Cell type deconvolution of RNAseq data- Create signature matrix of cells
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JG13 • 0
@eeb93914
Last seen 9 days ago
Greece

I would like to use my RNAseq expression matrix (an example of the matrix below ) from parkinson data for deconvolution in specific cell types (oligodendrocytes ,microglia ,neurons ,astrocytes).

GENE    C_0002  C_0003  C_0004  C_0005  C_0006  C_0008  C_0009  C_0010  C_0011  C_0012  C_0013  C_0014  C_0015  C_0016  C_0017  C_0018  C_0019  C_0020  C_0021  C_0022  C_0023  C_0024  C_0025  C_0026  C_0029  C_0031  C_0032  C_0035  C_0038  C_0039  C_0050  C_0053  C_0060  C_0061  C_0062  C_0065  C_0069  C_0070  C_0075  C_0076  C_0081  C_0082  C_0083  C_0087  P_0003  P_0006  P_0013  P_0014  P_0015  P_0016  P_0018  P_0019  P_0020  P_0021  P_0022  P_0023  P_0026  P_0027  P_0028  P_0029  P_0030  P_0031  P_0033  P_0012  P_0034  P_0063  P_0126  P_0130  P_0132  P_0133  P_0134  P_0135  P_0136
AAK1    642.871561  294.583928  1280.83903  1890.80641  1140.25563  880.130415  222.81526   551.979173  1107.54424  1223.94835  1260.36174  661.40837   1836.24324  1271.75586  1018.4964   1502.85202  859.992854  1984.86234  654.760191  1118.8933   428.602762  1137.80167  1194.67317  745.578479  480.158696  346.885588  1601.82995  1688.99632  1088.21906  274.408964  1447.86657  253.212737  191.496691  409.662659  996.499745  261.112599  444.872978  221.117901  315.463679  2180.77471  1344.04119  543.838229  1098.49585  1759.28396  1389.71144  794.906536  1184.48301  585.778738  503.989755  1160.32589  704.414117  740.580518  717.496298  262.271928  587.539195  647.2961    288.165828  1412.57678  448.232465  665.492767  592.393925  672.042946  228.23937   800.911947  252.275799  394.449632  215.222639  261.490151  295.981708  235.174547  1072.55123  185.240602  207.513983
AANAT   32.2535333  38.8211379  51.7108924  48.1260094  17.3517161  33.1707443  28.6298938  17.5875717  80.0393309  11.2288839  33.6424684  52.3887817  11.2308455  11.5404343  29.9557764  26.3658249  14.8019424  21.7700686  28.5713538  31.0803695  23.1052702  12.327212   15.5996497  22.6313872  48.6236654  14.8665252  5.73789834  9.6102209   4.75204828  10.3161265  25.9530673  24.5312832  25.7618866  18.9201629  15.7757216  14.726524   8.74750237  17.4895515  17.0740651  11.3083651  5.27074976  13.9894078  10.2743182  19.48574    26.9385342  17.7251886  50.0185997  32.6036403  47.5742541  30.2275543  22.4445674  28.2476815  42.0290718  114.840962  99.6487181  81.1277778  54.4460781  42.3157531  39.3186373  40.5605073  58.8860761  56.8925245  46.8183323  23.8156636  20.5783884  12.9859961  24.6814953  31.0519554  51.3437656  18.7880492  23.771584   78.8459999  38.0759602
ABAT    11524.0408  5909.94734  11505.6735  10001.7755  9987.15201  9385.10925  1573.39938  8960.19133  18597.1385  7061.72034  8888.17605  11841.1744  11842.3027  9714.73756  8924.75544  8108.85491  10373.2012  12458.1584  9366.64215  10370.0848  6991.65476  10888.6264  8897.0002   11364.7283  8814.55884  6580.91515  10628.5004  11941.9007  9278.37427  7988.80833  11922.6818  6326.57637  9848.76925  8566.72074  9277.87713  9204.07751  8831.22846  8834.0974   9805.39169  13032.4558  10524.8088  7181.22935  9310.24468  10734.787   7710.75925  8399.01246  9361.99194  10569.0134  5549.83408  9807.46739  8623.03016  6957.52676  8704.02064  2754.63119  11997.9645  8526.18422  9298.32777  10632.7947  11229.4028  10897.2563  9194.47192  10501.4118  3891.77387  10234.5609  9406.61 7251.05559  5043.91039  9417.73122  5150.48441  8027.67993  10324.2253  8275.03018  11556.0539
ACSL6   4989.03517  1895.38497  4656.96363  4278.74954  4071.45624  3412.1639   601.227769  4494.30101  4973.44392  3098.54814  3319.93725  3705.19659  4986.49541  3825.65396  4057.45826  7375.15764  4567.87943  4233.80508  3719.03788  3189.32407  3575.54056  4999.9172   4525.19838  3692.68802  3438.60484  4367.7851   6153.89597  5154.68224  4691.45967  3665.31973  5888.98691  2856.02347  3499.32293  5427.61892  6510.99086  3153.74176  6120.12755  3734.01925  5058.80158  5912.53519  5809.24469  3999.80485  6295.58848  5695.40344  2555.9915   2046.57755  3801.41357  3304.92234  1929.73068  5151.73704  2802.11792  3947.30644  3118.15685  484.194328  4411.72052  2382.91271  2766.12636  4223.11216  2895.16232  3076.58959  3297.62026  2925.22397  702.274985  5023.3409   5658.29466  5000.42014  1983.40497  3843.08806  2733.30046  3081.88794  5411.43131  2263.73515  2554.89693
ADRB2   79.1677634  79.925872   82.5385397  52.5913092  37.1822487  70.7642545  78.4210134  52.7627151  75.0368727  45.5393626  100.927405  61.5568186  30.5728572  98.0936912  40.2853544  17.2741611  86.5913631  33.1283653  63.0950729  75.3101262  64.6947565  53.0070118  54.5987739  65.3795631  118.520184  64.4216092  30.6021245  33.6357732  32.0763259  46.422569   62.9165268  120.993278  51.5237732  53.4700257  42.9450198  82.6950964  42.4878686  58.0902961  72.3615141  14.787862   103.658079  32.0590596  64.2144888  38.97148    33.2770128  107.714608  64.917757   89.116617   87.715031   50.8372504  75.1029757  95.7964849  49.0339172  121.048582  170.826374  193.325768  123.49964   72.3214689  64.2204409  78.1165325  89.5068357  168.307052  134.602705  49.3954505  58.6865152  132.294836  156.97431   100.510277  70.4718352  74.5043331  49.2411384  70.2964337  137.073457

Most of the tools like granulator, dtangle of even CIBERSORTx use their signature matrixes with proportions -expression of genes in each cell type. I don't have this file and I would like to create this for the particular cell types (oligodendrocytes ,microglia ,neurons ,astrocytes). Is it possible to download or create this? Is any database where I can find marker genes and their expression for those particular cell types ?

I can only find from PangalaoDB (for example https://panglaodb.se/markers.html?cell_type=%27Neurons%27) the marker genes for each one but not a signature matrix with expression for each cell type, 

deconvolution rnaseqGene RNAseq • 126 views
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