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,