Program: 5. Cancer Associated Fibroblast: Inflammatory.

Program: 5. Cancer Associated Fibroblast: Inflammatory.

Program description and justification of annotation: 5.
Submit a comment on this gene expression program’s interpretation: CLICK

QQ-plot of gene loadings, averaged over both independent splits of the data
 This plot highlights the relative contribution of each gene to the GEP

Interactive QQ Plot

Top genes driving this program.
 Note: Decartes website is buggy, try refreshing. Also, Decartes fetal adrenal data have been collected at specific time points (89-122 days), all possible cell types of interest may not be represented, do not overinterpret.
The Mean Count column shows the mean read count in cells scoring highly (H > 50) on this gene expression program.

Gene Loading Gene.Name GTEx DepMap Descartes Mean.Counts Mean.Tpm
1 C7 0.0087669 complement C7 GTEx DepMap Descartes 0.86 408.39
2 TNC 0.0085546 tenascin C GTEx DepMap Descartes 2.06 488.76
3 EXOC3L4 0.0069854 exocyst complex component 3 like 4 GTEx DepMap Descartes 0.11 103.34
4 IGFBP7 0.0068017 insulin like growth factor binding protein 7 GTEx DepMap Descartes 3.11 3421.62
5 PAPLN 0.0065595 papilin, proteoglycan like sulfated glycoprotein GTEx DepMap Descartes 0.32 70.55
6 SULF1 0.0062347 sulfatase 1 GTEx DepMap Descartes 2.85 906.06
7 POSTN 0.0054233 periostin GTEx DepMap Descartes 1.57 862.81
8 ADAM12 0.0048947 ADAM metallopeptidase domain 12 GTEx DepMap Descartes 1.38 307.75
9 TIMP1 0.0046397 TIMP metallopeptidase inhibitor 1 GTEx DepMap Descartes 2.87 4863.81
10 FN1 0.0043083 fibronectin 1 GTEx DepMap Descartes 4.35 844.41
11 PRRX1 0.0041227 paired related homeobox 1 GTEx DepMap Descartes 0.57 231.54
12 PARD3B 0.0039587 par-3 family cell polarity regulator beta GTEx DepMap Descartes 1.33 270.30
13 CLU 0.0037933 clusterin GTEx DepMap Descartes 1.14 494.10
14 PRKG1 0.0037786 protein kinase cGMP-dependent 1 GTEx DepMap Descartes 2.21 477.99
15 ADAMTS12 0.0035537 ADAM metallopeptidase with thrombospondin type 1 motif 12 GTEx DepMap Descartes 0.40 77.21
16 BNC2 0.0034729 basonuclin 2 GTEx DepMap Descartes 1.14 164.39
17 NPY1R 0.0034116 neuropeptide Y receptor Y1 GTEx DepMap Descartes 0.04 29.00
18 SLC26A7 0.0033975 solute carrier family 26 member 7 GTEx DepMap Descartes 0.16 36.06
19 GEM 0.0033794 GTP binding protein overexpressed in skeletal muscle GTEx DepMap Descartes 0.81 697.57
20 ABI3BP 0.0033485 ABI family member 3 binding protein GTEx DepMap Descartes 0.38 97.20
21 UACA 0.0032723 uveal autoantigen with coiled-coil domains and ankyrin repeats GTEx DepMap Descartes 0.91 270.62
22 NFIA 0.0032102 nuclear factor I A GTEx DepMap Descartes 1.06 43.23
23 FGF11 0.0032060 fibroblast growth factor 11 GTEx DepMap Descartes 0.03 30.80
24 ANKRD29 0.0032047 ankyrin repeat domain 29 GTEx DepMap Descartes 0.14 48.71
25 B2M 0.0031452 beta-2-microglobulin GTEx DepMap Descartes 3.35 1835.87
26 HS3ST3A1 0.0030440 heparan sulfate-glucosamine 3-sulfotransferase 3A1 GTEx DepMap Descartes 0.19 86.58
27 PDE1A 0.0030304 phosphodiesterase 1A GTEx DepMap Descartes 0.49 163.95
28 BIRC3 0.0029385 baculoviral IAP repeat containing 3 GTEx DepMap Descartes 0.08 21.25
29 CYP7B1 0.0029235 cytochrome P450 family 7 subfamily B member 1 GTEx DepMap Descartes 0.45 126.85
30 IL33 0.0029119 interleukin 33 GTEx DepMap Descartes 0.14 103.70
31 ARHGAP42 0.0029005 Rho GTPase activating protein 42 GTEx DepMap Descartes 0.40 92.36
32 CCL2 0.0028949 C-C motif chemokine ligand 2 GTEx DepMap Descartes 0.64 1212.95
33 ARHGAP15 0.0028605 Rho GTPase activating protein 15 GTEx DepMap Descartes 0.82 386.03
34 PDGFRB 0.0028514 platelet derived growth factor receptor beta GTEx DepMap Descartes 0.50 162.41
35 OSMR 0.0028266 oncostatin M receptor GTEx DepMap Descartes 0.43 137.23
36 ITIH5 0.0028046 inter-alpha-trypsin inhibitor heavy chain 5 GTEx DepMap Descartes 0.19 37.14
37 KCNE4 0.0027821 potassium voltage-gated channel subfamily E regulatory subunit 4 GTEx DepMap Descartes 0.21 114.45
38 ZFPM2 0.0027781 zinc finger protein, FOG family member 2 GTEx DepMap Descartes 1.50 466.75
39 BACE2 0.0027780 beta-secretase 2 GTEx DepMap Descartes 0.47 NA
40 SLC9A9 0.0027771 solute carrier family 9 member A9 GTEx DepMap Descartes 0.52 269.29
41 RBPMS 0.0027029 RNA binding protein, mRNA processing factor GTEx DepMap Descartes 0.79 420.44
42 VCAM1 0.0026682 vascular cell adhesion molecule 1 GTEx DepMap Descartes 0.18 94.72
43 ID3 0.0026613 inhibitor of DNA binding 3, HLH protein GTEx DepMap Descartes 0.32 475.93
44 C3 0.0026599 complement C3 GTEx DepMap Descartes 1.04 311.89
45 TNFAIP3 0.0026434 TNF alpha induced protein 3 GTEx DepMap Descartes 0.15 48.07
46 GNA14 0.0026312 G protein subunit alpha 14 GTEx DepMap Descartes 0.35 206.93
47 CALD1 0.0026092 caldesmon 1 GTEx DepMap Descartes 3.33 1177.92
48 SVIL 0.0025921 supervillin GTEx DepMap Descartes 1.06 219.62
49 EPB41L2 0.0025726 erythrocyte membrane protein band 4.1 like 2 GTEx DepMap Descartes 0.50 170.75
50 EPHA3 0.0025716 EPH receptor A3 GTEx DepMap Descartes 0.28 104.30


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UMAP plots showing activity of gene expression program identified in community:5. Cancer Associated Fibroblast: Inflammatory

Interactive UMAP Plot
Interactive Boxplot

CNV Data procured from inferCNV.
 Outer tracks are putative CNV regions (gains = red, losses = blue) for each patient
Inner track is expression data representing:
    The top cells expressing this GEP (purple)
    Random cells (n =50) from the reference set used in inferCNV (orange)

Interactive BioCircos Plot

Gene set Enrichments for this program, caculated from top 50 genes


mSigDB Cell Types Gene Set:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
TRAVAGLINI_LUNG_VEIN_CELL 9.97e-09 49.98 16.33 1.12e-06 6.69e-06
6C7, TIMP1, CLU, ABI3BP, VCAM1, TNFAIP3
 40
DURANTE_ADULT_OLFACTORY_NEUROEPITHELIUM_FIBROBLASTS_STROMAL_CELLS 2.99e-08 27.08 9.96 2.23e-06 2.00e-05
7IGFBP7, POSTN, TIMP1, PRRX1, CCL2, KCNE4, CALD1
 82
AIZARANI_LIVER_C33_STELLATE_CELLS_2 1.26e-09 23.42 9.79 1.69e-07 8.47e-07
9C7, IGFBP7, PRKG1, UACA, NFIA, RBPMS, ID3, CALD1, EPB41L2
 126
LAKE_ADULT_KIDNEY_C28_INTERSTITIUM 4.16e-08 25.71 9.48 2.79e-06 2.79e-05
7C7, TNC, IGFBP7, PRKG1, UACA, NFIA, CALD1
 86
HU_FETAL_RETINA_FIBROBLAST 8.48e-12 14.48 7.28 1.90e-09 5.69e-09
15IGFBP7, SULF1, TIMP1, FN1, PRRX1, SLC26A7, UACA, NFIA, B2M, PDGFRB, ID3, CALD1, SVIL, EPB41L2, EPHA3
 385
TRAVAGLINI_LUNG_MYOFIBROBLAST_CELL 5.50e-06 23.11 6.92 2.31e-04 3.69e-03
5TNC, POSTN, CLU, GEM, HS3ST3A1
 65
LAKE_ADULT_KIDNEY_C26_MESANGIAL_CELLS 2.44e-08 16.33 6.87 2.05e-06 1.64e-05
9C7, IGFBP7, POSTN, PRKG1, UACA, B2M, PDGFRB, CALD1, EPB41L2
 177
MANNO_MIDBRAIN_NEUROTYPES_HPERIC 1.90e-13 11.71 6.32 1.27e-10 1.27e-10
21IGFBP7, ADAM12, TIMP1, FN1, PRKG1, GEM, UACA, B2M, ARHGAP42, CCL2, ARHGAP15, PDGFRB, OSMR, ITIH5, KCNE4, RBPMS, ID3, TNFAIP3, CALD1, SVIL, EPB41L2
 795
MURARO_PANCREAS_MESENCHYMAL_STROMAL_CELL 1.71e-12 11.60 6.16 5.72e-10 1.14e-09
19TNC, IGFBP7, SULF1, POSTN, ADAM12, TIMP1, FN1, PRRX1, PRKG1, GEM, UACA, IL33, PDGFRB, OSMR, KCNE4, RBPMS, ID3, CALD1, SVIL
 680
FAN_EMBRYONIC_CTX_BRAIN_ENDOTHELIAL_2 1.72e-08 12.07 5.52 1.65e-06 1.15e-05
11IGFBP7, ADAM12, TIMP1, FN1, PRKG1, UACA, ARHGAP42, PDGFRB, ITIH5, KCNE4, CALD1
 303
MENON_FETAL_KIDNEY_3_STROMAL_CELLS 1.62e-05 18.27 5.51 5.17e-04 1.09e-02
5TNC, POSTN, FN1, UACA, CALD1
 81
HAY_BONE_MARROW_STROMAL 1.21e-11 10.28 5.46 2.02e-09 8.10e-09
19C7, TNC, IGFBP7, SULF1, FN1, PRRX1, NPY1R, GEM, ABI3BP, PDE1A, CCL2, PDGFRB, OSMR, ITIH5, KCNE4, VCAM1, ID3, CALD1, EPHA3
 765
LAKE_ADULT_KIDNEY_C29_UNKNOWN_NOVEL_PT_CFH_POS_SUBPOPULATION_S2 2.16e-05 17.14 5.17 6.31e-04 1.45e-02
5PARD3B, BNC2, PDE1A, ZFPM2, SVIL
 86
AIZARANI_LIVER_C21_STELLATE_CELLS_1 7.76e-07 12.80 5.12 4.34e-05 5.20e-04
8C7, IGFBP7, TIMP1, GEM, NFIA, CCL2, RBPMS, CALD1
 194
DESCARTES_FETAL_LIVER_STELLATE_CELLS 2.67e-06 13.38 5.00 1.24e-04 1.79e-03
7POSTN, ADAMTS12, GEM, PDGFRB, ITIH5, KCNE4, EPHA3
 159
AIZARANI_LIVER_C32_MVECS_3 9.09e-06 14.32 4.89 3.31e-04 6.10e-03
6C7, IGFBP7, NFIA, B2M, IL33, VCAM1
 125
DURANTE_ADULT_OLFACTORY_NEUROEPITHELIUM_VASCULAR_SMOOTH_MUSCLE_CELLS 3.15e-05 15.77 4.77 8.14e-04 2.12e-02
5IGFBP7, GEM, CCL2, PDGFRB, CALD1
 93
DESCARTES_FETAL_PANCREAS_CCL19_CCL21_POSITIVE_CELLS 1.24e-04 17.81 4.52 2.60e-03 8.31e-02
4TNC, SLC26A7, FGF11, VCAM1
 65
LAKE_ADULT_KIDNEY_C22_ENDOTHELIAL_CELLS_GLOMERULAR_CAPILLARIES 1.53e-05 13.01 4.45 5.13e-04 1.03e-02
6PRKG1, UACA, NFIA, GNA14, CALD1, SVIL
 137
HU_FETAL_RETINA_RPE 1.59e-06 9.70 4.10 8.20e-05 1.07e-03
9IGFBP7, SULF1, GEM, UACA, B2M, PDGFRB, BACE2, ID3, CALD1
 292

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mSigDB Hallmark Gene Sets:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION 1.15e-11 20.99 9.83 5.75e-10 5.75e-10
12TNC, POSTN, ADAM12, TIMP1, FN1, PRRX1, GEM, ABI3BP, PDGFRB, VCAM1, TNFAIP3, CALD1
 200
HALLMARK_COMPLEMENT 1.24e-04 8.78 3.02 3.09e-03 6.18e-03
6TIMP1, FN1, CLU, ZFPM2, C3, TNFAIP3
 200
HALLMARK_TNFA_SIGNALING_VIA_NFKB 1.08e-03 7.12 2.18 1.80e-02 5.40e-02
5TNC, GEM, BIRC3, CCL2, TNFAIP3
 200
HALLMARK_COAGULATION 2.09e-03 8.11 2.09 2.62e-02 1.05e-01
4TIMP1, FN1, CLU, C3
 138
HALLMARK_APOPTOSIS 3.63e-03 6.92 1.79 3.63e-02 1.82e-01
4TIMP1, CLU, BIRC3, PDGFRB
 161
HALLMARK_ANGIOGENESIS 8.94e-03 15.30 1.73 4.97e-02 4.47e-01
2POSTN, TIMP1
 36
HALLMARK_MYOGENESIS 7.71e-03 5.55 1.44 4.82e-02 3.85e-01
4IGFBP7, ADAM12, CLU, SVIL
 200
HALLMARK_INTERFERON_GAMMA_RESPONSE 7.71e-03 5.55 1.44 4.82e-02 3.85e-01
4B2M, CCL2, VCAM1, TNFAIP3
 200
HALLMARK_KRAS_SIGNALING_UP 7.71e-03 5.55 1.44 4.82e-02 3.85e-01
4PRRX1, BIRC3, IL33, TNFAIP3
 200
HALLMARK_INFLAMMATORY_RESPONSE 4.35e-02 4.05 0.80 1.98e-01 1.00e+00
3TIMP1, CCL2, OSMR
 200
HALLMARK_ALLOGRAFT_REJECTION 4.35e-02 4.05 0.80 1.98e-01 1.00e+00
3TIMP1, B2M, CCL2
 200
HALLMARK_UV_RESPONSE_DN 1.10e-01 3.67 0.43 4.59e-01 1.00e+00
2PDGFRB, RBPMS
 144
HALLMARK_ADIPOGENESIS 1.85e-01 2.63 0.31 6.05e-01 1.00e+00
2ITIH5, C3
 200
HALLMARK_ESTROGEN_RESPONSE_EARLY 1.85e-01 2.63 0.31 6.05e-01 1.00e+00
2NPY1R, SVIL
 200
HALLMARK_APICAL_JUNCTION 1.85e-01 2.63 0.31 6.05e-01 1.00e+00
2VCAM1, EPB41L2
 200
HALLMARK_TGF_BETA_SIGNALING 1.94e-01 4.81 0.12 6.05e-01 1.00e+00
1ID3
 54
HALLMARK_CHOLESTEROL_HOMEOSTASIS 2.55e-01 3.49 0.09 7.50e-01 1.00e+00
1CLU
 74
HALLMARK_IL6_JAK_STAT3_SIGNALING 2.93e-01 2.97 0.07 7.87e-01 1.00e+00
1OSMR
 87
HALLMARK_INTERFERON_ALPHA_RESPONSE 3.20e-01 2.66 0.07 7.87e-01 1.00e+00
1B2M
 97
HALLMARK_ANDROGEN_RESPONSE 3.28e-01 2.58 0.06 7.87e-01 1.00e+00
1B2M
 100

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KEGG Pathways:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
KEGG_NOD_LIKE_RECEPTOR_SIGNALING_PATHWAY 1.88e-03 13.52 2.62 3.50e-01 3.50e-01
3BIRC3, CCL2, TNFAIP3
 62
KEGG_FOCAL_ADHESION 7.58e-03 5.57 1.44 7.05e-01 1.00e+00
4TNC, FN1, BIRC3, PDGFRB
 199
KEGG_CALCIUM_SIGNALING_PATHWAY 3.26e-02 4.56 0.90 9.43e-01 1.00e+00
3PDE1A, PDGFRB, GNA14
 178
KEGG_COMPLEMENT_AND_COAGULATION_CASCADES 3.05e-02 7.77 0.90 9.43e-01 1.00e+00
2C7, C3
 69
KEGG_PATHWAYS_IN_CANCER 3.70e-02 3.39 0.88 9.43e-01 1.00e+00
4FN1, FGF11, BIRC3, PDGFRB
 325
KEGG_MELANOMA 3.21e-02 7.55 0.87 9.43e-01 1.00e+00
2FGF11, PDGFRB
 71
KEGG_REGULATION_OF_ACTIN_CYTOSKELETON 5.07e-02 3.80 0.75 9.43e-01 1.00e+00
3FN1, FGF11, PDGFRB
 213
KEGG_ECM_RECEPTOR_INTERACTION 4.36e-02 6.35 0.74 9.43e-01 1.00e+00
2TNC, FN1
 84
KEGG_SMALL_CELL_LUNG_CANCER 4.36e-02 6.35 0.74 9.43e-01 1.00e+00
2FN1, BIRC3
 84
KEGG_GAP_JUNCTION 4.93e-02 5.92 0.69 9.43e-01 1.00e+00
2PRKG1, PDGFRB
 90
KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION 8.44e-02 3.05 0.60 1.00e+00 1.00e+00
3CCL2, PDGFRB, OSMR
 265
KEGG_VASCULAR_SMOOTH_MUSCLE_CONTRACTION 7.56e-02 4.61 0.54 1.00e+00 1.00e+00
2PRKG1, CALD1
 115
KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS 1.04e-01 3.80 0.44 1.00e+00 1.00e+00
2C7, C3
 139
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS 6.18e-02 16.98 0.40 1.00e+00 1.00e+00
1CYP7B1
 16
KEGG_GLYCOSAMINOGLYCAN_DEGRADATION 8.04e-02 12.74 0.30 1.00e+00 1.00e+00
1HS3ST3A1
 21
KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_HEPARAN_SULFATE 9.85e-02 10.19 0.24 1.00e+00 1.00e+00
1HS3ST3A1
 26
KEGG_MAPK_SIGNALING_PATHWAY 2.80e-01 1.97 0.23 1.00e+00 1.00e+00
2FGF11, PDGFRB
 267
KEGG_PRION_DISEASES 1.30e-01 7.50 0.18 1.00e+00 1.00e+00
1C7
 35
KEGG_TASTE_TRANSDUCTION 1.87e-01 5.00 0.12 1.00e+00 1.00e+00
1PDE1A
 52
KEGG_STEROID_HORMONE_BIOSYNTHESIS 1.97e-01 4.72 0.12 1.00e+00 1.00e+00
1CYP7B1
 55

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CHR Positional Gene Sets:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
chr5p13 1.40e-02 6.38 1.25 1.00e+00 1.00e+00
3C7, ADAMTS12, OSMR
 128
chr11q22 5.73e-02 5.42 0.63 1.00e+00 1.00e+00
2BIRC3, ARHGAP42
 98
chr6q23 6.57e-02 5.01 0.58 1.00e+00 1.00e+00
2TNFAIP3, EPB41L2
 106
chr8q22 1.22e-01 3.45 0.40 1.00e+00 1.00e+00
2GEM, ZFPM2
 153
chr3p11 9.13e-02 11.08 0.26 1.00e+00 1.00e+00
1EPHA3
 24
chr3q12 1.67e-01 5.67 0.14 1.00e+00 1.00e+00
1ABI3BP
 46
chr10p14 1.71e-01 5.54 0.13 1.00e+00 1.00e+00
1ITIH5
 47
chr7q33 1.87e-01 5.00 0.12 1.00e+00 1.00e+00
1CALD1
 52
chr17p12 2.22e-01 4.11 0.10 1.00e+00 1.00e+00
1HS3ST3A1
 63
chr15q23 2.28e-01 3.99 0.10 1.00e+00 1.00e+00
1UACA
 65
chr8p12 2.34e-01 3.86 0.09 1.00e+00 1.00e+00
1RBPMS
 67
chr2q22 2.37e-01 3.81 0.09 1.00e+00 1.00e+00
1ARHGAP15
 68
chr8q13 2.46e-01 3.64 0.09 1.00e+00 1.00e+00
1SULF1
 71
chr13q13 2.67e-01 3.31 0.08 1.00e+00 1.00e+00
1POSTN
 78
chr4q12 2.70e-01 3.27 0.08 1.00e+00 1.00e+00
1IGFBP7
 79
chr18q11 2.73e-01 3.23 0.08 1.00e+00 1.00e+00
1ANKRD29
 80
chr2q36 2.78e-01 3.15 0.08 1.00e+00 1.00e+00
1KCNE4
 82
chr8q12 2.95e-01 2.93 0.07 1.00e+00 1.00e+00
1CYP7B1
 88
chr1p21 3.25e-01 2.60 0.06 1.00e+00 1.00e+00
1VCAM1
 99
chr9p24 3.31e-01 2.55 0.06 1.00e+00 1.00e+00
1IL33
 101

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Transcription Factor Targets:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
HOX13_01 7.92e-04 18.54 3.56 3.03e-01 8.98e-01
3PRRX1, CALD1, SVIL
 46
TGCCAAR_NF1_Q6 6.46e-05 4.93 2.27 7.32e-02 7.32e-02
11PAPLN, POSTN, ADAM12, BNC2, SLC26A7, NFIA, PDE1A, SLC9A9, ID3, CALD1, EPHA3
 727
CART1_01 1.94e-03 6.20 1.90 3.03e-01 1.00e+00
5PRRX1, BNC2, ZFPM2, BACE2, CALD1
 229
CEBP_Q2 2.29e-03 5.96 1.83 3.03e-01 1.00e+00
5CLU, PRKG1, OSMR, RBPMS, ID3
 238
PAX4_02 2.42e-03 5.88 1.81 3.03e-01 1.00e+00
5SLC26A7, NFIA, B2M, ARHGAP15, BACE2
 241
OCT1_04 2.51e-03 5.84 1.79 3.03e-01 1.00e+00
5BNC2, SLC26A7, NFIA, PDE1A, ZFPM2
 243
GATA1_04 2.69e-03 5.74 1.76 3.03e-01 1.00e+00
5BNC2, SLC26A7, RBPMS, ID3, CALD1
 247
AFP1_Q6 3.79e-03 5.28 1.62 3.03e-01 1.00e+00
5SULF1, PRRX1, ZFPM2, BACE2, CALD1
 268
NF1_Q6 3.90e-03 5.24 1.61 3.03e-01 1.00e+00
5SLC26A7, NFIA, FGF11, B2M, VCAM1
 270
CEBP_Q2_01 4.03e-03 5.20 1.60 3.03e-01 1.00e+00
5SULF1, PRKG1, BNC2, ID3, CALD1
 272
STAT5A_03 4.15e-03 5.16 1.59 3.03e-01 1.00e+00
5FN1, SLC26A7, FGF11, ID3, SVIL
 274
NF1_Q6_01 4.28e-03 5.13 1.58 3.03e-01 1.00e+00
5POSTN, SLC26A7, NFIA, FGF11, B2M
 276
YTAATTAA_LHX3_01 6.70e-03 5.78 1.50 3.35e-01 1.00e+00
4SULF1, PRRX1, BNC2, BACE2
 192
ZNF449_TARGET_GENES 2.42e-03 2.96 1.41 3.03e-01 1.00e+00
12TNC, SULF1, FN1, GEM, ABI3BP, UACA, NFIA, B2M, BIRC3, RBPMS, SVIL, EPB41L2
 1346
MYOGNF1_01 1.55e-02 11.31 1.29 3.35e-01 1.00e+00
2NFIA, B2M
 48
IRF2_01 1.42e-02 6.33 1.24 3.35e-01 1.00e+00
3BNC2, B2M, KCNE4
 129
LHX3_01 1.27e-02 4.77 1.24 3.35e-01 1.00e+00
4SULF1, PRRX1, PRKG1, ID3
 232
TTANTCA_UNKNOWN 8.28e-03 2.87 1.22 3.35e-01 1.00e+00
9SULF1, TIMP1, PRRX1, BNC2, ABI3BP, PDE1A, ZFPM2, BACE2, SLC9A9
 967
ATF1_Q6 1.36e-02 4.67 1.21 3.35e-01 1.00e+00
4GEM, HS3ST3A1, PDE1A, CALD1
 237
GGGNNTTTCC_NFKB_Q6_01 1.57e-02 6.09 1.20 3.35e-01 1.00e+00
3BNC2, GEM, BIRC3
 134

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GO Biological Processes:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
GOBP_MICROGLIAL_CELL_PROLIFERATION 4.28e-04 86.37 8.33 2.67e-01 1.00e+00
2CLU, IL33
 8
GOBP_REGULATION_OF_APOPTOTIC_CELL_CLEARANCE 5.49e-04 74.10 7.33 2.67e-01 1.00e+00
2CCL2, C3
 9
GOBP_PROSTATE_GLAND_MORPHOGENESIS 1.62e-04 33.18 6.19 1.53e-01 1.00e+00
3TNC, SULF1, CYP7B1
 27
GOBP_MACROPHAGE_PROLIFERATION 9.99e-04 51.89 5.39 3.53e-01 1.00e+00
2CLU, IL33
 12
GOBP_REGULATION_OF_NUCLEOTIDE_BINDING_OLIGOMERIZATION_DOMAIN_CONTAINING_SIGNALING_PATHWAY 1.18e-03 47.19 4.96 3.81e-01 1.00e+00
2BIRC3, TNFAIP3
 13
GOBP_NEGATIVE_REGULATION_OF_SMOOTH_MUSCLE_CONTRACTION 1.37e-03 43.30 4.59 3.81e-01 1.00e+00
2PRKG1, ARHGAP42
 14
GOBP_POSITIVE_REGULATION_OF_NITRIC_OXIDE_SYNTHASE_BIOSYNTHETIC_PROCESS 1.58e-03 39.95 4.27 3.92e-01 1.00e+00
2IL33, CCL2
 15
GOBP_PROSTATE_GLAND_DEVELOPMENT 5.65e-04 20.97 4.00 2.67e-01 1.00e+00
3TNC, SULF1, CYP7B1
 41
GOBP_COMPLEMENT_ACTIVATION_ALTERNATIVE_PATHWAY 2.28e-03 32.49 3.53 4.87e-01 1.00e+00
2C7, C3
 18
GOBP_CHRONIC_INFLAMMATORY_RESPONSE 2.54e-03 30.58 3.34 4.90e-01 1.00e+00
2VCAM1, TNFAIP3
 19
GOBP_POSITIVE_REGULATION_OF_RECEPTOR_MEDIATED_ENDOCYTOSIS 1.01e-03 16.95 3.26 3.53e-01 1.00e+00
3CLU, B2M, C3
 50
GOBP_NITRIC_OXIDE_SYNTHASE_BIOSYNTHETIC_PROCESS 2.81e-03 28.89 3.17 4.90e-01 1.00e+00
2IL33, CCL2
 20
GOBP_POSITIVE_REGULATION_OF_CALCIUM_ION_IMPORT 2.81e-03 28.89 3.17 4.90e-01 1.00e+00
2CCL2, PDGFRB
 20
GOBP_EXTERNAL_ENCAPSULATING_STRUCTURE_ORGANIZATION 1.77e-05 7.09 3.01 1.32e-01 1.32e-01
9TNC, PAPLN, SULF1, POSTN, ADAM12, TIMP1, FN1, ADAMTS12, VCAM1
 396
GOBP_NEGATIVE_REGULATION_OF_MUSCLE_CONTRACTION 3.40e-03 26.01 2.87 5.42e-01 1.00e+00
2PRKG1, ARHGAP42
 22
GOBP_NEGATIVE_REGULATION_OF_REPRODUCTIVE_PROCESS 1.48e-03 14.76 2.85 3.81e-01 1.00e+00
3SULF1, TIMP1, ZFPM2
 57
GOBP_RESPONSE_TO_RETINOIC_ACID 7.16e-04 10.98 2.82 3.15e-01 1.00e+00
4TNC, IGFBP7, PDGFRB, EPHA3
 103
GOBP_INNERVATION 3.72e-03 24.78 2.74 5.56e-01 1.00e+00
2SULF1, VCAM1
 23
GOBP_ACUTE_INFLAMMATORY_RESPONSE 8.25e-04 10.55 2.71 3.43e-01 1.00e+00
4FN1, OSMR, VCAM1, C3
 107
GOBP_GLAND_MORPHOGENESIS 9.45e-04 10.15 2.61 3.53e-01 1.00e+00
4TNC, SULF1, CYP7B1, TNFAIP3
 111

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Immunological Gene Sets:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
GSE45365_NK_CELL_VS_BCELL_UP 1.17e-04 8.88 3.05 4.05e-01 5.71e-01
6GEM, BIRC3, CYP7B1, VCAM1, ID3, TNFAIP3
 198
GSE36891_POLYIC_TLR3_VS_PAM_TLR2_STIM_PERITONEAL_MACROPHAGE_UP 3.25e-04 9.38 2.87 4.05e-01 1.00e+00
5GEM, BIRC3, CCL2, KCNE4, TNFAIP3
 153
GSE37605_FOXP3_FUSION_GFP_VS_IRES_GFP_TREG_C57BL6_UP 7.65e-04 7.72 2.36 4.05e-01 1.00e+00
5GEM, NFIA, CCL2, KCNE4, ID3
 185
GSE9509_LPS_VS_LPS_AND_IL10_STIM_IL10_KO_MACROPHAGE_20MIN_UP 9.44e-04 7.35 2.25 4.05e-01 1.00e+00
5NFIA, BIRC3, BACE2, RBPMS, C3
 194
GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_UP 9.88e-04 7.27 2.23 4.05e-01 1.00e+00
5TNC, PRRX1, CCL2, ID3, TNFAIP3
 196
GSE17721_CTRL_VS_LPS_6H_BMDC_DN 1.06e-03 7.16 2.19 4.05e-01 1.00e+00
5TIMP1, SLC26A7, PDE1A, CCL2, ZFPM2
 199
GSE17721_LPS_VS_PAM3CSK4_1H_BMDC_DN 1.06e-03 7.16 2.19 4.05e-01 1.00e+00
5BIRC3, PDGFRB, VCAM1, EPB41L2, EPHA3
 199
GSE13306_RA_VS_UNTREATED_TCONV_DN 1.08e-03 7.12 2.18 4.05e-01 1.00e+00
5EXOC3L4, POSTN, ADAM12, NPY1R, B2M
 200
GSE14769_UNSTIM_VS_40MIN_LPS_BMDM_DN 1.08e-03 7.12 2.18 4.05e-01 1.00e+00
5EXOC3L4, BIRC3, CCL2, ID3, TNFAIP3
 200
GSE20715_0H_VS_24H_OZONE_LUNG_DN 1.08e-03 7.12 2.18 4.05e-01 1.00e+00
5PAPLN, TIMP1, IL33, OSMR, C3
 200
GSE20715_0H_VS_48H_OZONE_TLR4_KO_LUNG_DN 1.08e-03 7.12 2.18 4.05e-01 1.00e+00
5TNC, CLU, CYP7B1, IL33, OSMR
 200
GSE9601_NFKB_INHIBITOR_VS_PI3K_INHIBITOR_TREATED_HCMV_INF_MONOCYTE_DN 1.08e-03 7.12 2.18 4.05e-01 1.00e+00
5TIMP1, GEM, IL33, CCL2, KCNE4
 200
GSE43955_1H_VS_20H_ACT_CD4_TCELL_WITH_TGFB_IL6_DN 1.08e-03 7.12 2.18 4.05e-01 1.00e+00
5TNC, B2M, PDE1A, BIRC3, OSMR
 200
GSE36891_UNSTIM_VS_POLYIC_TLR3_STIM_PERITONEAL_MACROPHAGE_UP 2.76e-03 7.50 1.93 7.51e-01 1.00e+00
4ADAM12, CCL2, KCNE4, TNFAIP3
 149
GSE37605_TREG_VS_TCONV_NOD_FOXP3_FUSION_GFP_UP 2.83e-03 7.44 1.92 7.51e-01 1.00e+00
4BIRC3, CCL2, KCNE4, ID3
 150
GSE7218_IGM_VS_IGG_SIGNAL_THGOUGH_ANTIGEN_BCELL_DN 4.40e-03 6.55 1.69 7.51e-01 1.00e+00
4GEM, B2M, BIRC3, ARHGAP15
 170
GSE37605_TREG_VS_TCONV_NOD_FOXP3_FUSION_GFP_DN 4.40e-03 6.55 1.69 7.51e-01 1.00e+00
4HS3ST3A1, PDE1A, CCL2, ID3
 170
GSE6259_33D1_POS_VS_DEC205_POS_FLT3L_INDUCED_SPLENIC_DC_UP 4.87e-03 6.36 1.64 7.51e-01 1.00e+00
4FN1, PDGFRB, RBPMS, TNFAIP3
 175
GSE37605_FOXP3_FUSION_GFP_VS_IRES_GFP_TREG_C57BL6_DN 4.96e-03 6.32 1.63 7.51e-01 1.00e+00
4HS3ST3A1, PDE1A, SLC9A9, ID3
 176
GSE21360_SECONDARY_VS_QUATERNARY_MEMORY_CD8_TCELL_UP 5.58e-03 6.11 1.58 7.51e-01 1.00e+00
4CCL2, RBPMS, VCAM1, TNFAIP3
 182

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Top Ranked Transcription Factors for this Gene Expression Program:

Gene Symbol TF Rank DNA Binding Domain Motif Status IUPAC PWM GTEx DepMap Decartes
PRRX1 11 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
CLU 13 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None Included only because GO says positive regulation of NF-kappaB transcription factor activity, but there is no DBD and no evidence of DNA binding.
BNC2 16 Yes Inferred motif Monomer or homomultimer In vivo/Misc source Has a putative AT-hook None
NFIA 22 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
ZFPM2 38 Yes Likely to be sequence specific TF Monomer or homomultimer No motif None FOG-proteins use some of their zinc-fingers to interact with the GATA proteins. Other C2H2 ZFs are probably also capable of binding DNA (PMID: 10329627).
ID3 43 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None ID bHLH proteins lack the basic region and should not be able to bind DNA. The HT-SELEX motif for ID4 is likely by a co-precipitated protein or it is a contamination
TNFAIP3 45 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None Inhibits NFKB-activation. No evidence for direct binding to DNA
HOXA10 51 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
STK3 66 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None Kinase - included only because GO says it regulates TFs
TBX18 67 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
ERG 75 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
DEPTOR 83 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None None
NR2F2 92 Yes Known motif Monomer or homomultimer 100 perc ID - in vitro None None
HOXA7 96 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
NOTCH3 98 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None Fragment of NOTCH. Is a coactivator.
ETV6 100 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
LPP 108 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None znfLIM is probably not a DNA binding domain (PMID: 8506279). The protein has been reported to be coactivator for ETV4 (PMID: 16738319).
HOXA9 109 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
JUNB 114 Yes Known motif Monomer or homomultimer High-throughput in vitro None Prefers forming heterodimers with FOS; FOSB; FOSL1 and FOSL2 over homodimers (PMID:12805554); but, clearly can bind DNA specifically in vitro.
RARB 122 Yes Known motif Monomer or homomultimer High-throughput in vitro None None

QQ Plot showing correlations with other Gene Expression Programs in this dataset, calculated by Spearman correlation:

Interactive QQ-plot of gene loadings:

Interactive QQ Plot

A similar QQ-plot as above, but only for instances where the H value is e.g. > 25, i.e. we are confident that the expression program is active above noise. Agreemenet between these binary vectors is tested using the Jaccard Index, with the P-values calculated by an exact test:

Interactive QQ-plot:

Interactive QQ Plot

Singler cell type annotations for the top 50 cells on this program.


Cell ID Singler label Singler Delta Activity Score Top Singler Raw Scores
NB12_CAGTAACTCCGATATG-1 Smooth_muscle_cells:vascular 0.16 1200.23
Raw ScoresiPS_cells:CRL2097_foreskin: 0.26, Fibroblasts:breast: 0.25, Smooth_muscle_cells:vascular: 0.25, Smooth_muscle_cells:bronchial: 0.25, Smooth_muscle_cells:vascular:IL-17: 0.25, Smooth_muscle_cells:bronchial:vit_D: 0.25, Osteoblasts: 0.24, Osteoblasts:BMP2: 0.24, iPS_cells:adipose_stem_cells: 0.24, MSC: 0.24
NB13_GAAACTCAGGGTATCG-1 Fibroblasts:breast 0.15 1056.79
Raw ScoresOsteoblasts: 0.24, Osteoblasts:BMP2: 0.24, Smooth_muscle_cells:vascular: 0.24, Fibroblasts:breast: 0.24, iPS_cells:adipose_stem_cells: 0.24, iPS_cells:CRL2097_foreskin: 0.24, Smooth_muscle_cells:bronchial: 0.23, Tissue_stem_cells:BM_MSC: 0.23, Smooth_muscle_cells:bronchial:vit_D: 0.23, Smooth_muscle_cells:vascular:IL-17: 0.23
NB12_TCCCGATTCCATGAAC-1 Smooth_muscle_cells:bronchial:vit_D 0.09 914.74
Raw ScoresSmooth_muscle_cells:bronchial: 0.18, Smooth_muscle_cells:bronchial:vit_D: 0.18, Smooth_muscle_cells:vascular: 0.17, Osteoblasts: 0.17, Smooth_muscle_cells:vascular:IL-17: 0.17, Fibroblasts:breast: 0.16, iPS_cells:adipose_stem_cells: 0.16, iPS_cells:CRL2097_foreskin: 0.16, Osteoblasts:BMP2: 0.16, Tissue_stem_cells:BM_MSC: 0.16
NB13_ATCATCTGTCGCGTGT-1 Smooth_muscle_cells:vascular 0.16 672.36
Raw ScoresSmooth_muscle_cells:bronchial: 0.22, Fibroblasts:breast: 0.22, Smooth_muscle_cells:bronchial:vit_D: 0.22, Smooth_muscle_cells:vascular: 0.21, iPS_cells:adipose_stem_cells: 0.21, Smooth_muscle_cells:vascular:IL-17: 0.21, Osteoblasts: 0.2, iPS_cells:CRL2097_foreskin: 0.2, Osteoblasts:BMP2: 0.2, Tissue_stem_cells:BM_MSC:BMP2: 0.2
NB13_AGGGAGTCAAACGCGA-1 Chondrocytes:MSC-derived 0.07 528.84
Raw ScoresiPS_cells:CRL2097_foreskin: 0.16, Smooth_muscle_cells:bronchial: 0.16, Osteoblasts: 0.16, Chondrocytes:MSC-derived: 0.16, Fibroblasts:breast: 0.16, Smooth_muscle_cells:bronchial:vit_D: 0.16, Osteoblasts:BMP2: 0.16, Tissue_stem_cells:BM_MSC:TGFb3: 0.16, Smooth_muscle_cells:vascular: 0.16, iPS_cells:adipose_stem_cells: 0.15
NB05_TGCGTGGCAGACAAAT-1 Neurons:adrenal_medulla_cell_line 0.15 413.48
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.33, Neuroepithelial_cell:ESC-derived: 0.33, Astrocyte:Embryonic_stem_cell-derived: 0.32, Endothelial_cells:HUVEC:VEGF: 0.3, Endothelial_cells:lymphatic:TNFa_48h: 0.3, Neurons:ES_cell-derived_neural_precursor: 0.3, Endothelial_cells:lymphatic: 0.3, Endothelial_cells:HUVEC: 0.29, MSC: 0.29, iPS_cells:CRL2097_foreskin: 0.29
NB13_CTGATCCCATGGTTGT-1 Tissue_stem_cells:BM_MSC 0.09 400.44
Raw ScoresiPS_cells:CRL2097_foreskin: 0.28, Smooth_muscle_cells:bronchial: 0.28, iPS_cells:PDB_fibroblasts: 0.28, Chondrocytes:MSC-derived: 0.27, Smooth_muscle_cells:bronchial:vit_D: 0.27, Osteoblasts: 0.27, iPS_cells:skin_fibroblast: 0.27, Fibroblasts:breast: 0.27, iPS_cells:fibroblasts: 0.27, iPS_cells:adipose_stem_cells: 0.27
NB05_GTATCTTCACGCGAAA-1 Fibroblasts:breast 0.15 376.50
Raw ScoresiPS_cells:CRL2097_foreskin: 0.28, Smooth_muscle_cells:bronchial: 0.27, Fibroblasts:breast: 0.27, MSC: 0.27, Smooth_muscle_cells:bronchial:vit_D: 0.27, iPS_cells:adipose_stem_cells: 0.26, Smooth_muscle_cells:vascular: 0.26, Astrocyte:Embryonic_stem_cell-derived: 0.26, iPS_cells:foreskin_fibrobasts: 0.26, Chondrocytes:MSC-derived: 0.26
NB03_CTTGGCTCAGTGAGTG-1 Neurons:adrenal_medulla_cell_line 0.07 332.93
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.25, Astrocyte:Embryonic_stem_cell-derived: 0.24, Endothelial_cells:lymphatic:TNFa_48h: 0.23, Endothelial_cells:HUVEC:VEGF: 0.23, Endothelial_cells:lymphatic: 0.23, Smooth_muscle_cells:bronchial: 0.23, Neuroepithelial_cell:ESC-derived: 0.22, Smooth_muscle_cells:bronchial:vit_D: 0.22, iPS_cells:CRL2097_foreskin: 0.22, Neurons:ES_cell-derived_neural_precursor: 0.22
NB13_AGCATACGTTCCCTTG-1 Smooth_muscle_cells:vascular 0.11 314.48
Raw ScoresiPS_cells:CRL2097_foreskin: 0.19, Smooth_muscle_cells:bronchial: 0.18, Fibroblasts:breast: 0.18, Smooth_muscle_cells:vascular: 0.18, iPS_cells:adipose_stem_cells: 0.18, Osteoblasts: 0.18, Smooth_muscle_cells:bronchial:vit_D: 0.17, Smooth_muscle_cells:vascular:IL-17: 0.17, Tissue_stem_cells:BM_MSC: 0.17, iPS_cells:skin_fibroblast: 0.17
NB12_AACTCAGGTTATTCTC-1 Smooth_muscle_cells:vascular 0.13 312.12
Raw ScoresSmooth_muscle_cells:vascular: 0.22, Fibroblasts:breast: 0.21, Smooth_muscle_cells:bronchial: 0.21, Smooth_muscle_cells:bronchial:vit_D: 0.21, Smooth_muscle_cells:vascular:IL-17: 0.21, iPS_cells:CRL2097_foreskin: 0.21, iPS_cells:adipose_stem_cells: 0.21, MSC: 0.21, Tissue_stem_cells:BM_MSC: 0.21, Osteoblasts: 0.2
NB12_CAGCGACGTGCAGACA-1 Neurons:adrenal_medulla_cell_line 0.14 296.47
Raw ScoresNeuroepithelial_cell:ESC-derived: 0.21, Neurons:adrenal_medulla_cell_line: 0.21, Neurons:ES_cell-derived_neural_precursor: 0.2, iPS_cells:CRL2097_foreskin: 0.19, MSC: 0.19, Astrocyte:Embryonic_stem_cell-derived: 0.19, Fibroblasts:breast: 0.19, Tissue_stem_cells:lipoma-derived_MSC: 0.19, iPS_cells:skin_fibroblast: 0.18, iPS_cells:PDB_fibroblasts: 0.18
NB13_CATCGGGAGATGAGAG-1 iPS_cells:adipose_stem_cells 0.10 293.97
Raw ScoresiPS_cells:CRL2097_foreskin: 0.25, iPS_cells:adipose_stem_cells: 0.25, Fibroblasts:breast: 0.25, Osteoblasts: 0.24, Smooth_muscle_cells:bronchial: 0.24, iPS_cells:skin_fibroblast: 0.24, Smooth_muscle_cells:bronchial:vit_D: 0.24, iPS_cells:PDB_fibroblasts: 0.24, iPS_cells:fibroblasts: 0.24, Tissue_stem_cells:BM_MSC:TGFb3: 0.24
NB12_AAACGGGGTCTTCAAG-1 Osteoblasts 0.09 259.85
Raw ScoresSmooth_muscle_cells:bronchial: 0.16, Smooth_muscle_cells:bronchial:vit_D: 0.16, Osteoblasts: 0.16, Osteoblasts:BMP2: 0.15, Fibroblasts:breast: 0.15, iPS_cells:CRL2097_foreskin: 0.15, Tissue_stem_cells:BM_MSC:TGFb3: 0.15, Tissue_stem_cells:BM_MSC:BMP2: 0.15, Smooth_muscle_cells:vascular: 0.15, Tissue_stem_cells:iliac_MSC: 0.15
NB02_GCAATCATCATAACCG-1 iPS_cells:adipose_stem_cells 0.09 226.34
Raw ScoresSmooth_muscle_cells:bronchial: 0.14, Fibroblasts:breast: 0.14, Smooth_muscle_cells:bronchial:vit_D: 0.13, iPS_cells:CRL2097_foreskin: 0.13, Smooth_muscle_cells:vascular: 0.13, Smooth_muscle_cells:vascular:IL-17: 0.13, Osteoblasts: 0.13, iPS_cells:adipose_stem_cells: 0.13, Tissue_stem_cells:BM_MSC:TGFb3: 0.13, Chondrocytes:MSC-derived: 0.12
NB12_GATGAGGTCCCTTGTG-1 Smooth_muscle_cells:vascular 0.11 219.51
Raw ScoresSmooth_muscle_cells:bronchial: 0.18, Fibroblasts:breast: 0.18, Smooth_muscle_cells:bronchial:vit_D: 0.18, iPS_cells:adipose_stem_cells: 0.17, iPS_cells:CRL2097_foreskin: 0.17, Smooth_muscle_cells:vascular: 0.17, Osteoblasts: 0.17, Chondrocytes:MSC-derived: 0.16, Smooth_muscle_cells:vascular:IL-17: 0.16, Tissue_stem_cells:BM_MSC:TGFb3: 0.16
NB13_CAGCAGCCAGCTTAAC-1 Chondrocytes:MSC-derived 0.05 218.32
Raw ScoresAstrocyte:Embryonic_stem_cell-derived: 0.09, Chondrocytes:MSC-derived: 0.09, Osteoblasts: 0.08, iPS_cells:CRL2097_foreskin: 0.08, Fibroblasts:breast: 0.08, Smooth_muscle_cells:bronchial: 0.08, Smooth_muscle_cells:vascular: 0.08, Endothelial_cells:HUVEC:Serum_Amyloid_A: 0.08, Smooth_muscle_cells:bronchial:vit_D: 0.08, MSC: 0.08
NB12_AGCTTGACAAGTTAAG-1 Neurons:adrenal_medulla_cell_line 0.16 212.03
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.23, Astrocyte:Embryonic_stem_cell-derived: 0.2, Neuroepithelial_cell:ESC-derived: 0.2, Neurons:ES_cell-derived_neural_precursor: 0.19, Embryonic_stem_cells: 0.17, iPS_cells:PDB_1lox-17Puro-10: 0.17, iPS_cells:PDB_1lox-21Puro-20: 0.16, iPS_cells:PDB_1lox-17Puro-5: 0.16, iPS_cells:PDB_1lox-21Puro-26: 0.16, iPS_cells:CRL2097_foreskin: 0.16
NB13_TTCTACATCCAGAAGG-1 iPS_cells:adipose_stem_cells 0.16 210.63
Raw ScoresFibroblasts:breast: 0.22, Osteoblasts: 0.22, iPS_cells:adipose_stem_cells: 0.22, iPS_cells:CRL2097_foreskin: 0.22, Smooth_muscle_cells:vascular: 0.22, Chondrocytes:MSC-derived: 0.21, Osteoblasts:BMP2: 0.21, Smooth_muscle_cells:bronchial: 0.21, Smooth_muscle_cells:bronchial:vit_D: 0.21, Smooth_muscle_cells:vascular:IL-17: 0.21
NB13_TTAGGACAGAGAGCTC-1 iPS_cells:adipose_stem_cells 0.14 207.97
Raw ScoresiPS_cells:adipose_stem_cells: 0.26, Fibroblasts:breast: 0.26, Smooth_muscle_cells:vascular: 0.25, iPS_cells:CRL2097_foreskin: 0.25, Chondrocytes:MSC-derived: 0.25, Smooth_muscle_cells:bronchial: 0.25, Smooth_muscle_cells:vascular:IL-17: 0.25, Tissue_stem_cells:BM_MSC: 0.25, Osteoblasts: 0.25, Osteoblasts:BMP2: 0.25
NB13_ACCGTAAGTACGCACC-1 Fibroblasts:breast 0.11 205.00
Raw ScoresFibroblasts:breast: 0.18, Tissue_stem_cells:BM_MSC: 0.18, iPS_cells:adipose_stem_cells: 0.18, Smooth_muscle_cells:bronchial: 0.18, MSC: 0.18, iPS_cells:skin_fibroblast: 0.18, Neurons:Schwann_cell: 0.18, Osteoblasts: 0.18, Chondrocytes:MSC-derived: 0.18, iPS_cells:CRL2097_foreskin: 0.18
NB12_TGTCCCACATGGTCAT-1 Endothelial_cells:lymphatic:TNFa_48h 0.19 202.01
Raw ScoresEndothelial_cells:lymphatic:TNFa_48h: 0.3, Endothelial_cells:lymphatic: 0.3, Endothelial_cells:HUVEC:VEGF: 0.29, Endothelial_cells:HUVEC:Serum_Amyloid_A: 0.27, Endothelial_cells:HUVEC: 0.27, Endothelial_cells:HUVEC:B._anthracis_LT: 0.26, Endothelial_cells:HUVEC:H5N1-infected: 0.26, Endothelial_cells:HUVEC:IL-1b: 0.26, Endothelial_cells:HUVEC:FPV-infected: 0.25, Endothelial_cells:HUVEC:PR8-infected: 0.25
NB12_ATGAGGGTCTGGTGTA-1 Fibroblasts:breast 0.20 193.73
Raw ScoresFibroblasts:breast: 0.27, iPS_cells:adipose_stem_cells: 0.26, Osteoblasts: 0.26, Tissue_stem_cells:BM_MSC:TGFb3: 0.25, Smooth_muscle_cells:vascular: 0.25, iPS_cells:CRL2097_foreskin: 0.25, Chondrocytes:MSC-derived: 0.25, Osteoblasts:BMP2: 0.25, Smooth_muscle_cells:vascular:IL-17: 0.24, Smooth_muscle_cells:bronchial:vit_D: 0.24
NB12_GTGGGTCAGAGGGATA-1 Neurons:adrenal_medulla_cell_line 0.17 181.78
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.28, Astrocyte:Embryonic_stem_cell-derived: 0.24, Neuroepithelial_cell:ESC-derived: 0.24, Neurons:ES_cell-derived_neural_precursor: 0.23, iPS_cells:PDB_1lox-21Puro-20: 0.21, iPS_cells:PDB_1lox-21Puro-26: 0.21, iPS_cells:PDB_1lox-17Puro-10: 0.21, iPS_cells:PDB_1lox-17Puro-5: 0.2, Embryonic_stem_cells: 0.2, iPS_cells:PDB_2lox-22: 0.19
NB12_AGCGTATTCTCTAAGG-1 Neurons:adrenal_medulla_cell_line 0.08 176.46
Raw ScoresSmooth_muscle_cells:vascular: 0.16, Fibroblasts:breast: 0.16, Smooth_muscle_cells:bronchial: 0.15, Osteoblasts: 0.15, iPS_cells:CRL2097_foreskin: 0.15, Smooth_muscle_cells:vascular:IL-17: 0.15, Tissue_stem_cells:BM_MSC:BMP2: 0.15, Chondrocytes:MSC-derived: 0.15, iPS_cells:adipose_stem_cells: 0.15, Tissue_stem_cells:BM_MSC:TGFb3: 0.15
NB09_TCCACACCAATGGATA-1 Osteoblasts 0.11 169.99
Raw ScoresiPS_cells:CRL2097_foreskin: 0.19, MSC: 0.19, Smooth_muscle_cells:bronchial: 0.19, Chondrocytes:MSC-derived: 0.18, Osteoblasts: 0.18, Tissue_stem_cells:BM_MSC:TGFb3: 0.18, Fibroblasts:breast: 0.18, Smooth_muscle_cells:bronchial:vit_D: 0.18, Smooth_muscle_cells:vascular: 0.18, iPS_cells:adipose_stem_cells: 0.18
NB03_AAGCCGCCACCAGCAC-1 Smooth_muscle_cells:bronchial 0.05 169.87
Raw ScoresSmooth_muscle_cells:bronchial: 0.13, Smooth_muscle_cells:bronchial:vit_D: 0.13, iPS_cells:CRL2097_foreskin: 0.13, iPS_cells:skin_fibroblast: 0.12, Tissue_stem_cells:BM_MSC:TGFb3: 0.12, iPS_cells:fibroblasts: 0.12, iPS_cells:adipose_stem_cells: 0.12, Astrocyte:Embryonic_stem_cell-derived: 0.12, Fibroblasts:breast: 0.12, NK_cell:IL2: 0.12
NB12_CAGCTAAGTATGAATG-1 Neurons:adrenal_medulla_cell_line 0.13 166.79
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.19, Astrocyte:Embryonic_stem_cell-derived: 0.17, Neuroepithelial_cell:ESC-derived: 0.16, Neurons:ES_cell-derived_neural_precursor: 0.16, Smooth_muscle_cells:bronchial: 0.15, iPS_cells:CRL2097_foreskin: 0.14, Smooth_muscle_cells:bronchial:vit_D: 0.14, MSC: 0.14, Smooth_muscle_cells:vascular: 0.14, Embryonic_stem_cells: 0.14
NB06_AGTAGTCAGGTCATCT-1 Neuroepithelial_cell:ESC-derived 0.07 164.26
Raw ScoresOsteoblasts: 0.17, iPS_cells:adipose_stem_cells: 0.17, iPS_cells:CRL2097_foreskin: 0.17, Fibroblasts:breast: 0.17, Smooth_muscle_cells:vascular: 0.17, Chondrocytes:MSC-derived: 0.17, Osteoblasts:BMP2: 0.17, Smooth_muscle_cells:vascular:IL-17: 0.16, Smooth_muscle_cells:bronchial: 0.16, Tissue_stem_cells:BM_MSC: 0.16
NB09_TTGTAGGGTTCAGGCC-1 Smooth_muscle_cells:vascular 0.09 156.89
Raw ScoresFibroblasts:breast: 0.14, Smooth_muscle_cells:vascular: 0.14, Smooth_muscle_cells:vascular:IL-17: 0.13, Neuroepithelial_cell:ESC-derived: 0.13, Neurons:ES_cell-derived_neural_precursor: 0.13, MSC: 0.13, iPS_cells:adipose_stem_cells: 0.13, Osteoblasts: 0.13, iPS_cells:CRL2097_foreskin: 0.13, Osteoblasts:BMP2: 0.13
NB14_CAGAGAGTCGCGTTTC-1 Tissue_stem_cells:BM_MSC 0.15 155.86
Raw ScoresChondrocytes:MSC-derived: 0.19, Fibroblasts:breast: 0.18, Smooth_muscle_cells:bronchial: 0.18, Smooth_muscle_cells:bronchial:vit_D: 0.18, iPS_cells:CRL2097_foreskin: 0.18, Osteoblasts: 0.18, iPS_cells:adipose_stem_cells: 0.18, Tissue_stem_cells:BM_MSC: 0.18, Smooth_muscle_cells:vascular: 0.18, Tissue_stem_cells:BM_MSC:TGFb3: 0.18
NB07_AACCGCGCATTAGCCA-1 Neurons:adrenal_medulla_cell_line 0.17 144.08
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.29, Neuroepithelial_cell:ESC-derived: 0.26, Astrocyte:Embryonic_stem_cell-derived: 0.25, Neurons:ES_cell-derived_neural_precursor: 0.23, Embryonic_stem_cells: 0.21, iPS_cells:PDB_1lox-21Puro-20: 0.21, iPS_cells:PDB_1lox-17Puro-10: 0.21, iPS_cells:PDB_1lox-21Puro-26: 0.21, iPS_cells:PDB_1lox-17Puro-5: 0.21, iPS_cells:PDB_2lox-22: 0.21
NB12_GATGAGGTCTCTGTCG-1 Osteoblasts 0.09 144.00
Raw ScoresSmooth_muscle_cells:bronchial: 0.14, Smooth_muscle_cells:bronchial:vit_D: 0.14, iPS_cells:CRL2097_foreskin: 0.14, Osteoblasts: 0.14, Fibroblasts:breast: 0.14, Osteoblasts:BMP2: 0.13, iPS_cells:adipose_stem_cells: 0.13, MSC: 0.13, Smooth_muscle_cells:vascular: 0.13, iPS_cells:skin_fibroblast: 0.13
NB06_CACTCCACAATCTACG-1 Neurons:adrenal_medulla_cell_line 0.19 138.24
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.33, Neuroepithelial_cell:ESC-derived: 0.31, Astrocyte:Embryonic_stem_cell-derived: 0.31, Neurons:ES_cell-derived_neural_precursor: 0.3, Embryonic_stem_cells: 0.26, iPS_cells:PDB_1lox-17Puro-10: 0.25, iPS_cells:PDB_1lox-21Puro-20: 0.25, iPS_cells:PDB_1lox-21Puro-26: 0.25, MSC: 0.25, Tissue_stem_cells:CD326-CD56+: 0.25
NB13_CAGATCAAGGCGCTCT-1 Tissue_stem_cells:BM_MSC:BMP2 0.06 137.53
Raw ScoresTissue_stem_cells:BM_MSC:BMP2: 0.19, iPS_cells:adipose_stem_cells: 0.19, Smooth_muscle_cells:bronchial: 0.19, Tissue_stem_cells:BM_MSC:TGFb3: 0.19, Fibroblasts:breast: 0.19, Smooth_muscle_cells:bronchial:vit_D: 0.19, Osteoblasts: 0.19, Chondrocytes:MSC-derived: 0.19, Osteoblasts:BMP2: 0.19, Tissue_stem_cells:BM_MSC: 0.18
NB13_GTTCTCGGTACGCACC-1 Tissue_stem_cells:BM_MSC:BMP2 0.12 134.48
Raw ScoresSmooth_muscle_cells:bronchial: 0.17, Osteoblasts: 0.17, Smooth_muscle_cells:bronchial:vit_D: 0.17, Fibroblasts:breast: 0.17, Osteoblasts:BMP2: 0.16, Tissue_stem_cells:BM_MSC:TGFb3: 0.16, Tissue_stem_cells:BM_MSC:BMP2: 0.16, Smooth_muscle_cells:vascular: 0.16, iPS_cells:adipose_stem_cells: 0.16, iPS_cells:CRL2097_foreskin: 0.16
NB14_GGCCGATGTCCGCTGA-1 Tissue_stem_cells:BM_MSC 0.15 131.91
Raw ScoresOsteoblasts: 0.2, Smooth_muscle_cells:bronchial: 0.2, Chondrocytes:MSC-derived: 0.2, Smooth_muscle_cells:bronchial:vit_D: 0.2, iPS_cells:adipose_stem_cells: 0.19, Osteoblasts:BMP2: 0.19, iPS_cells:CRL2097_foreskin: 0.19, Tissue_stem_cells:BM_MSC: 0.19, Fibroblasts:breast: 0.19, Smooth_muscle_cells:vascular: 0.19
NB07_CGCTATCTCAGAAATG-1 Neurons:adrenal_medulla_cell_line 0.17 131.05
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.26, Astrocyte:Embryonic_stem_cell-derived: 0.22, Neuroepithelial_cell:ESC-derived: 0.21, Neurons:ES_cell-derived_neural_precursor: 0.21, iPS_cells:CRL2097_foreskin: 0.18, Smooth_muscle_cells:bronchial: 0.18, Embryonic_stem_cells: 0.17, Smooth_muscle_cells:bronchial:vit_D: 0.17, iPS_cells:PDB_1lox-21Puro-20: 0.17, iPS_cells:PDB_1lox-17Puro-10: 0.17
NB13_CTAACTTAGCCGCCTA-1 Neurons:adrenal_medulla_cell_line 0.23 128.27
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.42, Astrocyte:Embryonic_stem_cell-derived: 0.34, Neuroepithelial_cell:ESC-derived: 0.33, Neurons:ES_cell-derived_neural_precursor: 0.31, iPS_cells:PDB_1lox-21Puro-20: 0.3, iPS_cells:PDB_1lox-21Puro-26: 0.3, iPS_cells:PDB_1lox-17Puro-10: 0.3, iPS_cells:PDB_1lox-17Puro-5: 0.3, Embryonic_stem_cells: 0.29, iPS_cells:PDB_2lox-22: 0.29
NB12_GGGCATCGTGTGTGCC-1 Neurons:adrenal_medulla_cell_line 0.18 125.71
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.27, Neuroepithelial_cell:ESC-derived: 0.24, Astrocyte:Embryonic_stem_cell-derived: 0.23, Neurons:ES_cell-derived_neural_precursor: 0.23, iPS_cells:PDB_1lox-21Puro-20: 0.21, iPS_cells:PDB_1lox-21Puro-26: 0.21, Embryonic_stem_cells: 0.21, iPS_cells:PDB_1lox-17Puro-10: 0.21, iPS_cells:PDB_1lox-17Puro-5: 0.2, iPS_cells:PDB_2lox-22: 0.2
NB11_GCAAACTAGTGGGATC-1 Fibroblasts:breast 0.15 122.45
Raw ScoresSmooth_muscle_cells:bronchial: 0.18, Fibroblasts:breast: 0.18, iPS_cells:CRL2097_foreskin: 0.18, iPS_cells:adipose_stem_cells: 0.18, Smooth_muscle_cells:bronchial:vit_D: 0.18, Chondrocytes:MSC-derived: 0.17, Osteoblasts: 0.17, Smooth_muscle_cells:vascular: 0.16, Osteoblasts:BMP2: 0.16, iPS_cells:PDB_fibroblasts: 0.16
NB03_TTGCGTCTCGAACTGT-1 iPS_cells:skin_fibroblast 0.06 121.61
Raw ScoresiPS_cells:adipose_stem_cells: 0.15, Smooth_muscle_cells:bronchial: 0.15, iPS_cells:skin_fibroblast: 0.15, iPS_cells:CRL2097_foreskin: 0.14, Osteoblasts: 0.14, Fibroblasts:breast: 0.14, Smooth_muscle_cells:vascular: 0.14, Smooth_muscle_cells:bronchial:vit_D: 0.14, Tissue_stem_cells:BM_MSC:TGFb3: 0.14, iPS_cells:PDB_fibroblasts: 0.14
NB13_CAAGGCCTCAACACAC-1 Neurons:adrenal_medulla_cell_line 0.07 121.21
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.19, Astrocyte:Embryonic_stem_cell-derived: 0.17, Neuroepithelial_cell:ESC-derived: 0.16, Neurons:ES_cell-derived_neural_precursor: 0.16, iPS_cells:skin_fibroblast: 0.15, iPS_cells:CRL2097_foreskin: 0.15, MSC: 0.15, Neurons:Schwann_cell: 0.15, Endothelial_cells:HUVEC:VEGF: 0.15, iPS_cells:PDB_fibroblasts: 0.15
NB02_TATGCCCTCAACGCTA-1 Fibroblasts:breast 0.10 121.05
Raw ScoresOsteoblasts: 0.16, Chondrocytes:MSC-derived: 0.16, Fibroblasts:breast: 0.15, iPS_cells:adipose_stem_cells: 0.15, Tissue_stem_cells:BM_MSC:TGFb3: 0.15, Tissue_stem_cells:BM_MSC:BMP2: 0.15, Tissue_stem_cells:BM_MSC: 0.15, Tissue_stem_cells:BM_MSC:osteogenic: 0.14, Smooth_muscle_cells:vascular: 0.14, Smooth_muscle_cells:vascular:IL-17: 0.14
NB13_CTAATGGGTATAGTAG-1 Smooth_muscle_cells:bronchial:vit_D 0.12 118.87
Raw ScoresSmooth_muscle_cells:bronchial:vit_D: 0.2, iPS_cells:adipose_stem_cells: 0.2, Smooth_muscle_cells:bronchial: 0.2, Fibroblasts:breast: 0.2, Chondrocytes:MSC-derived: 0.2, iPS_cells:CRL2097_foreskin: 0.2, Osteoblasts: 0.19, Tissue_stem_cells:BM_MSC:TGFb3: 0.19, Tissue_stem_cells:BM_MSC:BMP2: 0.19, Smooth_muscle_cells:vascular: 0.19
NB02_GCTTCCACATTCTCAT-1 iPS_cells:adipose_stem_cells 0.17 118.48
Raw ScoresFibroblasts:breast: 0.27, Osteoblasts: 0.27, iPS_cells:adipose_stem_cells: 0.27, Chondrocytes:MSC-derived: 0.26, Osteoblasts:BMP2: 0.26, Smooth_muscle_cells:vascular:IL-17: 0.26, Tissue_stem_cells:BM_MSC: 0.26, iPS_cells:CRL2097_foreskin: 0.26, Smooth_muscle_cells:vascular: 0.26, Tissue_stem_cells:BM_MSC:osteogenic: 0.25
NB12_CAGCATAAGATACACA-1 Neurons:adrenal_medulla_cell_line 0.09 117.32
Raw ScoresNeurons:ES_cell-derived_neural_precursor: 0.14, iPS_cells:CRL2097_foreskin: 0.14, Fibroblasts:breast: 0.14, Neuroepithelial_cell:ESC-derived: 0.14, Smooth_muscle_cells:bronchial: 0.14, Smooth_muscle_cells:bronchial:vit_D: 0.14, iPS_cells:adipose_stem_cells: 0.14, MSC: 0.14, Smooth_muscle_cells:vascular: 0.13, Osteoblasts: 0.13
NB13_CGAGAAGTCACAACGT-1 Neurons:adrenal_medulla_cell_line 0.12 116.42
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.22, Neuroepithelial_cell:ESC-derived: 0.19, Astrocyte:Embryonic_stem_cell-derived: 0.19, Neurons:ES_cell-derived_neural_precursor: 0.18, Tissue_stem_cells:CD326-CD56+: 0.17, Neurons:Schwann_cell: 0.16, Embryonic_stem_cells: 0.16, Endothelial_cells:lymphatic:TNFa_48h: 0.16, Endothelial_cells:HUVEC:VEGF: 0.16, MSC: 0.16
NB12_GATGCTACACATCTTT-1 Neurons:adrenal_medulla_cell_line 0.08 114.29
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.13, Astrocyte:Embryonic_stem_cell-derived: 0.11, Neurons:ES_cell-derived_neural_precursor: 0.11, Neuroepithelial_cell:ESC-derived: 0.11, MSC: 0.09, Smooth_muscle_cells:umbilical_vein: 0.09, iPS_cells:skin_fibroblast: 0.09, iPS_cells:fibroblasts: 0.09, iPS_cells:CRL2097_foreskin: 0.09, Smooth_muscle_cells:bronchial: 0.09
NB13_ATTATCCCACCAGGCT-1 Tissue_stem_cells:BM_MSC 0.07 112.00
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.17, MSC: 0.17, iPS_cells:CRL2097_foreskin: 0.17, Osteoblasts: 0.17, Smooth_muscle_cells:bronchial: 0.17, Smooth_muscle_cells:bronchial:vit_D: 0.17, Osteoblasts:BMP2: 0.17, Chondrocytes:MSC-derived: 0.16, iPS_cells:skin_fibroblast: 0.16, Fibroblasts:breast: 0.16


Below shows the significant enrichments of this GEP for literature curated gene lists
   This data was procured from existing single cell RNA-seq maps of neuroblastoma or related relevant data.
  High ranks indicate this gene is a driver of this GEP.
  These curated gene list are ranked by the P-value (on this GEP) of their constituent genes.
  The Mean Count column shows the mean read count in cells scoring highly (H > 50) on this gene expression program.


Myofibroblastic CAF
These marker genes were curated across cancer subtypes in multiple organ systems as reviewed in Lavie et. al. (PMID 35883004) and contain myofibroblastic specific CAF genes:
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.03e-07
Mean rank of genes in gene set: 3592.31
Rank on gene expression program of genes in gene set:
Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
TNC 0.0085546 2 GTEx DepMap Descartes 2.06 488.76
IGFBP7 0.0068017 4 GTEx DepMap Descartes 3.11 3421.62
POSTN 0.0054233 7 GTEx DepMap Descartes 1.57 862.81
FN1 0.0043083 10 GTEx DepMap Descartes 4.35 844.41
BGN 0.0016672 117 GTEx DepMap Descartes 0.65 661.27
IGFBP3 0.0015960 125 GTEx DepMap Descartes 0.25 101.61
COL4A1 0.0015230 135 GTEx DepMap Descartes 0.96 277.42
ACTA2 0.0015138 140 GTEx DepMap Descartes 0.51 515.87
MEF2C 0.0012116 212 GTEx DepMap Descartes 0.72 89.27
TPM1 0.0011275 236 GTEx DepMap Descartes 1.08 367.27
COL14A1 0.0009719 314 GTEx DepMap Descartes 0.38 108.17
TAGLN 0.0008694 371 GTEx DepMap Descartes 0.43 171.46
TGFBR2 0.0008106 419 GTEx DepMap Descartes 0.35 85.12
MYH11 0.0007970 432 GTEx DepMap Descartes 0.11 24.98
THBS2 0.0007479 468 GTEx DepMap Descartes 0.91 342.88
MMP11 0.0006621 561 GTEx DepMap Descartes 0.04 27.65
COL5A2 0.0006453 580 GTEx DepMap Descartes 1.28 376.18
MYL9 0.0006399 591 GTEx DepMap Descartes 0.32 185.96
COL3A1 0.0006366 601 GTEx DepMap Descartes 3.72 1343.30
COL10A1 0.0006104 632 GTEx DepMap Descartes 0.03 23.70
VCAN 0.0005827 664 GTEx DepMap Descartes 1.34 201.70
COL5A1 0.0005633 691 GTEx DepMap Descartes 0.69 160.34
WNT5A 0.0005314 744 GTEx DepMap Descartes 0.03 4.17
THY1 0.0005127 784 GTEx DepMap Descartes 0.31 116.89
COL15A1 0.0005095 795 GTEx DepMap Descartes 0.18 63.88
TPM2 0.0004858 851 GTEx DepMap Descartes 0.36 351.06
CNN2 0.0004831 858 GTEx DepMap Descartes 0.12 84.17
ITGA7 0.0003383 1328 GTEx DepMap Descartes 0.11 33.49
MYLK 0.0003235 1413 GTEx DepMap Descartes 0.14 17.62
DCN 0.0002902 1600 GTEx DepMap Descartes 0.44 108.52
VEGFA 0.0002853 1633 GTEx DepMap Descartes 0.23 35.30
COL13A1 0.0002536 1879 GTEx DepMap Descartes 0.06 25.68
TGFB1 0.0002402 1991 GTEx DepMap Descartes 0.20 106.63
HOPX 0.0001995 2399 GTEx DepMap Descartes 0.03 8.68
TGFB2 0.0001992 2403 GTEx DepMap Descartes 0.09 14.72
PGF 0.0000349 5377 GTEx DepMap Descartes 0.08 24.96
TGFBR1 -0.0000141 6761 GTEx DepMap Descartes 0.26 67.30
COL1A1 -0.0000431 7753 GTEx DepMap Descartes 4.85 1426.45
CNN3 -0.0000930 9249 GTEx DepMap Descartes 0.25 203.88
TMEM119 -0.0001305 10215 GTEx DepMap Descartes 0.07 28.14
COL12A1 -0.0002393 11715 GTEx DepMap Descartes 0.47 67.66
RGS5 -0.0002548 11828 GTEx DepMap Descartes 0.73 118.19
ACTG2 -0.0003723 12216 GTEx DepMap Descartes 0.00 0.00
LUM -0.0005435 12402 GTEx DepMap Descartes 0.48 293.95
THBS1 -0.0006937 12473 GTEx DepMap Descartes 0.87 237.57
MMP2 -0.0007342 12486 GTEx DepMap Descartes 0.23 105.86
COL8A1 -0.0008538 12501 GTEx DepMap Descartes 0.53 174.85
COL11A1 -0.0009265 12512 GTEx DepMap Descartes 0.15 29.31
COL1A2 -0.0013785 12545 GTEx DepMap Descartes 4.21 1365.65


Inflammatory CAF
These marker genes were curated across cancer subtypes in multiple organ systems as reviewed in Lavie et. al. (PMID 35883004) and contain inflammatory specific CAF genes:
Wilcoxon ranksum test P-value for gene set overrepresentation: 3.88e-07
Mean rank of genes in gene set: 2698.44
Rank on gene expression program of genes in gene set:

Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
C7 0.0087669 1 GTEx DepMap Descartes 0.86 408.39
IL33 0.0029119 30 GTEx DepMap Descartes 0.14 103.70
CCL2 0.0028949 32 GTEx DepMap Descartes 0.64 1212.95
PDGFRB 0.0028514 34 GTEx DepMap Descartes 0.50 162.41
C3 0.0026599 44 GTEx DepMap Descartes 1.04 311.89
CXCL14 0.0012992 187 GTEx DepMap Descartes 0.05 35.69
CXCL12 0.0011452 228 GTEx DepMap Descartes 0.19 94.43
PDGFRA 0.0009306 332 GTEx DepMap Descartes 0.14 51.02
SERPING1 0.0005859 659 GTEx DepMap Descartes 0.29 201.15
SCARA3 0.0005619 693 GTEx DepMap Descartes 0.08 28.75
GPX3 0.0005264 757 GTEx DepMap Descartes 0.13 123.60
IGFBP6 0.0004160 1053 GTEx DepMap Descartes 0.08 106.27
PDPN 0.0004063 1081 GTEx DepMap Descartes 0.06 44.41
SOD2 0.0003601 1242 GTEx DepMap Descartes 0.47 54.75
PDGFD 0.0001929 2488 GTEx DepMap Descartes 0.24 88.23
IL1R1 0.0001174 3569 GTEx DepMap Descartes 0.31 132.12
RGMA 0.0001165 3589 GTEx DepMap Descartes 0.08 11.46
CFB 0.0001033 3849 GTEx DepMap Descartes 0.03 13.32
SCARA5 0.0000937 4034 GTEx DepMap Descartes 0.00 0.00
CXCL2 0.0000843 4213 GTEx DepMap Descartes 0.07 138.00
HGF 0.0000710 4477 GTEx DepMap Descartes 0.03 7.16
CFD 0.0000113 6041 GTEx DepMap Descartes 0.03 48.95
LIF 0.0000037 6250 GTEx DepMap Descartes 0.06 29.27
IL10 -0.0001265 10129 GTEx DepMap Descartes 0.00 0.00
IGF1 -0.0006415 12449 GTEx DepMap Descartes 0.26 64.88


Stromal 2 (Hanemaaijer)
Marker genes obtained from Supplementary Table SD of Hanemaaijer et al (PMID 33500353). The authors generated single-cell RNA-seq data (sort-seq, 2,229 cells total) from mouse adrenal glads at E13.5, E14.5, E17.5, E18.5, P1 and P5. These were marker genes that matched with a similar dataset generated by Furlan et al (PMID 28684471). This particular set of markers are for Stroma subcluster:
Wilcoxon ranksum test P-value for gene set overrepresentation: 4.68e-05
Mean rank of genes in gene set: 2191.33
Rank on gene expression program of genes in gene set:

Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
POSTN 0.0054233 7 GTEx DepMap Descartes 1.57 862.81
FBN1 0.0013597 168 GTEx DepMap Descartes 0.94 119.61
FSTL1 0.0013010 186 GTEx DepMap Descartes 0.48 164.74
FBN2 0.0010006 297 GTEx DepMap Descartes 0.09 13.56
COL14A1 0.0009719 314 GTEx DepMap Descartes 0.38 108.17
IGFBP5 0.0009462 326 GTEx DepMap Descartes 0.58 137.03
GSN 0.0008514 390 GTEx DepMap Descartes 0.44 107.03
COL5A2 0.0006453 580 GTEx DepMap Descartes 1.28 376.18
GAS1 0.0004077 1077 GTEx DepMap Descartes 0.06 29.61
SFRP1 0.0000665 4599 GTEx DepMap Descartes 0.10 43.55
ITM2A -0.0000270 7180 GTEx DepMap Descartes 0.01 1.87
PENK -0.0001840 11172 GTEx DepMap Descartes 0.00 0.00




Below shows ranks on this GEP for literature curated gene lists for large gene sets
  These include those reported as mesenchymal/adrenergic by Van Groningen et al.
  High ranks indicate this gene is a driver of this GEP (note these results are not ordered).
  The Mean Count column shows the mean read count in cells scoring highly (H > 50) on this gene expression program.


VanGroningen Adrenergic Genes
Adrenergic marker genes from Supplementary Table 2 of Van Groningen et al. Nature Genetics 2017. These genes were identified by differential expression analysis of mesenchymal-like and adrenergic-like neuroblastoma cell lines.
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.00e+00
Mean rank of genes in gene set: 9000.03
Median rank of genes in gene set: 10048
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
CELF2 0.0008081 422 GTEx DepMap Descartes 0.70 106.62
AKAP12 0.0005613 697 GTEx DepMap Descartes 0.68 146.95
SYNPO2 0.0005259 761 GTEx DepMap Descartes 0.76 70.73
CXCR4 0.0005233 767 GTEx DepMap Descartes 0.14 55.75
RBP1 0.0004738 884 GTEx DepMap Descartes 0.40 227.63
RTN1 0.0004684 895 GTEx DepMap Descartes 2.36 728.71
NPY 0.0004082 1075 GTEx DepMap Descartes 4.37 6313.43
ABLIM1 0.0003148 1458 GTEx DepMap Descartes 0.31 44.99
EXOC5 0.0003097 1493 GTEx DepMap Descartes 0.33 33.88
SLIT3 0.0003026 1521 GTEx DepMap Descartes 1.66 236.13
ICA1 0.0002914 1592 GTEx DepMap Descartes 2.45 1115.95
CDKN2C 0.0002511 1899 GTEx DepMap Descartes 0.05 27.45
LYN 0.0002370 2023 GTEx DepMap Descartes 0.11 28.35
LSM3 0.0002330 2058 GTEx DepMap Descartes 0.16 91.86
FKBP1B 0.0002300 2083 GTEx DepMap Descartes 0.03 27.70
POLB 0.0002279 2107 GTEx DepMap Descartes 0.12 122.06
TMEM178B 0.0002135 2247 GTEx DepMap Descartes 2.04 NA
INSM2 0.0002035 2358 GTEx DepMap Descartes 0.10 48.36
PPP2R3C 0.0001974 2425 GTEx DepMap Descartes 0.16 135.50
LIN28B 0.0001889 2548 GTEx DepMap Descartes 0.25 52.96
DPYSL3 0.0001838 2603 GTEx DepMap Descartes 0.93 232.20
PARP6 0.0001788 2652 GTEx DepMap Descartes 0.23 90.34
PHPT1 0.0001773 2682 GTEx DepMap Descartes 0.31 322.02
ALK 0.0001712 2752 GTEx DepMap Descartes 2.27 379.23
TUBB4B 0.0001590 2911 GTEx DepMap Descartes 0.23 143.00
RNF150 0.0001385 3196 GTEx DepMap Descartes 0.74 87.74
RUFY3 0.0001376 3216 GTEx DepMap Descartes 0.65 190.52
MCM7 0.0001361 3237 GTEx DepMap Descartes 0.53 154.15
DAPK1 0.0001360 3239 GTEx DepMap Descartes 0.35 60.92
CCNI 0.0001225 3469 GTEx DepMap Descartes 0.72 391.17


VanGroningen Mesenchymal Genes
Mesenchymal marker genes from Supplementary Table 2 of Van Groningen et al. Nature Genetics 2017. These genes were identified by differential expression analysis of mesenchymal-like and adrenergic-like neuroblastoma cell lines.
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.47e-34
Mean rank of genes in gene set: 4192.22
Median rank of genes in gene set: 2568
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
TNC 0.0085546 2 GTEx DepMap Descartes 2.06 488.76
POSTN 0.0054233 7 GTEx DepMap Descartes 1.57 862.81
TIMP1 0.0046397 9 GTEx DepMap Descartes 2.87 4863.81
FN1 0.0043083 10 GTEx DepMap Descartes 4.35 844.41
PRRX1 0.0041227 11 GTEx DepMap Descartes 0.57 231.54
BNC2 0.0034729 16 GTEx DepMap Descartes 1.14 164.39
NFIA 0.0032102 22 GTEx DepMap Descartes 1.06 43.23
B2M 0.0031452 25 GTEx DepMap Descartes 3.35 1835.87
HS3ST3A1 0.0030440 26 GTEx DepMap Descartes 0.19 86.58
ID3 0.0026613 43 GTEx DepMap Descartes 0.32 475.93
CALD1 0.0026092 47 GTEx DepMap Descartes 3.33 1177.92
SVIL 0.0025921 48 GTEx DepMap Descartes 1.06 219.62
EPHA3 0.0025716 50 GTEx DepMap Descartes 0.28 104.30
FLRT2 0.0025077 52 GTEx DepMap Descartes 0.73 33.90
COL27A1 0.0024809 53 GTEx DepMap Descartes 0.21 67.95
TFPI 0.0024692 54 GTEx DepMap Descartes 0.56 98.10
PLEKHH2 0.0024500 55 GTEx DepMap Descartes 0.19 63.33
COL6A3 0.0024122 56 GTEx DepMap Descartes 1.21 215.79
EDNRA 0.0023488 59 GTEx DepMap Descartes 0.35 154.74
RIN2 0.0023313 60 GTEx DepMap Descartes 0.43 177.56
COL4A2 0.0022438 64 GTEx DepMap Descartes 1.03 262.76
MGP 0.0021670 70 GTEx DepMap Descartes 1.16 1200.34
CDH11 0.0021492 72 GTEx DepMap Descartes 0.84 253.94
MAML2 0.0021475 73 GTEx DepMap Descartes 1.41 321.79
EPS8 0.0020320 81 GTEx DepMap Descartes 0.53 183.32
COL6A2 0.0020268 82 GTEx DepMap Descartes 1.44 669.08
PEAK1 0.0019873 87 GTEx DepMap Descartes 0.86 NA
CFH 0.0018385 101 GTEx DepMap Descartes 0.37 127.50
IFITM3 0.0017634 107 GTEx DepMap Descartes 0.47 1105.04
LPP 0.0017524 108 GTEx DepMap Descartes 1.81 174.80


Descartes adrenocortical markers
Top 50 marker genes of adrenocortical cells in the Decartes fetal adrenal single cell map (https://atlas.brotmanbaty.org/bbi/human-gene-expression-during-development/cell/adrenocortical/in/adrenal)
Wilcoxon ranksum test P-value for gene set overrepresentation: 8.97e-01
Mean rank of genes in gene set: 7038.67
Median rank of genes in gene set: 7903
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
CLU 0.0037933 13 GTEx DepMap Descartes 1.14 494.10
ERN1 0.0004081 1076 GTEx DepMap Descartes 0.18 29.45
SH3PXD2B 0.0002931 1585 GTEx DepMap Descartes 0.31 62.28
PAPSS2 0.0002832 1654 GTEx DepMap Descartes 0.15 74.61
LDLR 0.0002190 2193 GTEx DepMap Descartes 0.12 32.51
NPC1 0.0002183 2199 GTEx DepMap Descartes 0.26 58.32
INHA 0.0001476 3069 GTEx DepMap Descartes 0.02 15.94
IGF1R 0.0001333 3287 GTEx DepMap Descartes 1.01 86.23
CYB5B 0.0001193 3530 GTEx DepMap Descartes 0.23 66.06
SGCZ 0.0001188 3537 GTEx DepMap Descartes 0.19 34.86
FDX1 0.0001043 3820 GTEx DepMap Descartes 0.06 33.68
SCAP 0.0001020 3868 GTEx DepMap Descartes 0.19 58.47
TM7SF2 0.0000899 4111 GTEx DepMap Descartes 0.11 45.36
FDPS 0.0000841 4221 GTEx DepMap Descartes 0.36 267.71
PDE10A 0.0000494 5025 GTEx DepMap Descartes 0.35 66.46
SLC1A2 0.0000045 6224 GTEx DepMap Descartes 0.21 20.66
STAR -0.0000326 7381 GTEx DepMap Descartes 0.00 0.00
SH3BP5 -0.0000409 7680 GTEx DepMap Descartes 0.14 61.32
SCARB1 -0.0000552 8126 GTEx DepMap Descartes 0.09 18.89
HMGCR -0.0000580 8216 GTEx DepMap Descartes 0.11 26.18
POR -0.0000692 8581 GTEx DepMap Descartes 0.13 46.58
DHCR7 -0.0000705 8631 GTEx DepMap Descartes 0.05 17.77
FREM2 -0.0000766 8807 GTEx DepMap Descartes 0.00 0.00
DHCR24 -0.0000890 9155 GTEx DepMap Descartes 0.14 25.49
MSMO1 -0.0001154 9861 GTEx DepMap Descartes 0.07 36.13
FDXR -0.0001722 10999 GTEx DepMap Descartes 0.03 8.69
SLC16A9 -0.0001801 11109 GTEx DepMap Descartes 0.08 11.84
APOC1 -0.0001854 11194 GTEx DepMap Descartes 0.21 667.55
HMGCS1 -0.0001974 11350 GTEx DepMap Descartes 0.11 20.73
BAIAP2L1 -0.0002128 11500 GTEx DepMap Descartes 0.05 11.14


Descartes chromaffin markers
Top 50 marker genes of chromaffin cells in the Decartes fetal adrenal single cell map (https://atlas.brotmanbaty.org/bbi/human-gene-expression-during-development/cell/chromaffin/in/adrenal)
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.00e+00
Mean rank of genes in gene set: 10601.22
Median rank of genes in gene set: 12083
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
SYNPO2 0.0005259 761 GTEx DepMap Descartes 0.76 70.73
NPY 0.0004082 1075 GTEx DepMap Descartes 4.37 6313.43
ALK 0.0001712 2752 GTEx DepMap Descartes 2.27 379.23
RPH3A 0.0000126 5998 GTEx DepMap Descartes 0.05 7.40
PLXNA4 -0.0000011 6394 GTEx DepMap Descartes 0.43 28.00
MAB21L2 -0.0000065 6552 GTEx DepMap Descartes 0.13 38.57
MAB21L1 -0.0000510 8016 GTEx DepMap Descartes 0.14 66.26
GREM1 -0.0000742 8737 GTEx DepMap Descartes 0.04 6.58
GAL -0.0001069 9630 GTEx DepMap Descartes 0.45 598.17
EYA4 -0.0001261 10115 GTEx DepMap Descartes 0.46 91.43
SLC6A2 -0.0001313 10233 GTEx DepMap Descartes 0.14 28.61
CCND1 -0.0001534 10692 GTEx DepMap Descartes 1.52 411.85
EYA1 -0.0001785 11085 GTEx DepMap Descartes 0.57 101.86
IL7 -0.0002074 11462 GTEx DepMap Descartes 1.49 692.33
FAT3 -0.0002367 11697 GTEx DepMap Descartes 0.31 13.35
CNTFR -0.0002462 11766 GTEx DepMap Descartes 0.13 53.45
PTCHD1 -0.0002518 11803 GTEx DepMap Descartes 0.06 3.38
REEP1 -0.0002800 11966 GTEx DepMap Descartes 0.15 44.33
GAP43 -0.0002937 12016 GTEx DepMap Descartes 0.73 351.68
MLLT11 -0.0003076 12071 GTEx DepMap Descartes 0.37 144.66
TMEM132C -0.0003120 12083 GTEx DepMap Descartes 1.91 315.50
KCNB2 -0.0003402 12154 GTEx DepMap Descartes 1.11 227.60
TUBB2A -0.0003872 12245 GTEx DepMap Descartes 0.52 293.83
SLC44A5 -0.0004186 12285 GTEx DepMap Descartes 0.19 54.08
BASP1 -0.0004226 12294 GTEx DepMap Descartes 0.74 450.07
TMEFF2 -0.0004245 12298 GTEx DepMap Descartes 0.16 52.66
ISL1 -0.0004304 12307 GTEx DepMap Descartes 0.40 169.30
EPHA6 -0.0004333 12310 GTEx DepMap Descartes 0.26 53.66
RGMB -0.0004568 12331 GTEx DepMap Descartes 0.19 56.92
TUBB2B -0.0005016 12371 GTEx DepMap Descartes 1.33 652.68


Descartes Vascular_endothelial markers
Top 50 marker genes of Vascular_endothelial cells in the Decartes fetal adrenal single cell map (https://atlas.brotmanbaty.org/bbi/human-gene-expression-during-development/cell/vascular_endothelial/in/adrenal)
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.83e-01
Mean rank of genes in gene set: 5745.42
Median rank of genes in gene set: 5001.5
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
ARHGAP29 0.0014406 154 GTEx DepMap Descartes 0.40 66.47
NPR1 0.0006756 547 GTEx DepMap Descartes 0.04 23.86
MMRN2 0.0005641 689 GTEx DepMap Descartes 0.08 24.91
FLT4 0.0004609 925 GTEx DepMap Descartes 0.06 10.64
SLCO2A1 0.0004157 1055 GTEx DepMap Descartes 0.08 22.83
ROBO4 0.0004026 1097 GTEx DepMap Descartes 0.08 22.31
F8 0.0003950 1123 GTEx DepMap Descartes 0.04 3.89
CEACAM1 0.0003816 1161 GTEx DepMap Descartes 0.10 31.18
ESM1 0.0003553 1255 GTEx DepMap Descartes 0.08 29.38
RASIP1 0.0003153 1452 GTEx DepMap Descartes 0.09 38.73
KANK3 0.0002968 1559 GTEx DepMap Descartes 0.06 29.86
KDR 0.0002120 2271 GTEx DepMap Descartes 0.09 12.28
CDH5 0.0001609 2883 GTEx DepMap Descartes 0.04 9.02
PTPRB 0.0001584 2922 GTEx DepMap Descartes 0.21 17.01
TIE1 0.0001386 3193 GTEx DepMap Descartes 0.11 23.62
SHE 0.0001320 3307 GTEx DepMap Descartes 0.04 10.59
CLDN5 0.0001097 3723 GTEx DepMap Descartes 0.13 46.58
IRX3 0.0000594 4784 GTEx DepMap Descartes 0.00 0.00
EHD3 0.0000543 4907 GTEx DepMap Descartes 0.04 9.00
BTNL9 0.0000465 5096 GTEx DepMap Descartes 0.02 3.50
HYAL2 0.0000205 5796 GTEx DepMap Descartes 0.07 15.64
NR5A2 0.0000063 6185 GTEx DepMap Descartes 0.11 19.18
PODXL 0.0000005 6353 GTEx DepMap Descartes 0.09 17.86
RAMP2 -0.0000057 6532 GTEx DepMap Descartes 0.11 111.66
CYP26B1 -0.0000159 6816 GTEx DepMap Descartes 0.01 1.26
CRHBP -0.0000568 8175 GTEx DepMap Descartes 0.01 11.27
CALCRL -0.0000661 8467 GTEx DepMap Descartes 0.25 35.82
ID1 -0.0001293 10192 GTEx DepMap Descartes 0.06 95.43
GALNT15 -0.0001468 10563 GTEx DepMap Descartes 0.01 NA
PLVAP -0.0001471 10569 GTEx DepMap Descartes 0.17 47.65


Descartes stromal markers
Top 50 marker genes of stromal cells in the Decartes fetal adrenal single cell map (https://atlas.brotmanbaty.org/bbi/human-gene-expression-during-development/cell/stromal/in/adrenal)
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.87e-09
Mean rank of genes in gene set: 3060.8
Median rank of genes in gene set: 799
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
C7 0.0087669 1 GTEx DepMap Descartes 0.86 408.39
POSTN 0.0054233 7 GTEx DepMap Descartes 1.57 862.81
PRRX1 0.0041227 11 GTEx DepMap Descartes 0.57 231.54
COL27A1 0.0024809 53 GTEx DepMap Descartes 0.21 67.95
COL6A3 0.0024122 56 GTEx DepMap Descartes 1.21 215.79
EDNRA 0.0023488 59 GTEx DepMap Descartes 0.35 154.74
MGP 0.0021670 70 GTEx DepMap Descartes 1.16 1200.34
ABCA6 0.0021566 71 GTEx DepMap Descartes 0.19 51.22
CDH11 0.0021492 72 GTEx DepMap Descartes 0.84 253.94
ABCC9 0.0018517 99 GTEx DepMap Descartes 0.21 32.80
IGFBP3 0.0015960 125 GTEx DepMap Descartes 0.25 101.61
ACTA2 0.0015138 140 GTEx DepMap Descartes 0.51 515.87
ITGA11 0.0013564 169 GTEx DepMap Descartes 0.28 48.14
ADAMTS2 0.0012748 191 GTEx DepMap Descartes 0.41 112.97
GLI2 0.0011415 231 GTEx DepMap Descartes 0.24 70.73
ADAMTSL3 0.0010642 266 GTEx DepMap Descartes 0.12 27.21
PDGFRA 0.0009306 332 GTEx DepMap Descartes 0.14 51.02
CCDC80 0.0008862 362 GTEx DepMap Descartes 0.36 51.55
BICC1 0.0008271 406 GTEx DepMap Descartes 1.12 463.63
DKK2 0.0007736 449 GTEx DepMap Descartes 0.05 19.05
COL3A1 0.0006366 601 GTEx DepMap Descartes 3.72 1343.30
ISLR 0.0006159 622 GTEx DepMap Descartes 0.22 184.51
PAMR1 0.0004395 976 GTEx DepMap Descartes 0.09 40.65
ELN 0.0004197 1040 GTEx DepMap Descartes 0.41 181.12
RSPO3 0.0003427 1314 GTEx DepMap Descartes 0.00 NA
DCN 0.0002902 1600 GTEx DepMap Descartes 0.44 108.52
PCDH18 0.0002794 1684 GTEx DepMap Descartes 0.03 6.07
LRRC17 0.0002545 1872 GTEx DepMap Descartes 0.04 43.44
LAMC3 0.0001783 2665 GTEx DepMap Descartes 0.03 7.90
GAS2 0.0001704 2758 GTEx DepMap Descartes 0.08 44.42


Descartes sympathoblasts markers
Top 50 marker genes of sympathoblasts cells in the Decartes fetal adrenal single cell map (https://atlas.brotmanbaty.org/bbi/human-gene-expression-during-development/cell/sympathoblasts/in/adrenal)
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.00e+00
Mean rank of genes in gene set: 9518.82
Median rank of genes in gene set: 11315.5
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
LAMA3 0.0011355 234 GTEx DepMap Descartes 0.23 34.23
CNTN3 0.0005565 706 GTEx DepMap Descartes 0.08 11.13
TENM1 0.0003639 1226 GTEx DepMap Descartes 0.57 NA
AGBL4 0.0002627 1814 GTEx DepMap Descartes 1.99 417.04
SLC35F3 0.0000826 4253 GTEx DepMap Descartes 0.25 72.87
CDH12 0.0000744 4413 GTEx DepMap Descartes 0.12 15.14
SORCS3 0.0000720 4456 GTEx DepMap Descartes 0.03 4.39
DGKK 0.0000651 4636 GTEx DepMap Descartes 0.01 0.16
HTATSF1 -0.0000364 7522 GTEx DepMap Descartes 0.13 48.92
SLC24A2 -0.0000440 7786 GTEx DepMap Descartes 0.05 6.23
CHGA -0.0000607 8292 GTEx DepMap Descartes 1.38 651.57
ARC -0.0001009 9463 GTEx DepMap Descartes 0.03 17.24
KSR2 -0.0001172 9902 GTEx DepMap Descartes 0.35 15.71
PACRG -0.0001225 10033 GTEx DepMap Descartes 0.39 158.68
TBX20 -0.0001318 10243 GTEx DepMap Descartes 0.12 84.41
C1QL1 -0.0001579 10760 GTEx DepMap Descartes 0.04 28.74
TIAM1 -0.0001626 10839 GTEx DepMap Descartes 0.40 57.37
CDH18 -0.0001768 11065 GTEx DepMap Descartes 0.21 44.74
PENK -0.0001840 11172 GTEx DepMap Descartes 0.00 0.00
CCSER1 -0.0002073 11459 GTEx DepMap Descartes 1.22 NA
ST18 -0.0002698 11915 GTEx DepMap Descartes 0.02 4.60
EML6 -0.0003059 12062 GTEx DepMap Descartes 0.19 25.56
GALNTL6 -0.0003077 12073 GTEx DepMap Descartes 0.16 36.78
GCH1 -0.0003171 12095 GTEx DepMap Descartes 0.24 88.60
SPOCK3 -0.0003184 12100 GTEx DepMap Descartes 0.08 17.54
ROBO1 -0.0003674 12207 GTEx DepMap Descartes 2.27 336.13
SLC18A1 -0.0004306 12308 GTEx DepMap Descartes 0.14 31.41
PCSK1N -0.0004559 12330 GTEx DepMap Descartes 1.13 866.15
PCSK2 -0.0004772 12348 GTEx DepMap Descartes 0.16 28.98
UNC80 -0.0004806 12353 GTEx DepMap Descartes 0.47 31.00


Descartes erythroblasts markers
Top 50 marker genes of erythroblasts cells in the Decartes fetal adrenal single cell map (https://atlas.brotmanbaty.org/bbi/human-gene-expression-during-development/cell/erythroblasts/in/adrenal)
Wilcoxon ranksum test P-value for gene set overrepresentation: 5.41e-02
Mean rank of genes in gene set: 5195.31
Median rank of genes in gene set: 5038
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
MICAL2 0.0010076 295 GTEx DepMap Descartes 0.31 98.50
GYPC 0.0009309 330 GTEx DepMap Descartes 0.07 46.18
RHD 0.0009114 343 GTEx DepMap Descartes 0.08 32.65
MARCH3 0.0006509 571 GTEx DepMap Descartes 0.33 NA
BLVRB 0.0004987 819 GTEx DepMap Descartes 0.06 94.16
SLC25A37 0.0004799 865 GTEx DepMap Descartes 0.21 57.83
TSPAN5 0.0003211 1424 GTEx DepMap Descartes 0.76 207.05
SPECC1 0.0003111 1481 GTEx DepMap Descartes 0.08 9.90
DENND4A 0.0002665 1788 GTEx DepMap Descartes 0.62 85.43
SELENBP1 0.0002462 1938 GTEx DepMap Descartes 0.03 10.64
CAT 0.0002146 2231 GTEx DepMap Descartes 0.09 74.73
SLC25A21 0.0001911 2517 GTEx DepMap Descartes 0.04 16.50
XPO7 0.0001530 2999 GTEx DepMap Descartes 0.18 43.32
GCLC 0.0000897 4116 GTEx DepMap Descartes 0.11 52.11
ANK1 0.0000491 5038 GTEx DepMap Descartes 0.24 39.16
TRAK2 0.0000326 5444 GTEx DepMap Descartes 0.14 23.56
CPOX -0.0000227 7023 GTEx DepMap Descartes 0.04 17.57
TMCC2 -0.0000232 7042 GTEx DepMap Descartes 0.03 1.91
SLC4A1 -0.0000355 7493 GTEx DepMap Descartes 0.00 0.00
TFR2 -0.0000359 7504 GTEx DepMap Descartes 0.20 63.35
ABCB10 -0.0000534 8071 GTEx DepMap Descartes 0.11 26.20
ALAS2 -0.0000803 8909 GTEx DepMap Descartes 0.00 0.00
EPB41 -0.0000813 8939 GTEx DepMap Descartes 0.52 55.18
RAPGEF2 -0.0000972 9373 GTEx DepMap Descartes 0.54 83.45
RGS6 -0.0001127 9793 GTEx DepMap Descartes 0.03 4.38
SPTB -0.0001236 10045 GTEx DepMap Descartes 0.05 7.74
SNCA -0.0001627 10841 GTEx DepMap Descartes 0.18 48.50
FECH -0.0001706 10974 GTEx DepMap Descartes 0.06 7.54
SOX6 -0.0006618 12458 GTEx DepMap Descartes 0.58 75.08
NA NA NA NA NA NA NA NA


Descartes myeloid markers
Top 50 marker genes of myeloid cells in the Decartes fetal adrenal single cell map (https://atlas.brotmanbaty.org/bbi/human-gene-expression-during-development/cell/myeloid/in/adrenal)
Wilcoxon ranksum test P-value for gene set overrepresentation: 8.43e-01
Mean rank of genes in gene set: 6865.42
Median rank of genes in gene set: 7883.5
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
SLC9A9 0.0027771 40 GTEx DepMap Descartes 0.52 269.29
SLCO2B1 0.0015027 144 GTEx DepMap Descartes 0.14 27.84
PTPRE 0.0014366 156 GTEx DepMap Descartes 0.58 162.30
CD74 0.0013409 179 GTEx DepMap Descartes 0.82 282.02
ITPR2 0.0010349 281 GTEx DepMap Descartes 0.60 76.08
CST3 0.0008485 393 GTEx DepMap Descartes 0.55 214.35
CTSS 0.0006027 638 GTEx DepMap Descartes 0.14 49.34
ABCA1 0.0005804 666 GTEx DepMap Descartes 0.25 50.05
HRH1 0.0004683 896 GTEx DepMap Descartes 0.14 42.75
CTSC 0.0003375 1332 GTEx DepMap Descartes 0.11 30.08
RGL1 0.0002577 1851 GTEx DepMap Descartes 0.21 57.29
CSF1R 0.0002239 2138 GTEx DepMap Descartes 0.06 21.74
FGL2 0.0001719 2742 GTEx DepMap Descartes 0.04 14.12
WWP1 0.0001563 2959 GTEx DepMap Descartes 0.23 80.98
IFNGR1 0.0001508 3027 GTEx DepMap Descartes 0.16 76.26
FGD2 0.0000602 4753 GTEx DepMap Descartes 0.05 10.11
HCK 0.0000331 5426 GTEx DepMap Descartes 0.03 22.01
MARCH1 0.0000238 5694 GTEx DepMap Descartes 0.14 NA
CTSD 0.0000014 6328 GTEx DepMap Descartes 0.47 402.40
SFMBT2 -0.0000997 9439 GTEx DepMap Descartes 0.25 42.97
CPVL -0.0001293 10191 GTEx DepMap Descartes 0.08 25.95
RBPJ -0.0001486 10608 GTEx DepMap Descartes 0.48 110.99
AXL -0.0001704 10967 GTEx DepMap Descartes 0.16 37.85
ATP8B4 -0.0001807 11117 GTEx DepMap Descartes 0.04 9.75
CD163 -0.0001920 11279 GTEx DepMap Descartes 0.02 3.43
CTSB -0.0001932 11297 GTEx DepMap Descartes 0.33 140.02
MERTK -0.0002228 11596 GTEx DepMap Descartes 0.07 22.36
CYBB -0.0002295 11647 GTEx DepMap Descartes 0.03 3.64
ADAP2 -0.0003276 12127 GTEx DepMap Descartes 0.06 18.81
MS4A4A -0.0003298 12135 GTEx DepMap Descartes 0.00 0.00


Descartes Schwann markers
Top 50 marker genes of Schwann cells in the Decartes fetal adrenal single cell map (https://atlas.brotmanbaty.org/bbi/human-gene-expression-during-development/cell/schwann/in/adrenal)
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.89e-01
Mean rank of genes in gene set: 5794.61
Median rank of genes in gene set: 4252
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
NRXN3 0.0021702 69 GTEx DepMap Descartes 0.81 159.27
XKR4 0.0021460 74 GTEx DepMap Descartes 0.42 23.03
GAS7 0.0015207 137 GTEx DepMap Descartes 0.47 106.10
COL18A1 0.0011483 227 GTEx DepMap Descartes 0.91 219.05
VIM 0.0010974 250 GTEx DepMap Descartes 1.12 718.14
LAMC1 0.0010211 288 GTEx DepMap Descartes 0.60 127.66
EDNRB 0.0009662 317 GTEx DepMap Descartes 0.06 13.04
LAMA4 0.0009109 344 GTEx DepMap Descartes 0.23 48.35
STARD13 0.0008260 407 GTEx DepMap Descartes 0.46 141.46
COL5A2 0.0006453 580 GTEx DepMap Descartes 1.28 376.18
VCAN 0.0005827 664 GTEx DepMap Descartes 1.34 201.70
GRIK3 0.0004236 1030 GTEx DepMap Descartes 0.06 8.99
HMGA2 0.0003993 1112 GTEx DepMap Descartes 0.04 12.97
OLFML2A 0.0003335 1352 GTEx DepMap Descartes 0.04 9.17
PLCE1 0.0003140 1467 GTEx DepMap Descartes 0.15 16.85
FIGN 0.0002957 1565 GTEx DepMap Descartes 0.31 45.60
COL25A1 0.0001713 2751 GTEx DepMap Descartes 0.04 5.91
PTN 0.0001492 3050 GTEx DepMap Descartes 0.28 178.37
IL1RAPL1 0.0001486 3057 GTEx DepMap Descartes 0.25 82.32
LAMB1 0.0001078 3756 GTEx DepMap Descartes 0.52 122.54
ERBB3 0.0001010 3887 GTEx DepMap Descartes 0.03 6.18
PTPRZ1 0.0001001 3905 GTEx DepMap Descartes 0.01 0.74
SFRP1 0.0000665 4599 GTEx DepMap Descartes 0.10 43.55
PLP1 0.0000626 4695 GTEx DepMap Descartes 0.01 6.35
KCTD12 0.0000293 5531 GTEx DepMap Descartes 0.08 15.05
EGFLAM -0.0000062 6543 GTEx DepMap Descartes 0.10 28.82
GFRA3 -0.0000545 8104 GTEx DepMap Descartes 0.17 67.65
SLC35F1 -0.0000682 8548 GTEx DepMap Descartes 0.06 14.73
MDGA2 -0.0000864 9093 GTEx DepMap Descartes 0.00 0.00
MPZ -0.0001051 9585 GTEx DepMap Descartes 0.00 0.00


Descartes Megakaryocytes markers
Top 50 marker genes of Megakaryocytes cells in the Decartes fetal adrenal single cell map (https://atlas.brotmanbaty.org/bbi/human-gene-expression-during-development/cell/megakaryocytes/in/adrenal)
Wilcoxon ranksum test P-value for gene set overrepresentation: 4.76e-03
Mean rank of genes in gene set: 4877.11
Median rank of genes in gene set: 2443
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
SLC2A3 0.0019557 91 GTEx DepMap Descartes 0.62 238.12
SLC24A3 0.0011881 217 GTEx DepMap Descartes 0.31 106.46
MYH9 0.0008616 379 GTEx DepMap Descartes 0.55 119.24
GSN 0.0008514 390 GTEx DepMap Descartes 0.44 107.03
TRPC6 0.0008334 400 GTEx DepMap Descartes 0.08 15.96
LTBP1 0.0008174 413 GTEx DepMap Descartes 0.25 64.28
MMRN1 0.0007712 453 GTEx DepMap Descartes 0.08 15.49
ARHGAP6 0.0006473 578 GTEx DepMap Descartes 0.16 33.76
VCL 0.0005363 733 GTEx DepMap Descartes 0.44 93.02
FLNA 0.0005110 792 GTEx DepMap Descartes 0.57 99.28
ACTN1 0.0004814 861 GTEx DepMap Descartes 0.63 189.07
TMSB4X 0.0004501 947 GTEx DepMap Descartes 5.19 3018.20
GP1BA 0.0004453 961 GTEx DepMap Descartes 0.03 10.41
TPM4 0.0004187 1044 GTEx DepMap Descartes 0.37 111.58
MYLK 0.0003235 1413 GTEx DepMap Descartes 0.14 17.62
PDE3A 0.0003206 1427 GTEx DepMap Descartes 0.82 207.09
ANGPT1 0.0002934 1582 GTEx DepMap Descartes 0.08 23.39
STOM 0.0002730 1736 GTEx DepMap Descartes 0.14 47.62
DOK6 0.0002700 1754 GTEx DepMap Descartes 0.38 59.74
RAP1B 0.0002674 1781 GTEx DepMap Descartes 0.37 45.73
LIMS1 0.0002426 1974 GTEx DepMap Descartes 0.50 204.60
TGFB1 0.0002402 1991 GTEx DepMap Descartes 0.20 106.63
FLI1 0.0001960 2443 GTEx DepMap Descartes 0.29 59.48
STON2 0.0001874 2562 GTEx DepMap Descartes 0.19 38.08
FERMT3 0.0001244 3435 GTEx DepMap Descartes 0.05 42.66
ZYX 0.0000202 5807 GTEx DepMap Descartes 0.12 103.91
HIPK2 0.0000113 6042 GTEx DepMap Descartes 0.57 51.74
CD9 -0.0000062 6544 GTEx DepMap Descartes 0.25 158.89
MED12L -0.0000249 7103 GTEx DepMap Descartes 0.06 6.74
TUBB1 -0.0000276 7200 GTEx DepMap Descartes 0.00 0.00


Descartes Lyphoid markers
Top 50 marker genes of Lyphoid cells in the Decartes fetal adrenal single cell map (https://atlas.brotmanbaty.org/bbi/human-gene-expression-during-development/cell/lymphoid/in/adrenal)
Wilcoxon ranksum test P-value for gene set overrepresentation: 8.60e-07
Mean rank of genes in gene set: 3605.38
Median rank of genes in gene set: 702.5
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
B2M 0.0031452 25 GTEx DepMap Descartes 3.35 1835.87
ARHGAP15 0.0028605 33 GTEx DepMap Descartes 0.82 386.03
SP100 0.0013444 177 GTEx DepMap Descartes 0.36 102.36
DOCK10 0.0012650 193 GTEx DepMap Descartes 0.74 129.45
FOXP1 0.0012487 199 GTEx DepMap Descartes 2.97 484.52
MBNL1 0.0010805 260 GTEx DepMap Descartes 1.15 265.05
ARID5B 0.0010575 270 GTEx DepMap Descartes 0.62 130.30
ETS1 0.0010137 290 GTEx DepMap Descartes 0.35 99.57
NCALD 0.0010029 296 GTEx DepMap Descartes 0.52 191.98
CCND3 0.0008970 352 GTEx DepMap Descartes 0.30 226.91
PLEKHA2 0.0008919 358 GTEx DepMap Descartes 0.21 67.31
SKAP1 0.0008701 368 GTEx DepMap Descartes 0.18 113.44
SAMD3 0.0008464 396 GTEx DepMap Descartes 0.08 35.29
LEF1 0.0008196 411 GTEx DepMap Descartes 0.15 53.50
CELF2 0.0008081 422 GTEx DepMap Descartes 0.70 106.62
RCSD1 0.0007997 428 GTEx DepMap Descartes 0.13 30.74
IKZF1 0.0007772 444 GTEx DepMap Descartes 0.09 15.64
ITPKB 0.0007618 458 GTEx DepMap Descartes 0.17 37.38
PRKCH 0.0006873 533 GTEx DepMap Descartes 0.30 92.56
MSN 0.0005701 681 GTEx DepMap Descartes 0.22 88.21
MCTP2 0.0005623 692 GTEx DepMap Descartes 0.16 30.91
ANKRD44 0.0005504 713 GTEx DepMap Descartes 0.52 96.19
CCL5 0.0004022 1101 GTEx DepMap Descartes 0.05 36.83
LCP1 0.0003655 1217 GTEx DepMap Descartes 0.06 31.34
WIPF1 0.0003169 1444 GTEx DepMap Descartes 0.31 90.79
ABLIM1 0.0003148 1458 GTEx DepMap Descartes 0.31 44.99
PITPNC1 0.0003032 1514 GTEx DepMap Descartes 0.93 185.19
BACH2 0.0001911 2516 GTEx DepMap Descartes 0.76 111.43
ARHGDIB 0.0001783 2659 GTEx DepMap Descartes 0.06 45.44
PTPRC 0.0000835 4234 GTEx DepMap Descartes 0.10 19.60


Below shows the ranks on this GEP for immune marker gene lists curated by CellTypist (https://www.celltypist.org/encyclopedia).
   High ranks indicate this gene is a driver of this GEP.
  These curated gene list are ranked by P-value (on this GEP) of their constituent genes.
  The Mean Count column shows the mean read count in cells scoring highly (H > 50) on this gene expression program.


Fibroblasts: Fibroblasts (model markers)
the most common cells of connective tissues which synthesize the extracellular matrix and collagen to maintain tissue homeostasis:
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.55e-04
Mean rank of genes in gene set: 1920.22
Rank on gene expression program of genes in gene set:
Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
PRRX1 0.0041227 11 GTEx DepMap Descartes 0.57 231.54
PDGFRA 0.0009306 332 GTEx DepMap Descartes 0.14 51.02
EBF2 0.0007511 464 GTEx DepMap Descartes 0.10 23.95
SMOC2 0.0004169 1050 GTEx DepMap Descartes 0.22 105.51
NTRK2 0.0003284 1389 GTEx DepMap Descartes 0.11 20.70
ANGPTL1 0.0002861 1630 GTEx DepMap Descartes 0.26 81.78
OLFML1 0.0002504 1910 GTEx DepMap Descartes 0.03 7.82
SFRP1 0.0000665 4599 GTEx DepMap Descartes 0.10 43.55
F10 0.0000170 5897 GTEx DepMap Descartes 0.01 4.36


B cells: Memory B cells (model markers)
long-lived mature B lymphocytes which are formed within germinal centers following primary infection and selected for higher-affinity immunoglobulin:
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.17e-02
Mean rank of genes in gene set: 467
Rank on gene expression program of genes in gene set:

Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
CD74 0.0013409 179 GTEx DepMap Descartes 0.82 282.02
HES1 0.0005265 755 GTEx DepMap Descartes 0.18 181.69


T cells: Tcm/Naive helper T cells (curated markers)
CD4+ helper T lymphocytes mainly localized in secondary lymphoid tissues and sustaining the responses by proliferating and producing new effectors:
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.78e-02
Mean rank of genes in gene set: 1879.33
Rank on gene expression program of genes in gene set:

Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
CCR7 0.0009624 319 GTEx DepMap Descartes 0.03 26.30
SELL 0.0004646 912 GTEx DepMap Descartes 0.03 7.28
CD4 0.0000746 4407 GTEx DepMap Descartes 0.02 3.72