What it does

MySort is a R program to estimate the fraction and abundance of immune cells based on gene expression profile in heterogeneous mixture tissues.

Citation: MySort - A Gene Profiling Deconvolution Approach to Estimating Immune Cell Composition from Complex Tissues.

Inputs

Comma-separated values (CSV) files ONLY!

• Mixture file

  Mixture file contains the gene expression profiles of samples. Each column refers to different experimental conditions. Each row represents the expression level of the gene symbol.

  
  

• Example:

          17-002          17-006          17-019          17-023          17-026          17-027          17-030          17-034          17-040
  7A5     22.31589866     25.28132198     27.09585        22.00866909     28.05138308     19.97328878     23.58830748     22.31589866     24.5900029
  A1BG    22.16175149     36.25228433     23.26356028     27.6651914      25.8125363      25.28132198     24.7610399      25.63423608     22.47111801
  A1CF    24.25146506     21.25897303     22.31589866     25.45716748     23.75237713     29.24260641     22.47111801     23.91758798     23.58830748
  A26C3   22.78480313     23.91758798     21.85664411     30.48441594     24.5900029      25.99207668     19.97328878     27.85761803     23.75237713
  A2BP1   42.51794605     22.627417       21.25897303     20.96629446     22.78480313     26.35491255     21.55573723     25.10669113     22.00866909
  

• Signature Matrix file

  Signature matrix file is the gene expression signature profiles of each cell type. Each column refers to a single immune cell type. Each row represents the expression value of selected signature genes, which are used to estimate the abundance of immune cells.

  
  

• Example:

          B cells naive           B cells memory          Plasma cells            T cells CD8             T cells CD4 naive       T cells CD4 memory resting      T cells CD4 memory activated    T cells follicular helper       T cells gamma delta     T cells regulatory (Tregs)
  TCL1A   11762.9329863964        762.792841906926        502.833875600303        117.986529083727        146.531410192506        116.955378976466                69.9673544104057                151.861066666539                117.846466554419        86.5298778848906
  ABCB4   564.157988776832        13.2126403514086        9.26333899427403        5.97542505311934        6.31286755665178        9.4956471407396                 10.249430943865                 8.46885165495616                11.1449931559612        9.09238846544857
  AIM2    343.391399738098        4326.07933616138        1381.15051817772        309.918863346619        64.3615794973278        266.515332409956                3191.32538714028                1101.14371410434                397.275565779613        327.315303371804
  ZBTB32  12.24039385599          205.845379902139        15.6385731015393        31.3998897051428        33.7819675891862        9.96626463470093                202.575397976579                28.9208257029714                27.0139061691596        77.8965632518407
  CD27    402.562878492026        3939.40425295768        6600.97908386608        5292.27278301393        3885.54504835221        4026.06694012145                1110.92273824715                5495.01448261848                1685.96543960432        6725.22726617645
  

  
  

Outputs

• Bar plot

  Bar plot where the x-axis is each experiment and y-axis is the proportion of immune cells.
  
  

• Cluster plot

  Cluster plot shows the hierarchical clustering results of each sample according to the immune cell composition.
  
  

• Output file

  Output file is the immune cell proportions of each experiment. Each column refers to a single immune cell type. Each row represents different experimental conditions.
  
  

• Example:

          B cells naive           B cells memory          Plasma cells            T cells CD8             T cells CD4 naive       T cells CD4 memory resting      T cells CD4 memory activated    T cells follicular helper       T cells gamma delta     T cells regulatory (Tregs)
  17-002  5.86519116086516        5.78172185517755        0                       28.0456263712606        0                       12.3463700780668                3.70682402906826                2.55582761241995                0                       0
  17-006  7.96659407050384        0                       0                       34.3437301458475        0                       21.6379512374475                0.410130270925141               6.40140829275814                0                       4.06406539184987
  17-019  12.1880447552976        4.4170765639818         0                       13.6844979546959        0.439003816720928       15.3209721030027                0                               0                               5.01299153386902        0
  17-023  9.29323882302043        4.11131568640441        0                       1.61292111594947        0                       32.1031844996338                0                               2.02029369036927                0                       2.03783408522463
  17-026  3.64445891248583        8.34951887822622        0                       28.1694480957887        0                       12.2910782773502                0                               3.11105683498932                0                       0
  17-027  7.14710082306742        8.58148089134017        0                       26.1872213672226        4.6902671438807         8.44373238507345                0                               3.4328987286918                 0                       0
  17-030  2.11818136872382        8.59539494368935        0                       16.3872716875959        0                       14.912550920905                 0                               1.8127028236438                 7.58859854878188        0
  17-034  7.25696740663024        0                       0.543172049350818       4.13758563880151        9.28035161185525        18.7470450023791                0                               1.36823975273019                8.49903967754987        0
  17-040  11.6655203206611        0                       0.328516427461942       10.7770898907558        0                       11.8748718361016                4.08443320076682                4.81389646437365                0.994290664613396       0