +chr1 5098753 5100098 5099525 30.34 26272 intragenic intron no-response 0.943752122 -53105 Atp6v1h chr1:5073253-5152630;5073253,5074497,5079089,5083443,5085695,5088109,5091150,5107470,5114357,5123164,5125892,5133830,5140028,5152185,-5073359,5074644,5079192,5083533,5085809,5088214,5091204,5107568,5114550,5123343,5126018,5133932,5140142,5152630, +chr1 24740336 24742942 24741035 14.761 55653 intragenic f_intron no-response 0.97898714 -82111 Lmbrd1 chr1:24685382-24823146;24685382,24742241,24749785,24761665,24762821,24768356,24771753,24785390,24788591,24800727,24801100,24801710,24803649,24805644,24819036,24819467,-24685655,24742418,24749846,24761763,24762889,24768445,24771827,24785516,24788744,24800792,24801203,24801815,24803799,24805723,24819128,24823146, +chr1 26742253 26745384 26743917 35.652 388 immediateDownstream f_intron NA 1 -5272 4931408C20Rik chr1:26738645-26744305;26738645,26744085,-26742756,26744305, +chr1 85080880 85082307 85081583 16.46 24845 5kbDownstream NA no-response 1.000134768 3130 A530032D15Rik chr1:85084713-85106428;85084713,85086101,85087651,85090871,85096051,85097106,85105911,-85085391,85086155,85087764,85090934,85096223,85097269,85106428, +chr1 85082307 85083866 85082969 17.508 23459 5kbDownstream NA no-response 1.000134768 1744 A530032D15Rik chr1:85084713-85106428;85084713,85086101,85087651,85090871,85096051,85097106,85105911,-85085391,85086155,85087764,85090934,85096223,85097269,85106428, +chr1 85083866 85085683 85084958 18.151 21470 intragenic exon no-response 1.000134768 -245 A530032D15Rik chr1:85084713-85106428;85084713,85086101,85087651,85090871,85096051,85097106,85105911,-85085391,85086155,85087764,85090934,85096223,85097269,85106428, +chr1 85086721 85088276 85087510 20.363 18918 intragenic intron no-response 1.000134768 -2797 A530032D15Rik chr1:85084713-85106428;85084713,85086101,85087651,85090871,85096051,85097106,85105911,-85085391,85086155,85087764,85090934,85096223,85097269,85106428, +chr1 85093203 85094671 85093546 16.67 12882 intragenic intron no-response 1.000134768 -8833 A530032D15Rik chr1:85084713-85106428;85084713,85086101,85087651,85090871,85096051,85097106,85105911,-85085391,85086155,85087764,85090934,85096223,85097269,85106428, +chr1 85240563 85242641 85241538 17.296 25603 5kbDownstream NA NA 1 1380 C130026I21Rik chr1:85242918-85267141;85242918,85244873,85250677,85251088,85256269,85257311,85266607,-85243711,85244954,85250758,85251151,85256441,85257474,85267141, +chr1 85246352 85247580 85247301 16.999 19840 intragenic intron NA 1 -4383 C130026I21Rik chr1:85242918-85267141;85242918,85244873,85250677,85251088,85256269,85257311,85266607,-85243711,85244954,85250758,85251151,85256441,85257474,85267141, +chr1 85253320 85257213 85254272 16.447 12869 intragenic intron NA 1 -11354 C130026I21Rik chr1:85242918-85267141;85242918,85244873,85250677,85251088,85256269,85257311,85266607,-85243711,85244954,85250758,85251151,85256441,85257474,85267141, +chr1 85257621 85259101 85258529 21.444 8612 intragenic f_intron NA 1 -15611 C130026I21Rik chr1:85242918-85267141;85242918,85244873,85250677,85251088,85256269,85257311,85266607,-85243711,85244954,85250758,85251151,85256441,85257474,85267141, +chr1 85259545 85260323 85259967 15.712 7174 intragenic f_intron NA 1 -17049 C130026I21Rik chr1:85242918-85267141;85242918,85244873,85250677,85251088,85256269,85257311,85266607,-85243711,85244954,85250758,85251151,85256441,85257474,85267141, +chr1 85270080 85271421 85271052 19.694 -3911 enhancer NA NA 1 -28134 C130026I21Rik chr1:85242918-85267141;85242918,85244873,85250677,85251088,85256269,85257311,85266607,-85243711,85244954,85250758,85251151,85256441,85257474,85267141, +chr1 85272884 85274153 85273226 22.711 -6085 enhancer NA NA 1 -30308 C130026I21Rik chr1:85242918-85267141;85242918,85244873,85250677,85251088,85256269,85257311,85266607,-85243711,85244954,85250758,85251151,85256441,85257474,85267141, +chr1 85274153 85275922 85274451 28.374 -7310 enhancer NA NA 1 -31533 C130026I21Rik chr1:85242918-85267141;85242918,85244873,85250677,85251088,85256269,85257311,85266607,-85243711,85244954,85250758,85251151,85256441,85257474,85267141, +chr1 85275922 85278661 85277009 21.258 -9868 enhancer NA NA 1 -34091 C130026I21Rik chr1:85242918-85267141;85242918,85244873,85250677,85251088,85256269,85257311,85266607,-85243711,85244954,85250758,85251151,85256441,85257474,85267141, +chr1 85280947 85281918 85281246 15.619 -14105 enhancer NA NA 1 -38328 C130026I21Rik chr1:85242918-85267141;85242918,85244873,85250677,85251088,85256269,85257311,85266607,-85243711,85244954,85250758,85251151,85256441,85257474,85267141, +chr1 85305760 85306442 85306162 16.12 -39021 intergenic NA NA 1 -63244 C130026I21Rik chr1:85242918-85267141;85242918,85244873,85250677,85251088,85253960,85256269,85257311,85266607,-85243711,85244954,85250758,85251151,85254044,85256441,85257474,85267141, +chr1 87377795 87378470 87378067 18.535 -119210 intergenic NA NA 1 -163544 Sp140 chr1:87497277-87541611;87497277,87506268,87507313,87511378,87511762,87516630,87518228,87522674,87527034,87529052,87532133,87534398,87538307,87539116,87539509,87539777,87541158,-87497766,87506431,87507485,87511429,87511846,87516732,87518282,87522740,87527139,87529195,87532181,87534440,87538423,87539222,87539587,87539921,87541611, +chr1 87484790 87486388 87485192 14.833 15274 intragenic intron no-response 0.998181719 -11718 Sp110 chr1:87473474-87500466;87473474,87475631,87476218,87480086,87481477,87482789,87484036,87485688,87488097,87490839,87492536,87495203,87500409,-87473920,87475774,87476320,87480155,87481627,87482870,87484114,87485766,87488364,87491008,87492684,87495354,87500466, +chr1 87484790 87486388 87485192 14.833 -12085 enhancer NA NA 1 -56419 Sp140 chr1:87497277-87541611;87497277,87506268,87507313,87511378,87511762,87516630,87518228,87522674,87527034,87529052,87532133,87534398,87538307,87539116,87539509,87539777,87541158,-87497766,87506431,87507485,87511429,87511846,87516732,87518282,87522740,87527139,87529195,87532181,87534440,87538423,87539222,87539587,87539921,87541611, +chr1 87487300 87490747 87487765 39.111 12701 intragenic intron no-response 0.998181719 -14291 Sp110 chr1:87473474-87500466;87473474,87475631,87476218,87480086,87481477,87482789,87484036,87485688,87488097,87490839,87492536,87495203,87500409,-87473920,87475774,87476320,87480155,87481627,87482870,87484114,87485766,87488364,87491008,87492684,87495354,87500466, +chr1 87487300 87490747 87487765 39.111 -9512 enhancer NA NA 1 -53846 Sp140 chr1:87497277-87541611;87497277,87506268,87507313,87511378,87511762,87516630,87518228,87522674,87527034,87529052,87532133,87534398,87538307,87539116,87539509,87539777,87541158,-87497766,87506431,87507485,87511429,87511846,87516732,87518282,87522740,87527139,87529195,87532181,87534440,87538423,87539222,87539587,87539921,87541611, +chr1 87517743 87519910 87518396 16.896 21119 intragenic intron NA 1 -23215 Sp140 chr1:87497277-87541611;87497277,87506268,87507313,87511378,87511762,87516630,87518228,87522674,87527034,87529052,87532133,87534398,87538307,87539116,87539509,87539777,87541158,-87497766,87506431,87507485,87511429,87511846,87516732,87518282,87522740,87527139,87529195,87532181,87534440,87538423,87539222,87539587,87539921,87541611, +chr1 87517743 87519910 87518396 16.896 -17930 enhancer NA no-response 0.998181719 -44922 Sp110 chr1:87473474-87500466;87473474,87475631,87476218,87480086,87481477,87482789,87484036,87485688,87488097,87490839,87492536,87495203,87500409,-87473920,87475774,87476320,87480155,87481627,87482870,87484114,87485766,87488364,87491008,87492684,87495354,87500466, +chr1 87519910 87523146 87521627 21.372 24350 intragenic intron NA 1 -19984 Sp140 chr1:87497277-87541611;87497277,87506268,87507313,87511378,87511762,87516630,87518228,87522674,87527034,87529052,87532133,87534398,87538307,87539116,87539509,87539777,87541158,-87497766,87506431,87507485,87511429,87511846,87516732,87518282,87522740,87527139,87529195,87532181,87534440,87538423,87539222,87539587,87539921,87541611, +chr1 87519910 87523146 87521627 21.372 -21161 enhancer NA no-response 0.998181719 -48153 Sp110 chr1:87473474-87500466;87473474,87475631,87476218,87480086,87481477,87482789,87484036,87485688,87488097,87490839,87492536,87495203,87500409,-87473920,87475774,87476320,87480155,87481627,87482870,87484114,87485766,87488364,87491008,87492684,87495354,87500466, +chr1 90112957 90116251 90114826 17.112 6293 intragenic exon NA 1 -1751 Ugt1a1 chr1:90108533-90116577;90108533,90111618,90112369,90112712,90114701,-90109446,90111750,90112457,90112932,90116577, +chr1 90112957 90116251 90114826 17.112 17641 intragenic exon NA 1 -1751 Ugt1a2 chr1:90097185-90116577;90097185,90111618,90112369,90112712,90114701,-90098075,90111750,90112457,90112932,90116577, +chr1 90112957 90116251 90114826 17.112 52240 intragenic exon NA 1 -1751 Ugt1a5 chr1:90062586-90116577;90062586,90111618,90112369,90112712,90114701,-90063478,90111750,90112457,90112932,90116577, +chr1 90112957 90116251 90114826 17.112 83443 intragenic exon no-response 0.999775929 -1751 Ugt1a6a chr1:90031383-90116577;90031383,90035047,90111618,90112369,90112712,90114701,-90031510,90035906,90111750,90112457,90112932,90116577, +chr1 90112957 90116251 90114826 17.112 114995 intragenic exon NA 1 -747 Ugt1a6b chr1:89999831-90115573;89999831,90003515,90111618,90112369,90112712,90114701,-89999953,90004374,90111750,90112457,90112932,90115573, +chr1 90112957 90116251 90114826 17.112 123251 intragenic exon NA 1 -1751 Ugt1a7c chr1:89991575-90116577;89991575,90111618,90112369,90112712,90114701,-89992553,90111750,90112457,90112932,90116577, +chr1 90112957 90116251 90114826 17.112 147473 intragenic exon no-response 1.00331233 -1751 Ugt1a9 chr1:89967353-90116577;89967353,90111618,90112369,90112712,90114701,-89968253,90111750,90112457,90112932,90116577, +chr1 90112957 90116251 90114826 17.112 162841 intragenic exon NA 1 -1751 Ugt1a10 chr1:89951985-90116577;89951985,90111618,90112369,90112712,90114701,-89952911,90111750,90112457,90112932,90116577, +chr1 90129280 90131003 90129865 18.014 6271 intragenic jonction NA 1 -28999 Heatr7b1 chr1:90123594-90158864;90123594,90124628,90124801,90126916,90127200,90128818,90129891,90130576,90131163,90131528,90131764,90131947,90133229,90134047,90134419,90135468,90136693,90137253,90137645,90138117,90138978,90139243,90140505,90141518,90142562,90143710,90144322,90145126,90146277,90146839,90147819,90148910,90151432,90151664,90152112,90152631,90152974,90153225,90154284,90155157,90155693,90156104,90156479,-90123803,90124721,90124983,90127048,90127363,90128917,90130043,90130691,90131185,90131637,90131843,90132061,90133306,90134167,90134530,90135616,90136734,90137395,90137698,90138225,90139098,90139366,90140658,90141641,90142642,90143819,90144418,90145231,90146401,90146958,90147972,90149065,90151592,90151868,90152255,90152746,90153124,90153408,90154440,90155289,90155796,90156170,90158864, +chr1 90149913 90155167 90154240 15.666 30646 intragenic jonction NA 1 -4624 Heatr7b1 chr1:90123594-90158864;90123594,90124628,90124801,90126916,90127200,90128818,90129891,90130576,90131163,90131528,90131764,90131947,90133229,90134047,90134419,90135468,90136693,90137253,90137645,90138117,90138978,90139243,90140505,90141518,90142562,90143710,90144322,90145126,90146277,90146839,90147819,90148910,90151432,90151664,90152112,90152631,90152974,90153225,90154284,90155157,90155693,90156104,90156479,-90123803,90124721,90124983,90127048,90127363,90128917,90130043,90130691,90131185,90131637,90131843,90132061,90133306,90134167,90134530,90135616,90136734,90137395,90137698,90138225,90139098,90139366,90140658,90141641,90142642,90143819,90144418,90145231,90146401,90146958,90147972,90149065,90151592,90151868,90152255,90152746,90153124,90153408,90154440,90155289,90155796,90156170,90158864, +chr1 90149913 90155167 90154240 15.666 19914 5kbDownstream NA NA 1 1190 Hjurp chr1:90155430-90174154;90155430,90164522,90165895,90166776,90169303,90171616,90173793,90173948,-90163233,90164601,90165988,90166874,90169340,90171672,90173860,90174154, +chr1 90161629 90167024 90164681 15.647 9451 intragenic intron NA 1 -3279 A730008H23Rik chr1:90161402-90174132;90161402,90164522,90171616,90173795,90173948,-90163233,90164601,90171674,90173860,90174132, +chr1 90161629 90167024 90164681 15.647 9473 intragenic intron NA 1 -9251 Hjurp chr1:90155430-90174154;90155430,90164522,90165895,90166776,90169303,90171616,90173793,90173948,-90163233,90164601,90165988,90166874,90169340,90171672,90173860,90174154, +chr1 90196885 90200154 90198304 17.008 -24172 enhancer NA NA 1 -36902 A730008H23Rik chr1:90161402-90174132;90161402,90164522,90171616,90173795,90173948,-90163233,90164601,90171674,90173860,90174132, +chr1 90196885 90200154 90198304 17.008 -24150 enhancer NA NA 1 -42874 Hjurp chr1:90155430-90174154;90155430,90164522,90165895,90166776,90169303,90171616,90173793,90173948,-90163233,90164601,90165988,90166874,90169340,90171672,90173860,90174154, +chr1 90200154 90202008 90201761 15.754 -1525 promoter NA no-response 1.002545611 -83665 Trpm8 chr1:90203286-90285426;90203286,90204384,90215539,90217438,90221956,90222979,90224725,90227270,90229249,90233687,90237879,90239807,90244618,90246421,90247430,90247924,90250983,90251705,90256226,90257159,90258485,90261614,90270823,90276314,90277543,90281237,90285115,-90203366,90204477,90215661,90217512,90222113,90223157,90224898,90227445,90229317,90233885,90237982,90239926,90244909,90246517,90247560,90248070,90251096,90251922,90256318,90257301,90258657,90261792,90271014,90276414,90277577,90281328,90285426, +chr1 90622832 90623575 90623101 18.059 -24335 enhancer NA no-response 1.001685567 -28301 Arl4c chr1:90594800-90598766;90594800,-90598766, +chr1 104524314 104525195 104524820 18.655 -2140575 intergenic NA no-response 0.999542308 -2367238 Cdh20 chr1:106665395-106892058;106665395,106830533,106837608,106838674,106841768,106843900,106850405,106867397,106871570,106875556,106881247,106890456,-106665475,106830919,106837903,106838794,106841936,106844088,106850659,106867534,106871692,106875674,106881499,106892058, +chr1 124253099 124254836 124253796 26.8 -789239 intergenic NA NA 1 -803385 Ddx18 chr1:123450411-123464557;123450411,123451792,123452267,123453981,123454987,123455742,123456708,123457857,123458266,123458635,123461069,123462457,123464367,-123450715,123451970,123452324,123454095,123455140,123455904,123456848,123458172,123458367,123458771,123461180,123462745,123464557, +chr1 128925924 128926872 128926604 23.313 -174958 intergenic NA no-response 0.851334441 -452945 Mgat5 chr1:129101562-129379549;129101562,129146366,129203210,129217180,129261724,129262979,129279497,129281344,129283919,129287320,129294083,129308703,129342818,129356412,129365768,129368077,129376041,129379103,-129102004,129146416,129203593,129217342,129261801,129263069,129279569,129281506,129284089,129287455,129294217,129308837,129342968,129356559,129365885,129368152,129376199,129379549, +chr1 172999429 173000226 172999818 20.122 -10284 enhancer NA no-response 0.998142456 -18519 Fcgr3 chr1:172981299-172989534;172981299,172984069,172987821,172988716,172989399,-172981983,172984324,172988079,172988737,172989534, +chr1 173004303 173004972 173004678 20 -15144 enhancer NA no-response 0.998142456 -23379 Fcgr3 chr1:172981299-172989534;172981299,172984069,172987821,172988716,172989399,-172981983,172984324,172988079,172988737,172989534, +chr1 173445362 173446039 173445660 15.539 19765 5kbDownstream NA no-response 1.004411374 2594 Itln1 chr1:173448254-173465425;173448254,173459251,173460624,173461164,173461636,173463496,173464884,173465351,-173448524,173459355,173460745,173461323,173461884,173463595,173464948,173465425, +chr1 173446039 173448068 173447027 15.857 18398 5kbDownstream NA no-response 1.004411374 1227 Itln1 chr1:173448254-173465425;173448254,173459251,173460624,173461164,173461636,173463496,173464884,173465351,-173448524,173459355,173460745,173461323,173461884,173463595,173464948,173465425, +chr1 173448068 173448969 173448585 15.122 16840 intragenic intron no-response 1.004411374 -331 Itln1 chr1:173448254-173465425;173448254,173459251,173460624,173461164,173461636,173463496,173464884,173465351,-173448524,173459355,173460745,173461323,173461884,173463595,173464948,173465425, +chr1 173459672 173460984 173460431 17.304 4994 intragenic intron no-response 1.004411374 -12177 Itln1 chr1:173448254-173465425;173448254,173459251,173460624,173461164,173461636,173463496,173464884,173465351,-173448524,173459355,173460745,173461323,173461884,173463595,173464948,173465425, +chr1 173460984 173462519 173461358 16.876 4067 intragenic jonction no-response 1.004411374 -13104 Itln1 chr1:173448254-173465425;173448254,173459251,173460624,173461164,173461636,173463496,173464884,173465351,-173448524,173459355,173460745,173461323,173461884,173463595,173464948,173465425, +chr1 173463168 173465077 173463594 20.211 1831 immediateDownstream jonction no-response 1.004411374 -15340 Itln1 chr1:173448254-173465425;173448254,173459251,173460624,173461164,173461636,173463496,173464884,173465351,-173448524,173459355,173460745,173461323,173461884,173463595,173464948,173465425, +chr1 173469908 173472042 173471498 20.587 -17825 enhancer NA no-response 1.012030021 -43949 Cd244 chr1:173489323-173515447;173489323,173503811,173504223,173507373,173507945,173509229,173510888,173511773,173512934,-173489516,173504135,173504499,173507478,173508100,173509301,173510951,173511830,173515447, +chr1 173480851 173483155 173481939 16.263 -16514 enhancer NA no-response 1.004411374 -33685 Itln1 chr1:173448254-173465425;173448254,173459251,173460624,173461164,173461636,173463496,173464884,173465351,-173448524,173459355,173460745,173461323,173461884,173463595,173464948,173465425, +chr1 173485968 173487517 173486922 16.472 -21497 enhancer NA no-response 1.004411374 -38668 Itln1 chr1:173448254-173465425;173448254,173459251,173460624,173461164,173461636,173463496,173464884,173465351,-173448524,173459355,173460745,173461323,173461884,173463595,173464948,173465425, +chr1 173488643 173490235 173489318 15.417 -5 promoter NA no-response 1.012030021 -26129 Cd244 chr1:173489323-173515447;173489323,173503811,173504223,173507373,173507945,173509229,173510888,173511773,173512934,-173489516,173504135,173504499,173507478,173508100,173509301,173510951,173511830,173515447, +chr1 173494034 173495040 173494357 17.452 5034 intragenic f_intron no-response 1.012030021 -21090 Cd244 chr1:173489323-173515447;173489323,173503811,173504223,173507373,173507945,173509229,173510888,173511773,173512934,-173489516,173504135,173504499,173507478,173508100,173509301,173510951,173511830,173515447, +chr1 173495040 173496926 173495733 14.89 6410 intragenic f_intron no-response 1.012030021 -19714 Cd244 chr1:173489323-173515447;173489323,173503811,173504223,173507373,173507945,173509229,173510888,173511773,173512934,-173489516,173504135,173504499,173507478,173508100,173509301,173510951,173511830,173515447, +chr1 173509347 173510690 173509867 16.537 20544 intragenic intron no-response 1.012030021 -5580 Cd244 chr1:173489323-173515447;173489323,173503811,173504223,173507373,173507945,173509229,173510888,173511773,173512934,-173489516,173504135,173504499,173507478,173508100,173509301,173510951,173511830,173515447, +chr1 180991269 180993616 180993114 14.523 455020 intragenic intron no-response 0.955740041 -107945 Smyd3 chr1:180885169-181448134;180885169,180902318,180973867,180980421,181016454,181022996,181024465,181335413,181340537,181341808,181353485,181447918,-180887693,180902427,180974042,180980509,181016565,181023099,181024533,181335550,181340595,181341916,181353549,181448134, +chr1 197067549 197068732 197067936 28.745 -65027 intergenic NA no-response 1.001152487 -104932 Cr2 chr1:196963004-197002909;196963004,196967368,196976165,196977116,196977765,196980325,196981318,196982077,196982473,196983330,196984253,196984605,196984771,196985609,196986463,196986789,196986972,196989391,197002746,-196965992,196967477,196976238,196977140,196977951,196980511,196981711,196982160,196982552,196983738,196984330,196984696,196984948,196986017,196986546,196986889,196987161,196989781,197002909,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_annotatePeaks_3.dat Wed May 25 09:43:12 2016 -0400 @@ -0,0 +1,34 @@ +ChIP: +Total genes : 25714 +Total Sites: 51 +Type Count Frequency +5kbDownstream 6 0.0923076923076923 +enhancer 17 0.261538461538462 +immediateDownstream 2 0.0307692307692308 +intergenic 6 0.0923076923076923 +intragenic 32 0.492307692307692 +promoter 2 0.0307692307692308 +exon 9 0.138461538461538 +f_exon 0 0 +f_intron 6 0.0923076923076923 +intron 15 0.230769230769231 +jonction 4 0.0615384615384615 + +Control: + +----------------- + +Total genes : 25714 +Total Sites: 52 +Type Count Frequency +5kbDownstream 4 0.0754716981132075 +enhancer 7 0.132075471698113 +immediateDownstream 2 0.0377358490566038 +intergenic 9 0.169811320754717 +intragenic 26 0.490566037735849 +promoter 5 0.0943396226415094 +exon 2 0.0377358490566038 +f_exon 1 0.0188679245283019 +f_intron 7 0.132075471698113 +intron 16 0.30188679245283 +jonction 2 0.0377358490566038
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_annotatePeaks_4.dat Wed May 25 09:43:12 2016 -0400 @@ -0,0 +1,54 @@ +Chromosome Start End Max Score DistTSS Type TypeIntra Reg FoldChange DistTE GeneName GeneCoordinates +chr1 51990184 51992754 51991506 185.232 -18688 enhancer NA no-response 0.99805296 -184897 Myo1b chr1:51806609-51972818;51806609,51812486,51813948,51814719,51817138,51819335,51820733,51823665,51825847,51827629,51830076,51831155,51833047,51835164,51836404,51838813,51841280,51850483,51851155,51853842,51854231,51856375,51858027,51869846,51876984,51880940,51891292,51920162,51939926,51972604,-51808140,51812614,51814101,51814852,51817245,51819470,51820808,51823752,51825934,51827698,51830226,51831249,51833248,51835391,51836605,51838876,51841385,51850549,51851242,51853961,51854379,51856479,51858126,51869910,51877031,51881045,51891387,51920278,51940070,51972818, +chr1 60126773 60128669 60127805 155.165 -27874 enhancer NA no-response 0.955993942 -81894 Ica1l chr1:60045911-60099931;60045911,60054294,60060499,60063077,60064651,60066952,60070663,60072555,60079421,60084911,60099640,-60048083,60054555,60060549,60063163,60064750,60067078,60070862,60072679,60079494,60085080,60099931, +chr1 75183604 75186098 75184689 127.048 3808 intragenic jonction NA 1 -7250 Atg9a chr1:75177439-75188497;75177439,75179165,75179467,75181029,75181262,75181626,75182239,75182524,75182763,75184258,75184518,75186136,75186685,75186876,75187396,75188397,-75178505,75179311,75179690,75181147,75181441,75181875,75182419,75182678,75183512,75184400,75184680,75186201,75186729,75187008,75187451,75188497, +chr1 134237109 134239637 134238461 126.426 25760 intergenic NA no-response 0.818992729 8396 Nuak2 chr1:134212701-134230065;134212701,134221529,134222782,134224273,134224707,134226534,134227135,134227897,-134213049,134221650,134222806,134224425,134224773,134226654,134227268,134230065, +chr1 165313138 165315235 165313947 124.948 19825 5kbDownstream NA NA 1 1092 Gorab chr1:165315039-165333772;165315039,165322540,165324721,165326942,165333653,-165316828,165322681,165324823,165327300,165333772, +chr1 64167272 64170229 64168852 113.558 -889 promoter NA up-regulated 0.59 -86606 Klf7 chr1:64082246-64167963;64082246,64088887,64125280,64167473,-64082338,64089011,64125908,64167963, +chr1 51986012 51989067 51987565 109.617 -14747 enhancer NA no-response 0.99805296 -180956 Myo1b chr1:51806609-51972818;51806609,51812486,51813948,51814719,51817138,51819335,51820733,51823665,51825847,51827629,51830076,51831155,51833047,51835164,51836404,51838813,51841280,51850483,51851155,51853842,51854231,51856375,51858027,51869846,51876984,51880940,51891292,51920162,51939926,51972604,-51808140,51812614,51814101,51814852,51817245,51819470,51820808,51823752,51825934,51827698,51830226,51831249,51833248,51835391,51836605,51838876,51841385,51850549,51851242,51853961,51854379,51856479,51858126,51869910,51877031,51881045,51891387,51920278,51940070,51972818, +chr1 182657743 182659706 182658573 108.679 2400 intragenic f_intron NA 1 -25762 Acbd3 chr1:182656173-182684335;182656173,182663296,182664507,182666822,182668593,182675201,182676924,182682289,-182656509,182663438,182664648,182666981,182668768,182675388,182677209,182684335, +chr1 88404369 88408894 88406101 101.37 -17209 enhancer NA NA 1 -21172 Ptma chr1:88423310-88427273;88423310,88425747,88426030,88426305,88426539,-88423525,88425819,88426127,88426379,88427273, +chr1 133366130 133369052 133367391 100.62 56547 intragenic intron NA 1 -185564 Srgap2 chr1:133181827-133423938;133181827,133189097,133192896,133194908,133196969,133207050,133213705,133216101,133217011,133221664,133228693,133230433,133232966,133240925,133242338,133246028,133252087,133253266,133260578,133308376,133333251,133421514,133423809,-133186317,133189422,133193043,133195089,133197049,133207275,133213811,133216236,133217089,133221725,133228718,133230461,133233051,133241123,133242440,133246253,133252216,133253482,133260641,133308539,133333444,133422170,133423938, +chr1 172637708 172641516 172639841 98.192 158061 intragenic exon NA 1 -5254 Atf6 chr1:172634587-172797902;172634587,172677236,172717476,172718738,172724087,172724787,172729744,172745553,172749377,172764950,172770811,172771816,172779247,172783035,172785243,172797780,-172640218,172677321,172717591,172718806,172724187,172724901,172729876,172745645,172749563,172765171,172771015,172771943,172779348,172783123,172785320,172797902, +chr1 89544861 89546487 89545464 95.246 28578 intragenic intron up-regulated 0.54 -71619 Inpp5d chr1:89516886-89617083;89516886,89531866,89561961,89564463,89566216,89572857,89578063,89578261,89580317,89588199,89591907,89593923,89594687,89595602,89596214,89597734,89597989,89599692,89602508,89604670,89606192,89607639,89608605,89609767,89611612,89614264,89615895,-89517206,89531930,89562112,89564638,89566357,89572945,89578144,89578333,89580441,89588306,89592010,89594120,89594805,89595699,89596353,89597843,89598078,89599774,89602598,89604784,89606275,89607727,89608755,89609864,89611888,89614859,89617083, +chr1 193146718 193150678 193149744 94.908 -99 promoter NA NA 1 -27060 Tmem206 chr1:193149843-193176804;193149843,193152061,193162660,193164605,193168855,193170638,193172246,193173567,-193149955,193152158,193162870,193164757,193168998,193170783,193172354,193176804, +chr1 36320224 36322856 36321174 93.869 -20027 enhancer NA NA 1 -124302 Uggt1 chr1:36196872-36301147;36196872,36202876,36203469,36206889,36208478,36211917,36213071,36214244,36214952,36216786,36218520,36219049,36220065,36221288,36222353,36227043,36230279,36230923,36231740,36233077,36233620,36234362,36236403,36239314,36241200,36242677,36248373,36249230,36252694,36254388,36258549,36259623,36264786,36266830,36268234,36272976,36278056,36284328,36287502,36291651,36300914,-36201096,36203030,36203586,36207004,36208639,36212100,36213156,36214346,36215041,36216871,36218606,36219208,36220255,36221368,36222456,36227139,36230410,36231055,36231947,36233172,36233644,36234461,36236524,36239479,36241332,36242813,36248459,36249350,36252845,36254480,36258610,36259723,36264887,36266909,36268331,36273151,36278169,36284459,36287585,36291787,36301147, +chr1 181474385 181478078 181476526 93.465 -133 promoter NA NA 1 -81078 Cnst chr1:181476659-181557604;181476659,181509468,181522815,181531832,181534649,181535083,181536378,181536567,181539916,181552897,181555129,-181476747,181509899,181522997,181531863,181534736,181535198,181536400,181536664,181540797,181553033,181557604, +chr1 87631082 87634013 87633129 93.188 52 immediateDownstream f_exon NA 1 -19472 A630001G21Rik chr1:87613657-87633181;87613657,87615599,87619672,87621695,87623033,87633046,-87614943,87615704,87619756,87621864,87623190,87633181, +chr1 53321101 53323020 53321996 92.607 31844 intragenic intron no-response 1.125816525 -75965 Pms1 chr1:53246031-53353840;53246031,53248943,53251771,53253666,53263405,53264419,53264806,53273074,53313472,53324671,53331913,53338784,53353729,-53246342,53249104,53251902,53254146,53264256,53264563,53264929,53273191,53313636,53324774,53332096,53338936,53353840, +chr1 133553853 133555841 133554639 91.135 19749 intragenic f_intron NA 1 -17445 Ctse chr1:133534890-133572084;133534890,133558452,133559189,133559887,133560860,133564613,133567262,133568780,133569021,133571357,-133535134,133558643,133559346,133560005,133560979,133564813,133567385,133568922,133569120,133572084, +chr1 24003670 24006731 24005152 85.071 7327 intragenic intron no-response 1.045612002 -2375 1110058L19Rik chr1:24002777-24012479;24002777,24009995,24012384,-24003199,24010145,24012479, +chr1 36186500 36189331 36187307 83.732 62063 intergenic NA no-response 1.145451072 24016 Hs6st1 chr1:36125244-36163291;36125244,36160357,-36126029,36163291, +chr1 182190527 182194213 182191254 82.962 -15173 enhancer NA up-regulated 0.64 -34120 Psen2 chr1:182157134-182176081;182157134,182158973,182159516,182159972,182163741,182165119,182166041,182169003,182170861,182175744,182175994,-182157859,182159092,182159618,182160056,182163840,182165340,182166109,182169145,182171076,182175888,182176081, +chr1 55038767 55040799 55039738 82.324 44584 5kbDownstream NA up-regulated 0.47 2274 Sf3b1 chr1:55042012-55084322;55042012,55044782,55047146,55051173,55052209,55053660,55053855,55054881,55056470,55056858,55057085,55057487,55057855,55058226,55059947,55060136,55062645,55063014,55064323,55068945,55071326,55073219,55073622,55076077,55084182,-55044336,55044999,55047419,55051305,55052330,55053772,55054038,55055103,55056596,55057005,55057231,55057758,55057942,55058406,55060049,55060334,55062767,55063227,55064561,55069116,55071406,55073334,55073727,55076244,55084322, +chr1 36975862 36978131 36976794 81.087 19578 intragenic f_intron NA 1 -127761 Tmem131 chr1:36849033-36996372;36849033,36850888,36851648,36851945,36852139,36853006,36855786,36856123,36858669,36861312,36864728,36865671,36867125,36868252,36869005,36869401,36872299,36872731,36872953,36875502,36875737,36875907,36879911,36881560,36882056,36882273,36883855,36884106,36884909,36886410,36890340,36891460,36891606,36894803,36897233,36898438,36911688,36929356,36938178,36946108,36996009,-36850050,36851043,36851746,36852042,36852261,36853169,36855936,36856248,36858797,36861491,36865321,36865830,36867311,36868439,36869148,36869553,36872366,36872841,36873092,36875620,36875813,36876060,36879998,36881665,36882191,36882384,36884026,36884260,36885018,36886519,36890402,36891517,36891757,36894884,36897356,36898555,36911812,36929425,36938219,36946170,36996372, +chr1 177454643 177455632 177455221 80.157 -32545 intergenic NA no-response 1.000705337 -466015 Rgs7 chr1:176989206-177422676;176989206,177008319,177009535,177014102,177016246,177019549,177021124,177023934,177051858,177052025,177053061,177079782,177083254,177119307,177200947,177421183,177422391,-176989925,177008409,177009722,177014228,177016357,177019611,177021223,177024009,177051940,177052102,177053126,177079834,177083361,177119358,177201044,177421307,177422676, +chr1 59886380 59888476 59887333 77.115 65853 intragenic intron up-regulated 0.35 -40370 Bmpr2 chr1:59821480-59927703;59821480,59870431,59872084,59898274,59899586,59902321,59903901,59908021,59909137,59916016,59920624,59924179,59927078,-59821572,59870602,59872255,59898385,59899678,59902552,59904016,59908182,59909285,59916153,59920797,59925459,59927703, +chr1 131672587 131675030 131673879 76.84 503999 intragenic intron no-response 0.990070994 -441976 Thsd7b chr1:131169880-132115855;131169880,131327373,131491946,131509686,131525453,131564390,131574625,131655022,131656845,131672869,131713219,131719168,131812129,131817824,131847966,131999647,132013136,132056150,132059396,132061625,132076928,132085036,132086432,132086707,132089130,132091683,132106817,132114675,-131170177,131327546,131492757,131509935,131525623,131564546,131574823,131655214,131657080,131672985,131713349,131719272,131812324,131818091,131848145,131999781,132013287,132056292,132059512,132061743,132077074,132085196,132086606,132086803,132089213,132091876,132106905,132115855, +chr1 52778801 52780335 52779661 76.839 4501 intragenic f_intron NA 1 -62832 Mfsd6 chr1:52716829-52784162;52716829,52719233,52720128,52733321,52765007,52783866,-52717931,52719332,52720290,52733419,52766599,52784162, +chr1 89522665 89524223 89523172 74.658 6286 intragenic f_intron up-regulated 0.54 -93911 Inpp5d chr1:89516886-89617083;89516886,89531866,89561961,89564463,89566216,89572857,89578063,89578261,89580317,89588199,89591907,89593923,89594687,89595602,89596214,89597734,89597989,89599692,89602508,89604670,89606192,89607639,89608605,89609767,89611612,89614264,89615895,-89517206,89531930,89562112,89564638,89566357,89572945,89578144,89578333,89580441,89588306,89592010,89594120,89594805,89595699,89596353,89597843,89598078,89599774,89602598,89604784,89606275,89607727,89608755,89609864,89611888,89614859,89617083, +chr1 74485100 74489344 74486296 71.038 104564 intragenic intron no-response 1.215744803 -4213 Usp37 chr1:74482083-74590860;74482083,74486533,74488105,74490986,74497068,74499260,74500401,74502652,74506488,74508139,74513488,74514840,74517110,74517869,74518128,74521559,74524620,74526225,74532554,74533192,74536663,74539478,74542203,74546529,74577636,74590748,-74486052,74486672,74488175,74491102,74497129,74499427,74500657,74502794,74506554,74508304,74513568,74514958,74517301,74517993,74518260,74521718,74524705,74526323,74532629,74533371,74536764,74539650,74542427,74546674,74577686,74590860, +chr1 74485100 74489344 74486296 71.038 30339 5kbDownstream NA no-response 1.000422122 4162 Vil1 chr1:74455957-74482134;74455957,74461642,74462539,74464933,74466142,74466368,74467826,74468134,74468352,74469500,74470248,74470436,74472110,74473125,74473813,74474052,74474640,74477190,74478864,74481451,-74456010,74461728,74462614,74465130,74466251,74466479,74468029,74468213,74468451,74469654,74470349,74470574,74472269,74473305,74473959,74474197,74474829,74477259,74479005,74482134, +chr1 162238528 162240823 162239250 70.216 42452 intragenic intron up-regulated 0.473333333 -89946 Rabgap1l chr1:162149304-162281702;162149304,162156615,162161926,162166756,162168661,162177589,162187573,162272166,162281351,-162154499,162156813,162161998,162166840,162168766,162177700,162187666,162272295,162281702, +chr1 32802637 32804951 32803364 69.949 -199226 intergenic NA NA 1 -202974 Gm5415 chr1:32600390-32604138;32600390,-32604138, +chr1 69700706 69703228 69701687 65.623 30847 intragenic intron up-regulated 0.3 -123904 Ikzf2 chr1:69577783-69732534;69577783,69588800,69595172,69617066,69624354,69729783,69730697,69732267,-69586066,69588944,69595310,69617234,69624621,69729888,69730746,69732534, +chr1 176088652 176090284 176089363 65.366 511 immediateDownstream exon NA 1 -535 Olfr420 chr1:176088852-176089898;176088852,-176089898, +chr1 71090915 71092995 71091901 64.35 57645 intragenic intron down-regulated 2.23 -17793 Bard1 chr1:71074108-71149546;71074108,71077932,71093251,71094213,71100186,71112052,71113681,71121116,71134682,71136044,71149241,-71077426,71078030,71093344,71094346,71100295,71112225,71113762,71122054,71134825,71136101,71149546, +chr1 174240799 174242815 174241504 63.82 -1033 promoter NA NA 1 -8462 Igsf8 chr1:174242537-174249966;174242537,174246281,174247485,174248167,174248684,174249423,174249714,-174242724,174246659,174247947,174248575,174249098,174249554,174249966, +chr1 174441338 174445046 174444305 63.671 -6955 enhancer NA no-response 0.998353417 -31696 Ccdc19 chr1:174451260-174476001;174451260,174457920,174459940,174462211,174462661,174464076,174465341,174468609,174470617,174471315,174475222,174475805,-174451312,174458046,174460083,174462356,174462832,174464255,174465471,174468756,174470731,174471509,174475447,174476001, +chr1 77294504 77296236 77295394 63.66 216269 intergenic NA no-response 0.997483622 68365 Epha4 chr1:77363759-77511663;77363759,77369484,77371345,77373988,77377438,77379443,77380097,77384371,77385047,77386607,77395068,77396212,77397774,77423125,77441439,77503122,77508257,77511515,-77366246,77370422,77371501,77374182,77377588,77379653,77380159,77384557,77385161,77386666,77395180,77396372,77397899,77423464,77441595,77503786,77508325,77511663, +chr1 133030179 133033471 133032788 63.153 2023 intragenic jonction NA 1 -7771 Dyrk3 chr1:133025017-133034811;133025017,133032836,133034656,-133026822,133032948,133034811, +chr1 172725485 172727078 172726046 63.096 71856 intragenic intron NA 1 -91459 Atf6 chr1:172634587-172797902;172634587,172677236,172717476,172718738,172724087,172724787,172729744,172745553,172749377,172764950,172770811,172771816,172779247,172783035,172785243,172797780,-172640218,172677321,172717591,172718806,172724187,172724901,172729876,172745645,172749563,172765171,172771015,172771943,172779348,172783123,172785320,172797902, +chr1 158850311 158852732 158851860 62.949 17658 intragenic f_intron NA 1 -117564 Ralgps2 chr1:158734296-158869518;158734296,158741575,158743568,158747871,158749943,158751517,158754121,158758270,158759102,158760515,158762795,158763025,158799571,158814663,158817221,158818077,158830716,158831916,158837769,158869482,-158739324,158741667,158743674,158747964,158750049,158751595,158754176,158758422,158759259,158760583,158762886,158763163,158799698,158814756,158817311,158818161,158830767,158832021,158837909,158869518, +chr1 71602712 71605736 71603691 62.939 -38 promoter NA no-response 1.074673726 -22286 Atic chr1:71603729-71625977;71603729,71604070,71605799,71607462,71610332,71610979,71611384,71614387,71615536,71616413,71617413,71619481,71622614,71623190,71624359,71625125,-71603848,71604197,71605876,71607529,71610421,71611131,71611541,71614513,71615644,71616499,71617503,71619610,71622707,71623373,71624515,71625977, +chr1 58798703 58801466 58800321 62.896 30192 intragenic intron up-regulated 0.41 -15405 Cflar chr1:58770129-58815726;58770129,58783149,58785899,58787995,58789096,58792501,58797106,58797808,58809182,58810627,-58770503,58783576,58786005,58788131,58789170,58792556,58797156,58797890,58809690,58815726, +chr1 193739853 193742679 193741009 62.815 10350 5kbDownstream NA no-response 1.012582131 3883 Slc30a1 chr1:193730659-193737126;193730659,193732729,-193731492,193737126, +chr1 167322574 167323781 167323352 62.662 67242 intragenic intron NA 1 -63721 Dcaf6 chr1:167259631-167390594;167259631,167263419,167266875,167268318,167270015,167281014,167281602,167282091,167287559,167318788,167320544,167322269,167329784,167341594,167350241,167352986,167354432,167359384,167390261,-167260134,167263525,167266964,167268475,167270154,167281411,167281671,167282207,167287677,167319046,167320664,167322363,167329999,167341730,167350355,167353172,167354525,167359446,167390594, +chr1 152920964 152923760 152921765 61.584 -81200 intergenic NA no-response 0.997202412 -512134 Hmcn1 chr1:152409631-152840565;152409631,152412446,152420605,152424401,152427357,152429352,152430296,152433484,152434078,152435341,152440085,152441041,152442248,152442976,152445065,152445385,152446001,152446610,152450920,152451225,152451974,152454418,152456752,152457747,152459756,152462239,152465970,152470030,152470293,152471616,152474159,152474502,152477345,152477783,152478296,152479535,152480739,152482251,152485982,152493707,152496016,152496708,152497091,152499641,152502922,152503583,152503822,152504200,152504507,152505608,152510987,152511902,152514956,152516502,152519041,152521425,152522642,152523105,152524365,152526638,152527740,152530719,152533794,152536645,152537683,152541966,152544549,152547566,152548961,152550298,152551266,152562830,152566224,152567746,152568742,152569491,152570387,152579932,152581574,152584311,152584607,152585717,152589393,152590716,152592082,152595301,152596074,152597780,152600699,152602385,152603652,152605397,152612486,152617363,152619565,152620893,152645851,152649946,152653497,152655662,152656816,152664150,152666488,152706268,152707348,152723554,152839913,-152411023,152412573,152420725,152424752,152427486,152429478,152430410,152433619,152434198,152435404,152440323,152441163,152442386,152443126,152445236,152445556,152446172,152446781,152451091,152451396,152452244,152454500,152456943,152457882,152459970,152462430,152466240,152470165,152470431,152471724,152474324,152474624,152477502,152477911,152478441,152479677,152480876,152482333,152486179,152493986,152496114,152496892,152497216,152499801,152503072,152503715,152503904,152504403,152504621,152505770,152511084,152512090,152515070,152516697,152519192,152521571,152522756,152523279,152524557,152526725,152527854,152530887,152534076,152536807,152537806,152542063,152544725,152547690,152549113,152550475,152551368,152562954,152566379,152567916,152568851,152569773,152570666,152580087,152581701,152584459,152584738,152585912,152589489,152590986,152592210,152595470,152596234,152597893,152600844,152602513,152603748,152605592,152612645,152617477,152619693,152621035,152646127,152650068,152653642,152655926,152656937,152664257,152666660,152706391,152707507,152723625,152840565, +chr1 153302455 153305763 153304378 61.456 28601 intragenic intron no-response 1.00010457 -935 1190005F20Rik chr1:153275777-153305313;153275777,153280923,153282857,153286645,153287935,153289716,153290376,153295383,153297029,153299177,153300206,153301014,153302107,153304592,153304811,-153276232,153281034,153282971,153286710,153288065,153289840,153290456,153295627,153297242,153299368,153300285,153301181,153302170,153304719,153305313, +chr1 133950420 133955071 133951138 60.097 13501 intragenic intron no-response 0.967262256 -17779 Mfsd4 chr1:133933359-133964639;133933359,133937116,133938434,133942882,133948956,133950125,133950635,133954292,133955736,133964239,-133935550,133937237,133938505,133943030,133949130,133950241,133950801,133954544,133955935,133964639, +chr1 71049725 71052248 71050410 58.989 99136 intergenic NA down-regulated 2.23 23698 Bard1 chr1:71074108-71149546;71074108,71077932,71093251,71094213,71100186,71112052,71113681,71121116,71134682,71136044,71149241,-71077426,71078030,71093344,71094346,71100295,71112225,71113762,71122054,71134825,71136101,71149546, +chr1 59432545 59435438 59434466 58.725 -104524 intergenic NA NA 1 -109333 Fzd7 chr1:59538990-59543799;59538990,-59543799, +chr1 181480625 181483262 181481634 58.126 4975 intragenic f_intron NA 1 -75970 Cnst chr1:181476659-181557604;181476659,181509468,181522815,181531832,181534649,181535083,181536378,181536567,181539916,181552897,181555129,-181476747,181509899,181522997,181531863,181534736,181535198,181536400,181536664,181540797,181553033,181557604, +chr1 122345198 122346897 122346334 57.37 55327 intergenic NA no-response 0.999153017 24780 Marco chr1:122371114-122401661;122371114,122373130,122373942,122374428,122375920,122381201,122381350,122382265,122382408,122384723,122385108,122387489,122388608,122390196,122390620,122391317,122401245,-122371366,122373307,122373987,122374527,122375965,122381264,122381449,122382301,122382507,122384831,122385153,122387534,122388707,122390232,122390839,122391419,122401661, +chr1 133649571 133653576 133651231 57.37 10633 intragenic intron NA 1 -15751 Slc26a9 chr1:133640598-133666982;133640598,133647156,133649420,133649696,133650403,133651948,133652765,133653213,133653964,133655047,133655335,133655974,133658282,133659332,133659491,133659721,133660370,133661563,133662460,133664385,133665777,-133640690,133647299,133649560,133649807,133650579,133652113,133652918,133653296,133654112,133655161,133655413,133656070,133658389,133659402,133659584,133659835,133660652,133661618,133662603,133664457,133666982,