Program: 31. Cancer-Associated Fibroblasts.

Program: 31. Cancer-Associated Fibroblasts.


Program description and justification of annotation generated by GPT5: Perivascular mural/pericyte and myofibroblastic CAF program (vascular smooth muscle-like).

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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 PDGFRB 0.0092657 platelet derived growth factor receptor beta GTEx DepMap Descartes 2.47 355.96
2 CCDC102B 0.0081381 coiled-coil domain containing 102B GTEx DepMap Descartes 8.98 2569.01
3 NOTCH3 0.0078635 notch receptor 3 GTEx DepMap Descartes 1.20 121.25
4 UACA 0.0072823 uveal autoantigen with coiled-coil domains and ankyrin repeats GTEx DepMap Descartes 5.98 631.89
5 PRKG1 0.0071061 protein kinase cGMP-dependent 1 GTEx DepMap Descartes 17.79 1873.76
6 PLXDC1 0.0068063 plexin domain containing 1 GTEx DepMap Descartes 1.23 168.26
7 RNF152 0.0063609 ring finger protein 152 GTEx DepMap Descartes 2.55 214.71
8 EDNRA 0.0062143 endothelin receptor type A GTEx DepMap Descartes 1.42 255.37
9 ENPEP 0.0060884 glutamyl aminopeptidase GTEx DepMap Descartes 1.27 145.07
10 ANO1 0.0059796 anoctamin 1 GTEx DepMap Descartes 1.48 235.16
11 COL18A1 0.0055041 collagen type XVIII alpha 1 chain GTEx DepMap Descartes 3.67 411.97
12 ABCC9 0.0053157 ATP binding cassette subfamily C member 9 GTEx DepMap Descartes 0.74 69.71
13 EPS8 0.0053155 EGFR pathway substrate 8, signaling adaptor GTEx DepMap Descartes 5.53 807.95
14 PDE1A 0.0052383 phosphodiesterase 1A GTEx DepMap Descartes 3.65 517.54
15 GUCY1A2 0.0051988 guanylate cyclase 1 soluble subunit alpha 2 GTEx DepMap Descartes 2.28 105.28
16 HEYL 0.0051389 hes related family bHLH transcription factor with YRPW motif like GTEx DepMap Descartes 0.83 151.42
17 LHFPL6 0.0049279 LHFPL tetraspan subfamily member 6 GTEx DepMap Descartes 9.98 NA
18 CACNA1C 0.0046669 calcium voltage-gated channel subunit alpha1 C GTEx DepMap Descartes 9.38 473.32
19 SPECC1 0.0046175 sperm antigen with calponin homology and coiled-coil domains 1 GTEx DepMap Descartes 1.77 158.44
20 ITGA1 0.0045000 integrin subunit alpha 1 GTEx DepMap Descartes 5.91 361.85
21 ADGRF5 0.0044881 adhesion G protein-coupled receptor F5 GTEx DepMap Descartes 2.36 NA
22 GUCY1A1 0.0044214 guanylate cyclase 1 soluble subunit alpha 1 GTEx DepMap Descartes 2.37 NA
23 NEURL1B 0.0043987 neuralized E3 ubiquitin protein ligase 1B GTEx DepMap Descartes 0.79 98.22
24 COL5A3 0.0043273 collagen type V alpha 3 chain GTEx DepMap Descartes 0.61 85.50
25 COL4A2 0.0042830 collagen type IV alpha 2 chain GTEx DepMap Descartes 9.48 1043.05
26 TRPC4 0.0041622 transient receptor potential cation channel subfamily C member 4 GTEx DepMap Descartes 0.66 57.10
27 STEAP4 0.0041233 STEAP4 metalloreductase GTEx DepMap Descartes 0.38 29.32
28 SEMA5B 0.0041148 semaphorin 5B GTEx DepMap Descartes 0.42 73.62
29 KIRREL1 0.0040736 kirre like nephrin family adhesion molecule 1 GTEx DepMap Descartes 1.47 NA
30 COL4A1 0.0040172 collagen type IV alpha 1 chain GTEx DepMap Descartes 10.82 1150.26
31 TRPC6 0.0040030 transient receptor potential cation channel subfamily C member 6 GTEx DepMap Descartes 0.54 90.07
32 SEMA5A 0.0039881 semaphorin 5A GTEx DepMap Descartes 3.24 199.70
33 PEAK1 0.0038406 pseudopodium enriched atypical kinase 1 GTEx DepMap Descartes 5.84 NA
34 PIEZO2 0.0037406 piezo type mechanosensitive ion channel component 2 GTEx DepMap Descartes 2.12 157.05
35 EBF2 0.0037318 EBF transcription factor 2 GTEx DepMap Descartes 1.87 272.71
36 SLC6A1 0.0037249 solute carrier family 6 member 1 GTEx DepMap Descartes 0.35 36.68
37 PDE3A 0.0037155 phosphodiesterase 3A GTEx DepMap Descartes 7.15 621.34
38 ARHGEF17 0.0037006 Rho guanine nucleotide exchange factor 17 GTEx DepMap Descartes 0.86 81.49
39 ADAMTS14 0.0035170 ADAM metallopeptidase with thrombospondin type 1 motif 14 GTEx DepMap Descartes 0.27 40.40
40 CSPG4 0.0034733 chondroitin sulfate proteoglycan 4 GTEx DepMap Descartes 0.20 21.39
41 IGFBP7 0.0034665 insulin like growth factor binding protein 7 GTEx DepMap Descartes 14.78 6708.68
42 CALD1 0.0034248 caldesmon 1 GTEx DepMap Descartes 12.46 1676.00
43 RCAN2 0.0034244 regulator of calcineurin 2 GTEx DepMap Descartes 1.52 336.65
44 NGF 0.0034217 nerve growth factor GTEx DepMap Descartes 0.47 350.47
45 ARHGAP6 0.0034017 Rho GTPase activating protein 6 GTEx DepMap Descartes 1.46 177.81
46 COL6A2 0.0033889 collagen type VI alpha 2 chain GTEx DepMap Descartes 2.83 574.80
47 FRY 0.0033797 FRY microtubule binding protein GTEx DepMap Descartes 4.31 207.56
48 NHSL2 0.0032892 NHS like 2 GTEx DepMap Descartes 1.45 75.55
49 JAG1 0.0032844 jagged canonical Notch ligand 1 GTEx DepMap Descartes 1.48 169.88
50 ARHGAP42 0.0032771 Rho GTPase activating protein 42 GTEx DepMap Descartes 2.57 218.54


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UMAP plots showing activity of gene expression program identified in GEP 31. Cancer-Associated Fibroblasts:

Interactive UMAP Plot

Boxlot showing activity of gene expression program identified in GEP 31. Cancer-Associated Fibroblasts:
Interactive Boxplot

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
DESCARTES_FETAL_MUSCLE_SMOOTH_MUSCLE_CELLS 3.74e-19 97.90 44.62 4.18e-17 2.51e-16
12PDGFRB, EDNRA, ENPEP, ANO1, ABCC9, GUCY1A2, CACNA1C, TRPC4, STEAP4, SEMA5B, SLC6A1, RCAN2
 78
FAN_EMBRYONIC_CTX_BRAIN_ENDOTHELIAL_2 4.76e-35 80.25 43.67 1.60e-32 3.19e-32
26PDGFRB, CCDC102B, NOTCH3, UACA, PRKG1, PLXDC1, EDNRA, COL18A1, ABCC9, EPS8, GUCY1A2, HEYL, LHFPL6, ITGA1, GUCY1A1, COL4A2, COL4A1, TRPC6, SEMA5A, SLC6A1, ARHGEF17, CSPG4, IGFBP7, CALD1, COL6A2, ARHGAP42
 303
TRAVAGLINI_LUNG_VASCULAR_SMOOTH_MUSCLE_CELL 2.19e-16 100.49 42.45 1.33e-14 1.47e-13
10NOTCH3, EPS8, HEYL, ITGA1, ADGRF5, SEMA5A, IGFBP7, CALD1, RCAN2, JAG1
 61
AIZARANI_LIVER_C33_STELLATE_CELLS_2 3.53e-20 71.20 34.48 4.73e-18 2.37e-17
14NOTCH3, UACA, PRKG1, LHFPL6, ITGA1, ADGRF5, COL4A2, COL4A1, SEMA5A, ARHGEF17, IGFBP7, CALD1, RCAN2, COL6A2
 126
TRAVAGLINI_LUNG_PERICYTE_CELL 6.34e-19 71.32 33.74 5.81e-17 4.25e-16
13PDGFRB, CCDC102B, NOTCH3, PLXDC1, GUCY1A2, ITGA1, ADGRF5, COL4A2, COL4A1, TRPC6, SEMA5A, ARHGEF17, CSPG4
 114
MANNO_MIDBRAIN_NEUROTYPES_HPERIC 5.85e-39 63.17 33.42 3.92e-36 3.92e-36
35PDGFRB, NOTCH3, UACA, PRKG1, PLXDC1, EDNRA, ENPEP, COL18A1, ABCC9, EPS8, GUCY1A2, HEYL, LHFPL6, CACNA1C, SPECC1, ITGA1, ADGRF5, GUCY1A1, COL5A3, COL4A2, KIRREL1, COL4A1, TRPC6, SEMA5A, PEAK1, PIEZO2, SLC6A1, PDE3A, ARHGEF17, CSPG4, IGFBP7, CALD1, ARHGAP6, JAG1, ARHGAP42
 795
DESCARTES_MAIN_FETAL_SMOOTH_MUSCLE_CELLS 1.13e-11 90.13 32.11 4.01e-10 7.62e-09
7PDGFRB, CCDC102B, NOTCH3, ANO1, ABCC9, EBF2, CSPG4
 44
LAKE_ADULT_KIDNEY_C28_INTERSTITIUM 8.12e-15 67.43 29.01 4.19e-13 5.45e-12
10UACA, PRKG1, EPS8, LHFPL6, CACNA1C, ITGA1, COL4A2, COL4A1, IGFBP7, CALD1
 86
LAKE_ADULT_KIDNEY_C27_VASCULAR_SMOOTH_MUSCLE_CELLS_AND_PERICYTES 6.93e-19 56.64 27.54 5.81e-17 4.65e-16
14PRKG1, COL18A1, EPS8, PDE1A, LHFPL6, CACNA1C, ITGA1, COL4A2, COL4A1, PDE3A, CALD1, RCAN2, ARHGAP6, FRY
 155
DESCARTES_FETAL_HEART_SMOOTH_MUSCLE_CELLS 1.13e-09 71.60 23.58 3.29e-08 7.56e-07
6PDGFRB, NOTCH3, ENPEP, ABCC9, SEMA5B, ARHGEF17
 45
DESCARTES_FETAL_PLACENTA_SMOOTH_MUSCLE_CELLS 8.06e-13 55.54 22.97 3.38e-11 5.41e-10
9CCDC102B, NOTCH3, ABCC9, GUCY1A2, HEYL, CACNA1C, COL5A3, SEMA5B, CSPG4
 90
LAKE_ADULT_KIDNEY_C26_MESANGIAL_CELLS 2.17e-16 43.95 21.05 1.33e-14 1.45e-13
13PDGFRB, UACA, PRKG1, EPS8, LHFPL6, ITGA1, ADGRF5, COL4A2, COL4A1, PIEZO2, PDE3A, IGFBP7, CALD1
 177
RUBENSTEIN_SKELETAL_MUSCLE_PERICYTES 3.65e-14 43.53 19.65 1.67e-12 2.45e-11
11PDGFRB, NOTCH3, ABCC9, EPS8, LHFPL6, COL4A2, STEAP4, COL4A1, IGFBP7, CALD1, COL6A2
 144
DURANTE_ADULT_OLFACTORY_NEUROEPITHELIUM_VASCULAR_SMOOTH_MUSCLE_CELLS 5.66e-11 46.00 18.09 1.81e-09 3.80e-08
8PDGFRB, NOTCH3, LHFPL6, GUCY1A1, STEAP4, IGFBP7, CALD1, RCAN2
 93
GAO_LARGE_INTESTINE_ADULT_CJ_IMMUNE_CELLS 6.67e-23 33.40 18.07 1.12e-20 4.47e-20
22PDGFRB, CCDC102B, NOTCH3, EDNRA, COL18A1, PDE1A, LHFPL6, ITGA1, ADGRF5, GUCY1A1, COL5A3, COL4A2, STEAP4, KIRREL1, COL4A1, ARHGEF17, CSPG4, IGFBP7, CALD1, ARHGAP6, COL6A2, FRY
 505
MURARO_PANCREAS_MESENCHYMAL_STROMAL_CELL 1.61e-24 31.37 17.19 3.61e-22 1.08e-21
25PDGFRB, CCDC102B, NOTCH3, UACA, PRKG1, PLXDC1, EDNRA, ANO1, COL18A1, EPS8, GUCY1A2, HEYL, LHFPL6, ITGA1, COL5A3, COL4A2, COL4A1, PEAK1, PIEZO2, PDE3A, ARHGEF17, IGFBP7, CALD1, COL6A2, JAG1
 680
FAN_EMBRYONIC_CTX_BIG_GROUPS_BRAIN_ENDOTHELIAL 5.05e-18 30.40 15.72 3.77e-16 3.39e-15
17PDGFRB, NOTCH3, UACA, PLXDC1, EDNRA, COL18A1, LHFPL6, ITGA1, ADGRF5, COL4A2, COL4A1, SEMA5A, CSPG4, IGFBP7, CALD1, COL6A2, JAG1
 365
LAKE_ADULT_KIDNEY_C22_ENDOTHELIAL_CELLS_GLOMERULAR_CAPILLARIES 3.68e-11 35.19 14.72 1.24e-09 2.47e-08
9UACA, PRKG1, CACNA1C, ITGA1, ADGRF5, COL4A2, COL4A1, PEAK1, CALD1
 137
DESCARTES_FETAL_LIVER_STELLATE_CELLS 1.39e-10 30.04 12.61 4.25e-09 9.34e-08
9PDGFRB, EDNRA, ABCC9, GUCY1A2, ITGA1, NEURL1B, STEAP4, SEMA5A, CSPG4
 159
CUI_DEVELOPING_HEART_CORONARY_VASCULAR_ENDOTHELIAL_CELL 2.90e-06 48.15 11.99 6.48e-05 1.94e-03
4UACA, COL4A2, COL4A1, IGFBP7
 41

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mSigDB Hallmark Gene Sets:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
HALLMARK_NOTCH_SIGNALING 6.33e-05 45.10 8.51 1.58e-03 3.17e-03
3NOTCH3, HEYL, JAG1
 32
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION 8.22e-06 14.43 4.97 4.11e-04 4.11e-04
6PDGFRB, COL5A3, COL4A2, COL4A1, CALD1, COL6A2
 200
HALLMARK_MYOGENESIS 1.23e-02 6.65 1.31 1.54e-01 6.17e-01
3COL4A2, IGFBP7, COL6A2
 200
HALLMARK_KRAS_SIGNALING_UP 1.23e-02 6.65 1.31 1.54e-01 6.17e-01
3ANO1, GUCY1A1, NGF
 200
HALLMARK_ANDROGEN_RESPONSE 2.44e-02 8.73 1.01 2.44e-01 1.00e+00
2GUCY1A1, STEAP4
 100
HALLMARK_ANGIOGENESIS 8.37e-02 11.97 0.29 6.93e-01 1.00e+00
1JAG1
 36
HALLMARK_WNT_BETA_CATENIN_SIGNALING 9.70e-02 10.22 0.25 6.93e-01 1.00e+00
1JAG1
 42
HALLMARK_CHOLESTEROL_HOMEOSTASIS 1.64e-01 5.74 0.14 1.00e+00 1.00e+00
1JAG1
 74
HALLMARK_PI3K_AKT_MTOR_SIGNALING 2.25e-01 4.03 0.10 1.00e+00 1.00e+00
1NGF
 105
HALLMARK_UV_RESPONSE_DN 2.95e-01 2.93 0.07 1.00e+00 1.00e+00
1PDGFRB
 144
HALLMARK_APOPTOSIS 3.23e-01 2.62 0.06 1.00e+00 1.00e+00
1PDGFRB
 161
HALLMARK_TNFA_SIGNALING_VIA_NFKB 3.84e-01 2.11 0.05 1.00e+00 1.00e+00
1JAG1
 200
HALLMARK_ADIPOGENESIS 3.84e-01 2.11 0.05 1.00e+00 1.00e+00
1COL4A1
 200
HALLMARK_COMPLEMENT 3.84e-01 2.11 0.05 1.00e+00 1.00e+00
1COL4A2
 200
HALLMARK_XENOBIOTIC_METABOLISM 3.84e-01 2.11 0.05 1.00e+00 1.00e+00
1ENPEP
 200
HALLMARK_HYPOXIA 1.00e+00 0.00 0.00 1.00e+00 1.00e+00
0
 200
HALLMARK_MITOTIC_SPINDLE 1.00e+00 0.00 0.00 1.00e+00 1.00e+00
0
 199
HALLMARK_TGF_BETA_SIGNALING 1.00e+00 0.00 0.00 1.00e+00 1.00e+00
0
 54
HALLMARK_IL6_JAK_STAT3_SIGNALING 1.00e+00 0.00 0.00 1.00e+00 1.00e+00
0
 87
HALLMARK_DNA_REPAIR 1.00e+00 0.00 0.00 1.00e+00 1.00e+00
0
 150

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KEGG Pathways:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
KEGG_VASCULAR_SMOOTH_MUSCLE_CONTRACTION 3.36e-07 25.65 8.76 6.24e-05 6.24e-05
6PRKG1, EDNRA, GUCY1A2, CACNA1C, GUCY1A1, CALD1
 115
KEGG_ECM_RECEPTOR_INTERACTION 1.80e-06 28.86 8.71 1.68e-04 3.35e-04
5ITGA1, COL5A3, COL4A2, COL4A1, COL6A2
 84
KEGG_GAP_JUNCTION 6.63e-05 20.75 5.31 3.08e-03 1.23e-02
4PDGFRB, PRKG1, GUCY1A2, GUCY1A1
 90
KEGG_FOCAL_ADHESION 7.99e-06 14.51 4.99 4.96e-04 1.49e-03
6PDGFRB, ITGA1, COL5A3, COL4A2, COL4A1, COL6A2
 199
KEGG_LONG_TERM_DEPRESSION 6.52e-04 19.56 3.80 2.02e-02 1.21e-01
3PRKG1, GUCY1A2, GUCY1A1
 70
KEGG_PURINE_METABOLISM 5.82e-04 11.52 2.97 2.02e-02 1.08e-01
4PDE1A, GUCY1A2, GUCY1A1, PDE3A
 159
KEGG_CALCIUM_SIGNALING_PATHWAY 8.84e-04 10.26 2.65 2.35e-02 1.64e-01
4PDGFRB, EDNRA, PDE1A, CACNA1C
 178
KEGG_NOTCH_SIGNALING_PATHWAY 5.80e-03 19.01 2.17 1.35e-01 1.00e+00
2NOTCH3, JAG1
 47
KEGG_ARRHYTHMOGENIC_RIGHT_VENTRICULAR_CARDIOMYOPATHY_ARVC 1.39e-02 11.88 1.37 2.87e-01 1.00e+00
2CACNA1C, ITGA1
 74
KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM 1.72e-02 10.56 1.22 2.98e-01 1.00e+00
2CACNA1C, ITGA1
 83
KEGG_SMALL_CELL_LUNG_CANCER 1.76e-02 10.43 1.21 2.98e-01 1.00e+00
2COL4A2, COL4A1
 84
KEGG_DILATED_CARDIOMYOPATHY 2.00e-02 9.72 1.13 3.11e-01 1.00e+00
2CACNA1C, ITGA1
 90
KEGG_MAPK_SIGNALING_PATHWAY 2.62e-02 4.96 0.98 3.74e-01 1.00e+00
3PDGFRB, CACNA1C, NGF
 267
KEGG_PATHWAYS_IN_CANCER 4.27e-02 4.07 0.81 4.96e-01 1.00e+00
3PDGFRB, COL4A2, COL4A1
 325
KEGG_AXON_GUIDANCE 3.88e-02 6.74 0.78 4.96e-01 1.00e+00
2SEMA5B, SEMA5A
 129
KEGG_RENIN_ANGIOTENSIN_SYSTEM 4.05e-02 26.18 0.61 4.96e-01 1.00e+00
1ENPEP
 17
KEGG_REGULATION_OF_ACTIN_CYTOSKELETON 9.29e-02 4.06 0.47 9.60e-01 1.00e+00
2PDGFRB, ITGA1
 213
KEGG_DORSO_VENTRAL_AXIS_FORMATION 5.67e-02 18.21 0.43 6.20e-01 1.00e+00
1NOTCH3
 24
KEGG_ABC_TRANSPORTERS 1.01e-01 9.74 0.24 9.92e-01 1.00e+00
1ABCC9
 44
KEGG_TYPE_II_DIABETES_MELLITUS 1.08e-01 9.11 0.22 1.00e+00 1.00e+00
1CACNA1C
 47

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CHR Positional Gene Sets:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
chr11q22 1.72e-03 13.80 2.70 3.07e-01 4.78e-01
3GUCY1A2, TRPC6, ARHGAP42
 98
chr12p12 2.21e-03 12.60 2.47 3.07e-01 6.14e-01
3ABCC9, EPS8, PDE3A
 107
chr13q13 1.53e-02 11.25 1.30 1.00e+00 1.00e+00
2TRPC4, FRY
 78
chr15q24 3.20e-02 7.50 0.87 1.00e+00 1.00e+00
2PEAK1, CSPG4
 116
chr21q22 2.06e-01 2.44 0.29 1.00e+00 1.00e+00
2COL18A1, COL6A2
 353
chr11q13 2.65e-01 2.04 0.24 1.00e+00 1.00e+00
2ANO1, ARHGEF17
 421
chr7q33 1.19e-01 8.21 0.20 1.00e+00 1.00e+00
1CALD1
 52
chr18q22 1.38e-01 6.98 0.17 1.00e+00 1.00e+00
1CCDC102B
 61
chr15q23 1.46e-01 6.55 0.16 1.00e+00 1.00e+00
1UACA
 65
chr4q12 1.74e-01 5.37 0.13 1.00e+00 1.00e+00
1IGFBP7
 79
chr19p13 7.03e-01 1.11 0.13 1.00e+00 1.00e+00
2NOTCH3, COL5A3
 773
chr5q11 1.86e-01 4.99 0.12 1.00e+00 1.00e+00
1ITGA1
 85
chr4q25 1.90e-01 4.87 0.12 1.00e+00 1.00e+00
1ENPEP
 87
chr20p12 2.23e-01 4.07 0.10 1.00e+00 1.00e+00
1JAG1
 104
chr2q32 2.30e-01 3.92 0.10 1.00e+00 1.00e+00
1PDE1A
 108
chr4q32 2.40e-01 3.74 0.09 1.00e+00 1.00e+00
1GUCY1A1
 113
chr8p21 2.67e-01 3.30 0.08 1.00e+00 1.00e+00
1EBF2
 128
chr3q21 2.84e-01 3.06 0.08 1.00e+00 1.00e+00
1SEMA5B
 138
chr17q12 2.93e-01 2.95 0.07 1.00e+00 1.00e+00
1PLXDC1
 143
chr3p25 2.96e-01 2.91 0.07 1.00e+00 1.00e+00
1SLC6A1
 145

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Transcription Factor Targets:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
OCT1_02 1.60e-04 10.91 3.35 1.81e-01 1.81e-01
5PDE1A, CACNA1C, TRPC4, ARHGAP6, JAG1
 214
PAX4_04 2.01e-03 8.15 2.11 4.61e-01 1.00e+00
4PDE1A, STEAP4, EBF2, CALD1
 223
AP3_Q6 3.07e-03 7.23 1.88 4.61e-01 1.00e+00
4EDNRA, ENPEP, EBF2, CALD1
 251
ICSBP_Q6 3.15e-03 7.17 1.86 4.61e-01 1.00e+00
4CACNA1C, COL4A2, COL4A1, FRY
 253
TEF_Q6 3.57e-03 6.92 1.80 4.61e-01 1.00e+00
4ENPEP, ITGA1, EBF2, FRY
 262
IRF1_Q6 3.62e-03 6.89 1.79 4.61e-01 1.00e+00
4EPS8, CACNA1C, SEMA5B, CALD1
 263
RAAGNYNNCTTY_UNKNOWN 5.47e-03 9.04 1.78 5.16e-01 1.00e+00
3RNF152, ITGA1, ARHGAP6
 148
TTAYRTAA_E4BP4_01 3.86e-03 6.76 1.76 4.61e-01 1.00e+00
4PRKG1, ENPEP, ANO1, FRY
 268
NR2E3_TARGET_GENES 1.45e-02 83.52 1.74 6.84e-01 1.00e+00
1EPS8
 6
CEBP_Q2_01 4.07e-03 6.66 1.73 4.61e-01 1.00e+00
4PRKG1, ANO1, EBF2, CALD1
 272
FREAC4_01 5.99e-03 8.74 1.72 5.22e-01 1.00e+00
3SEMA5B, CALD1, FRY
 153
HAND1E47_01 4.73e-03 6.38 1.66 4.87e-01 1.00e+00
4ITGA1, EBF2, CALD1, ARHGAP6
 284
AACTTT_UNKNOWN 8.42e-04 3.39 1.61 3.26e-01 9.55e-01
12RNF152, PDE1A, ITGA1, TRPC4, STEAP4, SEMA5A, EBF2, SLC6A1, ARHGEF17, CALD1, RCAN2, JAG1
 1928
TGGAAA_NFAT_Q4_01 8.64e-04 3.38 1.60 3.26e-01 9.79e-01
12RNF152, EDNRA, CACNA1C, EBF2, ADAMTS14, CSPG4, IGFBP7, CALD1, RCAN2, NGF, ARHGAP6, JAG1
 1934
YAATNANRNNNCAG_UNKNOWN 1.25e-02 12.58 1.45 6.84e-01 1.00e+00
2PDE1A, CALD1
 70
AP2REP_01 9.59e-03 7.32 1.44 6.41e-01 1.00e+00
3EBF2, CALD1, ARHGAP6
 182
WTTGKCTG_UNKNOWN 7.52e-03 4.44 1.37 5.88e-01 1.00e+00
5NOTCH3, RNF152, SEMA5B, CALD1, FRY
 519
HNF3_Q6 1.11e-02 6.93 1.37 6.81e-01 1.00e+00
3EBF2, ADAMTS14, CALD1
 192
TGTTTGY_HNF3_Q6 7.79e-03 3.78 1.31 5.88e-01 1.00e+00
6SEMA5B, KIRREL1, EBF2, SLC6A1, CALD1, JAG1
 748
CATTGTYY_SOX9_B1 1.14e-02 4.91 1.28 6.81e-01 1.00e+00
4NOTCH3, SPECC1, ADGRF5, CALD1
 368

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GO Biological Processes:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
GOBP_POSITIVE_REGULATION_OF_NITRIC_OXIDE_MEDIATED_SIGNAL_TRANSDUCTION 5.75e-05 281.71 23.16 2.39e-02 4.30e-01
2GUCY1A2, GUCY1A1
 5
GOBP_NEGATIVE_REGULATION_OF_SMOOTH_MUSCLE_CONTRACTION 4.81e-06 118.70 20.61 3.99e-03 3.60e-02
3PRKG1, GUCY1A1, ARHGAP42
 14
GOBP_CGMP_METABOLIC_PROCESS 8.93e-06 93.38 16.66 6.07e-03 6.68e-02
3PDE1A, GUCY1A2, GUCY1A1
 17
GOBP_RELAXATION_OF_VASCULAR_ASSOCIATED_SMOOTH_MUSCLE 1.20e-04 169.99 15.84 3.21e-02 9.01e-01
2PRKG1, GUCY1A1
 7
GOBP_NEGATIVE_REGULATION_OF_MUSCLE_CONTRACTION 2.00e-05 68.91 12.62 9.99e-03 1.50e-01
3PRKG1, GUCY1A1, ARHGAP42
 22
GOBP_REGULATION_OF_NITRIC_OXIDE_MEDIATED_SIGNAL_TRANSDUCTION 2.06e-04 121.74 12.04 4.66e-02 1.00e+00
2GUCY1A2, GUCY1A1
 9
GOBP_RELAXATION_OF_SMOOTH_MUSCLE 2.06e-04 121.74 12.04 4.66e-02 1.00e+00
2PRKG1, GUCY1A1
 9
GOBP_CGMP_BIOSYNTHETIC_PROCESS 3.13e-04 94.83 9.72 6.17e-02 1.00e+00
2GUCY1A2, GUCY1A1
 11
GOBP_NOTCH_SIGNALING_INVOLVED_IN_HEART_DEVELOPMENT 3.13e-04 94.83 9.72 6.17e-02 1.00e+00
2HEYL, JAG1
 11
GOBP_COLLAGEN_ACTIVATED_TYROSINE_KINASE_RECEPTOR_SIGNALING_PATHWAY 3.75e-04 85.24 8.86 7.02e-02 1.00e+00
2COL4A2, COL4A1
 12
GOBP_GAMMA_AMINOBUTYRIC_ACID_TRANSPORT 4.43e-04 77.52 8.14 7.70e-02 1.00e+00
2TRPC4, SLC6A1
 13
GOBP_GLOMERULUS_DEVELOPMENT 1.53e-05 30.76 7.79 8.81e-03 1.14e-01
4PDGFRB, ENPEP, HEYL, JAG1
 62
GOBP_VASODILATION 9.05e-05 39.67 7.53 2.75e-02 6.77e-01
3PRKG1, ITGA1, GUCY1A1
 36
GOBP_MANGANESE_ION_TRANSPORT 5.94e-04 65.66 7.01 9.88e-02 1.00e+00
2TRPC4, TRPC6
 15
GOBP_COLLAGEN_ACTIVATED_SIGNALING_PATHWAY 5.94e-04 65.66 7.01 9.88e-02 1.00e+00
2COL4A2, COL4A1
 15
GOBP_CYCLIC_NUCLEOTIDE_METABOLIC_PROCESS 1.24e-04 35.36 6.75 3.21e-02 9.30e-01
3PDE1A, GUCY1A2, GUCY1A1
 40
GOBP_VASCULAR_PROCESS_IN_CIRCULATORY_SYSTEM 1.15e-07 16.50 6.62 3.53e-04 8.57e-04
8PRKG1, EDNRA, ABCC9, ITGA1, GUCY1A1, SLC6A1, PDE3A, ARHGAP42
 245
GOBP_PULMONARY_VALVE_MORPHOGENESIS 7.67e-04 56.94 6.15 1.15e-01 1.00e+00
2HEYL, JAG1
 17
GOBP_REGULATION_OF_PHOSPHOLIPASE_C_ACTIVITY 1.89e-04 30.45 5.84 4.56e-02 1.00e+00
3PDGFRB, EDNRA, ARHGAP6
 46
GOBP_POSITIVE_REGULATION_OF_TRANSCRIPTION_OF_NOTCH_RECEPTOR_TARGET 8.61e-04 53.39 5.80 1.20e-01 1.00e+00
2NOTCH3, HEYL
 18

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Immunological Gene Sets:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
GSE28783_ANTI_MIR33_VS_CTRL_ATHEROSCLEROSIS_MACROPHAGE_DN 1.12e-04 11.82 3.62 2.85e-01 5.44e-01
5EDNRA, ENPEP, TRPC6, ARHGEF17, FRY
 198
GSE6259_FLT3L_INDUCED_DEC205_POS_DC_VS_CD4_TCELL_DN 2.89e-04 13.95 3.59 4.13e-01 1.00e+00
4PDGFRB, GUCY1A2, ARHGEF17, CSPG4
 132
GSE21670_STAT3_KO_VS_WT_CD4_TCELL_IL6_TREATED_DN 1.17e-04 11.70 3.59 2.85e-01 5.70e-01
5PRKG1, COL4A2, COL4A1, TRPC6, FRY
 200
GSE27859_MACROPHAGE_VS_CD11C_INT_F480_INT_DC_UP 7.62e-04 10.69 2.76 4.13e-01 1.00e+00
4PDGFRB, UACA, LHFPL6, SPECC1
 171
GSE36476_YOUNG_VS_OLD_DONOR_MEMORY_CD4_TCELL_DN 1.31e-03 9.20 2.38 4.13e-01 1.00e+00
4GUCY1A1, TRPC6, SEMA5A, PEAK1
 198
GSE21670_UNTREATED_VS_TGFB_TREATED_CD4_TCELL_DN 1.31e-03 9.20 2.38 4.13e-01 1.00e+00
4PRKG1, COL4A2, COL4A1, FRY
 198
GSE24574_BCL6_HIGH_TFH_VS_TCONV_CD4_TCELL_DN 1.31e-03 9.20 2.38 4.13e-01 1.00e+00
4ENPEP, GUCY1A2, TRPC6, CALD1
 198
GSE3982_MEMORY_CD4_TCELL_VS_BCELL_UP 1.33e-03 9.16 2.37 4.13e-01 1.00e+00
4PLXDC1, EDNRA, ANO1, FRY
 199
GSE9006_TYPE_1_VS_TYPE_2_DIABETES_PBMC_AT_DX_DN 1.33e-03 9.16 2.37 4.13e-01 1.00e+00
4EPS8, LHFPL6, GUCY1A1, TRPC4
 199
GSE28783_ANTI_MIR33_VS_UNTREATED_ATHEROSCLEROSIS_MACROPHAGE_DN 1.33e-03 9.16 2.37 4.13e-01 1.00e+00
4PRKG1, GUCY1A2, TRPC6, ARHGEF17
 199
GSE33374_CD8_ALPHAALPHA_VS_ALPHABETA_CD161_HIGH_TCELL_UP 1.33e-03 9.16 2.37 4.13e-01 1.00e+00
4COL18A1, TRPC4, SEMA5B, NHSL2
 199
GSE13306_TREG_RA_VS_TCONV_RA_DN 1.36e-03 9.11 2.36 4.13e-01 1.00e+00
4ANO1, COL18A1, ADGRF5, FRY
 200
GSE1460_INTRATHYMIC_T_PROGENITOR_VS_THYMIC_STROMAL_CELL_DN 1.36e-03 9.11 2.36 4.13e-01 1.00e+00
4EDNRA, SLC6A1, COL6A2, JAG1
 200
GSE12003_MIR223_KO_VS_WT_BM_PROGENITOR_4D_CULTURE_DN 1.36e-03 9.11 2.36 4.13e-01 1.00e+00
4COL18A1, COL5A3, TRPC4, EBF2
 200
GSE21379_WT_VS_SAP_KO_TFH_CD4_TCELL_UP 1.36e-03 9.11 2.36 4.13e-01 1.00e+00
4LHFPL6, COL4A2, COL4A1, NHSL2
 200
GSE41978_ID2_KO_VS_ID2_KO_AND_BIM_KO_KLRG1_LOW_EFFECTOR_CD8_TCELL_UP 1.36e-03 9.11 2.36 4.13e-01 1.00e+00
4PLXDC1, SPECC1, GUCY1A1, NHSL2
 200
GSE3720_UNSTIM_VS_LPS_STIM_VD1_GAMMADELTA_TCELL_DN 5.26e-03 9.16 1.80 6.68e-01 1.00e+00
3NOTCH3, EPS8, ADAMTS14
 146
GSE13522_CTRL_VS_T_CRUZI_BRAZIL_STRAIN_INF_SKIN_UP 5.36e-03 9.10 1.79 6.68e-01 1.00e+00
3PDGFRB, ADAMTS14, ARHGAP6
 147
GSE5589_WT_VS_IL6_KO_LPS_AND_IL10_STIM_MACROPHAGE_180MIN_DN 5.57e-03 8.98 1.77 6.68e-01 1.00e+00
3ITGA1, TRPC4, RCAN2
 149
GSE3720_UNSTIM_VS_LPS_STIM_VD2_GAMMADELTA_TCELL_DN 5.99e-03 8.74 1.72 6.68e-01 1.00e+00
3EPS8, COL4A1, FRY
 153

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Top Ranked Transcription Factors for this Gene Expression Program:

Gene Symbol Gene Loading Rank DNA Binding Domain Motif Status IUPAC PWM GTEx DepMap Decartes
NOTCH3 3 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None Fragment of NOTCH. Is a coactivator.
HEYL 16 Yes Inferred motif Monomer or homomultimer High-throughput in vitro None None
EBF2 35 Yes Known motif Monomer or homomultimer In vivo/Misc source Only known motifs are from Transfac or HocoMoco - origin is uncertain EBF1 has a nice HT-SELEX model and based on this paper (PMID:23499423). EBF2 binds similar motif to control brown/beige fat cell identity.
NR2F2 54 Yes Known motif Monomer or homomultimer 100 perc ID - in vitro None None
ZBTB46 57 Yes Likely to be sequence specific TF Monomer or homomultimer No motif None Specificity is unknown; functions in dendritic cells (PMID: 22615130).
HEY2 70 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
EBF1 71 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
LZTS1 83 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None Does not contain a bZIP domain. (PMID: 10097140) does not examine TF activity or DNA binding - GO needs to be corrected.
MEF2C 91 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
ID3 94 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
STK3 101 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None Kinase - included only because GO says it regulates TFs
GLI3 103 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
PRRX1 117 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
RUNX1 120 Yes Known motif Monomer or homomultimer In vivo/Misc source Only known motifs are from Transfac or HocoMoco - origin is uncertain None
ZEB2 125 Yes Inferred motif Monomer or homomultimer In vivo/Misc source None None
SOX5 131 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
HES4 132 Yes Inferred motif Monomer or homomultimer High-throughput in vitro None None
LPP 154 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).
TBX15 172 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
ID4 187 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

Druggable Genes for this Gene Expression Program:

Gene Symbol Gene Loading Rank Drug Names Drug Category GTEx DepMap
PDGFRB 1
7SORAFENIB, IMATINIB, REGORAFENIB, PAZOPANIB, NINTEDANIB, SUNITINIB, DASATINIB
 Small molecule GTEx DepMap
EDNRA 8
3MACITENTAN, BOSENTAN, AMBRISENTAN
 Small molecule GTEx DepMap
ANO1 10
1CROFELEMER
 Small molecule GTEx DepMap
ABCC9 12
2PINACIDIL, MINOXIDIL
 Small molecule GTEx DepMap
PDE1A 14
2PENTOXIFYLLINE, DIPYRIDAMOLE
 Small molecule GTEx DepMap
CACNA1C 18
15DILTIAZEM, NISOLDIPINE, ISRADIPINE, AMLODIPINE, BEPRIDIL, NICARDIPINE, GABAPENTIN ENACARBIL, CLEVIDIPINE, DRONEDARONE, VERAPAMIL, FELODIPINE, NIFEDIPINE, NIMODIPINE, GABAPENTIN, PREGABALIN
 Small molecule GTEx DepMap
SLC6A1 36
1TIAGABINE
 Small molecule GTEx DepMap
PDE3A 37
9THEOPHYLLINE SODIUM GLYCINATE, ANAGRELIDE, PENTOXIFYLLINE, THEOPHYLLINE, DYPHYLLINE, INAMRINONE, MILRINONE, CILOSTAZOL, DIPYRIDAMOLE
 Small molecule GTEx DepMap
NGF 44
2TANEZUMAB, FULRANUMAB
 Antibody GTEx DepMap
EPHA3 64
1VANDETANIB
 Small molecule GTEx DepMap
PTGIR 92
4TREPROSTINIL, ILOPROST, SELEXIPAG, EPOPROSTENOL
 Small molecule GTEx DepMap
PDE1C 110
2PENTOXIFYLLINE, DIPYRIDAMOLE
 Small molecule GTEx DepMap
ADRA1B 118
28DOXAZOSIN, MIDODRINE, PHENOXYBENZAMINE, HYDROXYAMPHETAMINE, ALFUZOSIN, NAPHAZOLINE, TOLAZOLINE, TETRAHYDROZOLINE, PHENYLEPHRINE, LABETALOL, NOREPINEPHRINE, EPINEPHRINE, METARAMINOL, ERGOTAMINE, ERGOLOID MESYLATES, RAUWOLFIA SERPENTINA, METHOXAMINE, DROXIDOPA, TAMSULOSIN, PHENTOLAMINE, TRIMIPRAMINE, OXYMETAZOLINE, DIPIVEFRIN, TERAZOSIN, ALSEROXYLON, CARVEDILOL, MEPHENTERMINE, PRAZOSIN
 Small molecule GTEx DepMap
HTR1F 164
2ALMOTRIPTAN, ELETRIPTAN
 Small molecule GTEx DepMap
KCNJ8 174
1DIAZOXIDE
 Small molecule GTEx DepMap
AVPR1A 178
1CONIVAPTAN
 Small molecule GTEx DepMap
PDE5A 206
6SILDENAFIL, AVANAFIL, PENTOXIFYLLINE, TADALAFIL, VARDENAFIL, DIPYRIDAMOLE
 Small molecule GTEx DepMap
CACNA1H 216
10PREGABALIN, BEPRIDIL, MIBEFRADIL, GABAPENTIN ENACARBIL, ETHOSUXIMIDE, METHSUXIMIDE, TRIMETHADIONE, PHENSUXIMIDE, GABAPENTIN, PARAMETHADIONE
 Small molecule GTEx DepMap
S1PR3 222
1FINGOLIMOD
 Small molecule GTEx DepMap
PTK2 230
5PF-562271, CEP-37440, BI-853520, GSK-2256098, VS-4718
 Small molecule GTEx DepMap


QQ Plot showing correlations with other GEPs 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
AATCGACCAAATGGTA-1_HTA4_1002_4007 Smooth_muscle_cells 0.18 3012.58
Raw ScoresOsteoblasts: 0.29, Fibroblasts: 0.29, Smooth_muscle_cells: 0.29, MSC: 0.29, Chondrocytes: 0.27, iPS_cells: 0.26, Tissue_stem_cells: 0.26, Astrocyte: 0.26, Neurons: 0.26, Neuroepithelial_cell: 0.25
GAGCTGCCAAGTGGGT-1_HTA4_1019_4075 Endothelial_cells 0.22 2992.32
Raw ScoresEndothelial_cells: 0.41, Osteoblasts: 0.4, Smooth_muscle_cells: 0.4, Fibroblasts: 0.39, Tissue_stem_cells: 0.38, Chondrocytes: 0.38, MSC: 0.37, iPS_cells: 0.36, Astrocyte: 0.33, Neurons: 0.33
CATAGACGTTAAGCAA-1_HTA4_1002_4007 Smooth_muscle_cells 0.25 2948.48
Raw ScoresFibroblasts: 0.38, Smooth_muscle_cells: 0.38, Osteoblasts: 0.37, MSC: 0.35, Chondrocytes: 0.35, Tissue_stem_cells: 0.35, iPS_cells: 0.35, Neurons: 0.31, Endothelial_cells: 0.3, Astrocyte: 0.29
GTCTCACTCAAAGGAT-1_HTA4_1012_4045 Smooth_muscle_cells 0.32 2472.32
Raw ScoresFibroblasts: 0.55, Osteoblasts: 0.55, Smooth_muscle_cells: 0.54, MSC: 0.52, iPS_cells: 0.51, Tissue_stem_cells: 0.51, Chondrocytes: 0.51, Neurons: 0.44, Endothelial_cells: 0.43, Astrocyte: 0.37
GTCATTTCATCTGGGC-1_HTA4_1018_4070 Smooth_muscle_cells 0.20 2468.99
Raw ScoresSmooth_muscle_cells: 0.33, Osteoblasts: 0.33, Fibroblasts: 0.33, Tissue_stem_cells: 0.32, MSC: 0.31, Chondrocytes: 0.31, iPS_cells: 0.3, Neurons: 0.28, Endothelial_cells: 0.27, Astrocyte: 0.27
ACCAAACCACCATTCC-1_HTA4_1002_4008 Smooth_muscle_cells 0.21 2435.99
Raw ScoresSmooth_muscle_cells: 0.31, Fibroblasts: 0.31, Osteoblasts: 0.3, MSC: 0.29, Chondrocytes: 0.28, Tissue_stem_cells: 0.28, iPS_cells: 0.27, Astrocyte: 0.26, Neurons: 0.26, Neuroepithelial_cell: 0.25
TCCTGCAAGCTGGTGA-1_HTA4_1002_4008 Smooth_muscle_cells 0.25 2428.04
Raw ScoresFibroblasts: 0.36, Smooth_muscle_cells: 0.36, Osteoblasts: 0.35, Chondrocytes: 0.35, Tissue_stem_cells: 0.33, MSC: 0.33, iPS_cells: 0.32, Neurons: 0.29, Astrocyte: 0.28, Endothelial_cells: 0.27
CGAGTTATCTTAGCAG-1_HTA4_1002_4008 Smooth_muscle_cells 0.22 2408.23
Raw ScoresFibroblasts: 0.33, Osteoblasts: 0.32, MSC: 0.31, Smooth_muscle_cells: 0.31, Chondrocytes: 0.29, iPS_cells: 0.29, Tissue_stem_cells: 0.28, Neurons: 0.26, Astrocyte: 0.24, Neuroepithelial_cell: 0.24
ACCTACCAGCACCAGA-1_HTA4_1002_4007 Smooth_muscle_cells 0.23 2362.08
Raw ScoresOsteoblasts: 0.36, Fibroblasts: 0.36, Smooth_muscle_cells: 0.36, Chondrocytes: 0.35, Tissue_stem_cells: 0.34, MSC: 0.34, iPS_cells: 0.32, Neurons: 0.29, Astrocyte: 0.28, Neuroepithelial_cell: 0.28
TCGACCTAGAAACCAT-1_HTA4_1008_4028 Neurons 0.22 2148.76
Raw ScoresMSC: 0.42, Fibroblasts: 0.4, Neuroepithelial_cell: 0.39, Neurons: 0.39, Endothelial_cells: 0.39, Osteoblasts: 0.39, Smooth_muscle_cells: 0.38, Astrocyte: 0.38, iPS_cells: 0.38, Tissue_stem_cells: 0.38
TTTGACTGTAGGACCA-1_HTA4_1018_4067 Smooth_muscle_cells 0.25 2143.22
Raw ScoresFibroblasts: 0.46, Osteoblasts: 0.46, Smooth_muscle_cells: 0.45, Chondrocytes: 0.45, Tissue_stem_cells: 0.44, MSC: 0.44, iPS_cells: 0.42, Neurons: 0.39, Endothelial_cells: 0.38, Astrocyte: 0.35
TTCCGTGCAACAGCCC-1_HTA4_1020_4079 Smooth_muscle_cells 0.23 2122.02
Raw ScoresSmooth_muscle_cells: 0.41, Fibroblasts: 0.41, Osteoblasts: 0.41, MSC: 0.4, Chondrocytes: 0.4, Endothelial_cells: 0.39, Tissue_stem_cells: 0.39, iPS_cells: 0.38, Astrocyte: 0.35, Neurons: 0.35
TACTGCCTCTAGTGTG-1_HTA4_1018_4070 Smooth_muscle_cells 0.24 2085.73
Raw ScoresFibroblasts: 0.4, Osteoblasts: 0.4, Smooth_muscle_cells: 0.4, Tissue_stem_cells: 0.37, Chondrocytes: 0.37, MSC: 0.37, iPS_cells: 0.36, Neurons: 0.32, Endothelial_cells: 0.31, Astrocyte: 0.29
TACCCGTTCCACTTTA-1_HTA4_1009_4031 Tissue_stem_cells 0.17 2062.84
Raw ScoresOsteoblasts: 0.36, Fibroblasts: 0.36, Smooth_muscle_cells: 0.34, Tissue_stem_cells: 0.34, MSC: 0.34, Chondrocytes: 0.33, iPS_cells: 0.32, Neurons: 0.3, Astrocyte: 0.29, Endothelial_cells: 0.29
ATCCACCCATTCGATG-1_HTA4_1002_4007 Neurons 0.22 2028.42
Raw ScoresAstrocyte: 0.31, Neuroepithelial_cell: 0.31, Neurons: 0.31, MSC: 0.31, Osteoblasts: 0.3, Fibroblasts: 0.3, Smooth_muscle_cells: 0.29, iPS_cells: 0.27, Embryonic_stem_cells: 0.27, Chondrocytes: 0.26
GGAACCCAGAAAGCGA-1_HTA4_1018_4070 Smooth_muscle_cells 0.20 1898.05
Raw ScoresFibroblasts: 0.34, Smooth_muscle_cells: 0.34, Osteoblasts: 0.34, Tissue_stem_cells: 0.32, Chondrocytes: 0.32, MSC: 0.32, iPS_cells: 0.3, Neurons: 0.29, Astrocyte: 0.28, Endothelial_cells: 0.27
CGATGCGAGTATTGCC-1_HTA4_1018_4069 MSC 0.18 1834.08
Raw ScoresMSC: 0.32, Smooth_muscle_cells: 0.31, Fibroblasts: 0.31, Osteoblasts: 0.31, Endothelial_cells: 0.3, Neurons: 0.3, Neuroepithelial_cell: 0.29, iPS_cells: 0.29, Astrocyte: 0.29, Tissue_stem_cells: 0.29
GAAACCTTCGCTTGAA-1_HTA4_1018_4071 Smooth_muscle_cells 0.20 1827.47
Raw ScoresSmooth_muscle_cells: 0.36, Fibroblasts: 0.35, Osteoblasts: 0.35, Tissue_stem_cells: 0.34, Chondrocytes: 0.34, MSC: 0.33, iPS_cells: 0.32, Neurons: 0.3, Endothelial_cells: 0.29, Astrocyte: 0.28
TCAGCCTCAAAGCTAA-1_HTA4_1009_4031 Tissue_stem_cells 0.19 1805.15
Raw ScoresFibroblasts: 0.36, Osteoblasts: 0.36, Tissue_stem_cells: 0.35, Smooth_muscle_cells: 0.34, Chondrocytes: 0.34, MSC: 0.32, iPS_cells: 0.32, Neurons: 0.29, Endothelial_cells: 0.28, Astrocyte: 0.27
TACGCTCCAAGTAGTA-1_HTA4_1018_4069 Smooth_muscle_cells 0.25 1779.91
Raw ScoresFibroblasts: 0.44, Smooth_muscle_cells: 0.43, Osteoblasts: 0.43, MSC: 0.4, Chondrocytes: 0.4, Tissue_stem_cells: 0.4, iPS_cells: 0.39, Endothelial_cells: 0.39, Astrocyte: 0.38, Neurons: 0.37
CCACAAACACCTCTAC-1_HTA4_1020_4078 Smooth_muscle_cells 0.18 1773.92
Raw ScoresOsteoblasts: 0.3, Smooth_muscle_cells: 0.29, Fibroblasts: 0.29, MSC: 0.29, Tissue_stem_cells: 0.27, Chondrocytes: 0.27, iPS_cells: 0.27, Endothelial_cells: 0.26, Astrocyte: 0.26, Neurons: 0.25
TCTTCCTGTCCGCAGT-1_HTA4_1017_4062 Smooth_muscle_cells 0.20 1684.57
Raw ScoresFibroblasts: 0.34, Osteoblasts: 0.34, Smooth_muscle_cells: 0.33, Tissue_stem_cells: 0.32, MSC: 0.31, Chondrocytes: 0.3, iPS_cells: 0.3, Endothelial_cells: 0.28, Neurons: 0.27, Astrocyte: 0.26
CATTGCCCATACACCA-1_HTA4_1018_4067 Endothelial_cells 0.17 1651.93
Raw ScoresEndothelial_cells: 0.34, Osteoblasts: 0.33, Smooth_muscle_cells: 0.33, Fibroblasts: 0.33, Chondrocytes: 0.31, Tissue_stem_cells: 0.31, MSC: 0.3, iPS_cells: 0.3, Astrocyte: 0.29, Neurons: 0.28
GTCATCCGTCTCTCAC-1_HTA4_1018_4070 Smooth_muscle_cells 0.34 1616.66
Raw ScoresFibroblasts: 0.47, Smooth_muscle_cells: 0.47, Osteoblasts: 0.46, Chondrocytes: 0.44, Tissue_stem_cells: 0.42, MSC: 0.41, iPS_cells: 0.41, Neurons: 0.34, Astrocyte: 0.32, Endothelial_cells: 0.31
TCCGAAAAGGGAGGAC-1_HTA4_1018_4069 Smooth_muscle_cells 0.25 1602.09
Raw ScoresSmooth_muscle_cells: 0.46, Osteoblasts: 0.46, Fibroblasts: 0.46, Tissue_stem_cells: 0.45, Chondrocytes: 0.45, MSC: 0.44, iPS_cells: 0.43, Neurons: 0.39, Endothelial_cells: 0.39, Astrocyte: 0.37
TTCATGTGTGCTGATT-1_HTA4_1018_4070 Smooth_muscle_cells 0.21 1581.30
Raw ScoresOsteoblasts: 0.37, Smooth_muscle_cells: 0.37, Fibroblasts: 0.36, Tissue_stem_cells: 0.35, Chondrocytes: 0.35, MSC: 0.34, iPS_cells: 0.33, Neurons: 0.32, Endothelial_cells: 0.3, Astrocyte: 0.27
TTGGATGGTATGCAAA-1_HTA4_1002_4007 Smooth_muscle_cells 0.24 1562.66
Raw ScoresFibroblasts: 0.37, Osteoblasts: 0.37, Smooth_muscle_cells: 0.37, Chondrocytes: 0.35, Tissue_stem_cells: 0.35, MSC: 0.34, iPS_cells: 0.33, Neurons: 0.3, Endothelial_cells: 0.29, Astrocyte: 0.28
ACCTGTCTCCTCTAAT-1_HTA4_1018_4070 Fibroblasts 0.20 1528.73
Raw ScoresSmooth_muscle_cells: 0.31, Fibroblasts: 0.31, Osteoblasts: 0.3, Tissue_stem_cells: 0.28, Chondrocytes: 0.28, MSC: 0.27, iPS_cells: 0.27, Neurons: 0.24, Endothelial_cells: 0.23, Astrocyte: 0.23
TGAGCATAGCACGATG-1_HTA4_1012_4046 Endothelial_cells 0.21 1519.40
Raw ScoresEndothelial_cells: 0.47, Fibroblasts: 0.46, Smooth_muscle_cells: 0.46, Osteoblasts: 0.45, Tissue_stem_cells: 0.44, Chondrocytes: 0.44, MSC: 0.42, iPS_cells: 0.42, Neurons: 0.4, Astrocyte: 0.37
GCACATAGTGCTCTTC-1_HTA4_1020_4077 Osteoblasts 0.23 1501.21
Raw ScoresOsteoblasts: 0.41, Fibroblasts: 0.39, Smooth_muscle_cells: 0.38, MSC: 0.38, Chondrocytes: 0.37, Tissue_stem_cells: 0.37, iPS_cells: 0.36, Endothelial_cells: 0.33, Neurons: 0.31, Astrocyte: 0.3
AGGGAGTAGTTTGGCT-1_HTA4_1008_4028 Neurons 0.22 1487.51
Raw ScoresNeuroepithelial_cell: 0.39, Neurons: 0.39, MSC: 0.38, Endothelial_cells: 0.38, Astrocyte: 0.38, Fibroblasts: 0.36, Embryonic_stem_cells: 0.35, Osteoblasts: 0.35, Smooth_muscle_cells: 0.35, iPS_cells: 0.35
TCAATTCTCCTCCACA-1_HTA4_1020_4078 Smooth_muscle_cells 0.18 1478.45
Raw ScoresOsteoblasts: 0.28, MSC: 0.27, Smooth_muscle_cells: 0.27, Fibroblasts: 0.26, Tissue_stem_cells: 0.25, iPS_cells: 0.25, Chondrocytes: 0.25, Neurons: 0.23, Endothelial_cells: 0.22, Astrocyte: 0.22
ATACCTTCACAGAGAC-1_HTA4_1018_4070 Smooth_muscle_cells 0.17 1466.55
Raw ScoresOsteoblasts: 0.32, Fibroblasts: 0.32, Smooth_muscle_cells: 0.31, Tissue_stem_cells: 0.3, MSC: 0.3, Chondrocytes: 0.3, iPS_cells: 0.3, Neurons: 0.27, Endothelial_cells: 0.26, Astrocyte: 0.25
TGATGGTGTGTAAATG-1_HTA4_1008_4028 Neurons 0.23 1465.94
Raw ScoresNeuroepithelial_cell: 0.38, Astrocyte: 0.37, Neurons: 0.37, MSC: 0.36, Embryonic_stem_cells: 0.34, Fibroblasts: 0.33, Osteoblasts: 0.32, iPS_cells: 0.32, Smooth_muscle_cells: 0.31, Tissue_stem_cells: 0.31
GAGTTACAGCCTGCCA-1_HTA4_1002_4007 Neurons 0.20 1459.47
Raw ScoresNeuroepithelial_cell: 0.34, Astrocyte: 0.33, Neurons: 0.33, Fibroblasts: 0.33, MSC: 0.33, Smooth_muscle_cells: 0.33, Osteoblasts: 0.32, iPS_cells: 0.31, Tissue_stem_cells: 0.3, Embryonic_stem_cells: 0.3
TGATGCAAGTTGCTGT-1_HTA4_1018_4067 Smooth_muscle_cells 0.20 1449.88
Raw ScoresOsteoblasts: 0.35, Fibroblasts: 0.34, Smooth_muscle_cells: 0.34, Chondrocytes: 0.33, Tissue_stem_cells: 0.33, MSC: 0.32, iPS_cells: 0.31, Neurons: 0.29, Astrocyte: 0.28, Endothelial_cells: 0.28
GCGTTTCTCGCTGACG-1_HTA4_1018_4070 Smooth_muscle_cells 0.21 1435.03
Raw ScoresOsteoblasts: 0.35, Smooth_muscle_cells: 0.35, Fibroblasts: 0.34, Chondrocytes: 0.33, Tissue_stem_cells: 0.33, MSC: 0.31, iPS_cells: 0.31, Endothelial_cells: 0.29, Neurons: 0.28, Astrocyte: 0.27
CATGCAACAAGTAGTA-1_HTA4_1020_4078 Neurons 0.09 1434.85
Raw ScoresAstrocyte: 0.22, Smooth_muscle_cells: 0.22, Osteoblasts: 0.22, Fibroblasts: 0.22, MSC: 0.21, Neurons: 0.21, Neuroepithelial_cell: 0.2, Tissue_stem_cells: 0.2, Endothelial_cells: 0.19, iPS_cells: 0.19
ACATCGACAACTGATC-1_HTA4_1018_4070 Smooth_muscle_cells 0.16 1418.49
Raw ScoresFibroblasts: 0.3, Osteoblasts: 0.3, Smooth_muscle_cells: 0.29, Chondrocytes: 0.29, Tissue_stem_cells: 0.28, MSC: 0.28, iPS_cells: 0.28, Neurons: 0.26, Endothelial_cells: 0.24, Astrocyte: 0.22
AGTACCATCTATACTC-1_HTA4_1018_4070 Smooth_muscle_cells 0.18 1409.61
Raw ScoresOsteoblasts: 0.33, Fibroblasts: 0.33, Smooth_muscle_cells: 0.33, Chondrocytes: 0.33, Tissue_stem_cells: 0.32, MSC: 0.32, iPS_cells: 0.31, Neurons: 0.29, Astrocyte: 0.27, Endothelial_cells: 0.26
CCACACTGTTTAGACC-1_HTA4_1018_4067 Smooth_muscle_cells 0.16 1404.26
Raw ScoresFibroblasts: 0.27, Osteoblasts: 0.27, Smooth_muscle_cells: 0.27, MSC: 0.25, Tissue_stem_cells: 0.25, Chondrocytes: 0.25, Endothelial_cells: 0.24, iPS_cells: 0.24, Neurons: 0.24, Astrocyte: 0.23
AGATCCATCCATTGCC-1_HTA4_1016_4061 Osteoblasts 0.15 1402.49
Raw ScoresFibroblasts: 0.26, Osteoblasts: 0.26, Tissue_stem_cells: 0.25, Smooth_muscle_cells: 0.25, MSC: 0.25, Neuroepithelial_cell: 0.25, Astrocyte: 0.24, Chondrocytes: 0.24, Neurons: 0.24, Endothelial_cells: 0.23
AAGAACAAGCAACCAG-1_HTA4_1002_4008 Smooth_muscle_cells 0.27 1400.61
Raw ScoresFibroblasts: 0.41, Osteoblasts: 0.39, Smooth_muscle_cells: 0.38, Chondrocytes: 0.38, iPS_cells: 0.36, MSC: 0.36, Tissue_stem_cells: 0.36, Neurons: 0.31, Neuroepithelial_cell: 0.29, Endothelial_cells: 0.28
TGTTCTATCAGGACAG-1_HTA4_1002_4008 Tissue_stem_cells 0.18 1395.49
Raw ScoresFibroblasts: 0.3, Osteoblasts: 0.3, Chondrocytes: 0.29, Smooth_muscle_cells: 0.29, MSC: 0.29, Tissue_stem_cells: 0.28, Astrocyte: 0.28, iPS_cells: 0.28, Neuroepithelial_cell: 0.27, Neurons: 0.27
TAGACCATCTCTGGTC-1_HTA4_1005_4016 Smooth_muscle_cells 0.20 1361.78
Raw ScoresFibroblasts: 0.35, Smooth_muscle_cells: 0.35, Osteoblasts: 0.34, Chondrocytes: 0.33, MSC: 0.33, iPS_cells: 0.31, Tissue_stem_cells: 0.31, Astrocyte: 0.3, Neurons: 0.29, Neuroepithelial_cell: 0.27
AAAGGGCCAACACGAG-1_HTA4_1009_4031 Smooth_muscle_cells 0.28 1355.21
Raw ScoresFibroblasts: 0.43, Smooth_muscle_cells: 0.43, Osteoblasts: 0.42, Chondrocytes: 0.41, Tissue_stem_cells: 0.4, MSC: 0.39, iPS_cells: 0.39, Neurons: 0.36, Astrocyte: 0.33, Endothelial_cells: 0.31
CTCATTATCTCATTGT-1_HTA4_1020_4078 Smooth_muscle_cells 0.23 1346.84
Raw ScoresOsteoblasts: 0.39, Fibroblasts: 0.38, Smooth_muscle_cells: 0.38, MSC: 0.37, Chondrocytes: 0.36, Endothelial_cells: 0.36, Tissue_stem_cells: 0.36, iPS_cells: 0.35, Neurons: 0.31, Astrocyte: 0.3
ATGTCCCGTTGGTGTT-1_HTA4_1018_4071 Smooth_muscle_cells 0.17 1344.00
Raw ScoresSmooth_muscle_cells: 0.31, Fibroblasts: 0.31, Osteoblasts: 0.3, Tissue_stem_cells: 0.3, Chondrocytes: 0.29, MSC: 0.28, iPS_cells: 0.28, Neurons: 0.26, Endothelial_cells: 0.25, Astrocyte: 0.23
CTAGGTATCCGGTAAT-1_HTA4_1018_4067 Smooth_muscle_cells 0.13 1306.53
Raw ScoresOsteoblasts: 0.33, Smooth_muscle_cells: 0.33, Fibroblasts: 0.32, Tissue_stem_cells: 0.32, Chondrocytes: 0.31, MSC: 0.29, iPS_cells: 0.29, Endothelial_cells: 0.29, Neurons: 0.29, Astrocyte: 0.26
GATCACAGTTAACCTG-1_HTA4_1008_4027 Neurons 0.26 1303.26
Raw ScoresNeuroepithelial_cell: 0.47, Neurons: 0.46, Astrocyte: 0.44, MSC: 0.43, Embryonic_stem_cells: 0.42, iPS_cells: 0.39, Fibroblasts: 0.39, Endothelial_cells: 0.38, Tissue_stem_cells: 0.38, Smooth_muscle_cells: 0.37


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: 1.30e-12
Mean rank of genes in gene set: 4360.12
Rank on gene expression program of genes in gene set:
Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
COL4A1 0.0040172 30 GTEx DepMap Descartes 10.82 1150.26
IGFBP7 0.0034665 41 GTEx DepMap Descartes 14.78 6708.68
ITGA7 0.0026557 74 GTEx DepMap Descartes 0.33 60.38
MMP11 0.0025836 81 GTEx DepMap Descartes 0.30 56.68
MEF2C 0.0023838 91 GTEx DepMap Descartes 2.14 183.97
COL5A1 0.0023439 95 GTEx DepMap Descartes 2.96 238.14
BGN 0.0021902 109 GTEx DepMap Descartes 1.48 408.48
ACTA2 0.0017911 158 GTEx DepMap Descartes 1.79 888.81
MYH11 0.0017872 159 GTEx DepMap Descartes 0.94 105.45
MYLK 0.0017175 173 GTEx DepMap Descartes 1.06 71.15
COL5A2 0.0016322 186 GTEx DepMap Descartes 3.98 374.57
MYL9 0.0015445 197 GTEx DepMap Descartes 0.83 197.98
PGF 0.0015205 202 GTEx DepMap Descartes 0.17 35.93
TPM2 0.0015188 203 GTEx DepMap Descartes 0.74 314.57
FN1 0.0014897 210 GTEx DepMap Descartes 8.83 595.20
TPM1 0.0013352 251 GTEx DepMap Descartes 3.64 619.57
COL1A2 0.0013263 254 GTEx DepMap Descartes 13.52 1351.25
POSTN 0.0013185 257 GTEx DepMap Descartes 2.98 535.40
TNC 0.0012629 276 GTEx DepMap Descartes 3.30 275.69
RGS5 0.0012262 292 GTEx DepMap Descartes 2.08 228.40
COL3A1 0.0011973 301 GTEx DepMap Descartes 12.13 1295.73
THY1 0.0011098 326 GTEx DepMap Descartes 1.23 162.20
COL1A1 0.0010090 374 GTEx DepMap Descartes 13.32 1330.68
COL12A1 0.0008653 462 GTEx DepMap Descartes 2.57 137.47
COL14A1 0.0008410 484 GTEx DepMap Descartes 2.15 172.96
TAGLN 0.0008049 518 GTEx DepMap Descartes 1.59 266.90
TGFB1 0.0006164 691 GTEx DepMap Descartes 0.63 149.58
COL13A1 0.0005273 825 GTEx DepMap Descartes 0.05 10.46
THBS2 0.0005006 873 GTEx DepMap Descartes 2.82 284.14
TMEM119 0.0002936 1454 GTEx DepMap Descartes 0.16 32.33
COL10A1 0.0002896 1470 GTEx DepMap Descartes 0.34 51.05
CNN3 0.0002726 1558 GTEx DepMap Descartes 1.17 353.81
COL15A1 0.0001950 2053 GTEx DepMap Descartes 1.17 111.17
TGFB2 0.0001732 2257 GTEx DepMap Descartes 0.31 32.04
CNN2 0.0001424 2589 GTEx DepMap Descartes 0.21 59.44
ACTG2 0.0001399 2629 GTEx DepMap Descartes 0.07 23.81
LUM 0.0000726 3898 GTEx DepMap Descartes 1.60 323.77
WNT5A 0.0000185 6181 GTEx DepMap Descartes 0.06 5.18
HOPX 0.0000131 6563 GTEx DepMap Descartes 0.19 28.32
THBS1 -0.0000087 10034 GTEx DepMap Descartes 3.83 308.94
TGFBR1 -0.0000379 13004 GTEx DepMap Descartes 0.89 78.63
VCAN -0.0001079 16387 GTEx DepMap Descartes 4.91 224.70
COL8A1 -0.0001746 18042 GTEx DepMap Descartes 2.29 217.97
VEGFA -0.0001754 18057 GTEx DepMap Descartes 0.66 29.84
MMP2 -0.0002988 19562 GTEx DepMap Descartes 0.25 43.39
DCN -0.0003064 19603 GTEx DepMap Descartes 1.90 162.81
IGFBP3 -0.0003404 19783 GTEx DepMap Descartes 0.31 68.00
TGFBR2 -0.0003496 19822 GTEx DepMap Descartes 1.63 151.93
COL11A1 -0.0007419 20507 GTEx DepMap Descartes 0.51 34.92


Stroma (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 the broad Stroma cluster:
Wilcoxon ranksum test P-value for gene set overrepresentation: 8.96e-05
Mean rank of genes in gene set: 337.2
Rank on gene expression program of genes in gene set:

Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
COL5A1 0.0023439 95 GTEx DepMap Descartes 2.96 238.14
COL6A1 0.0021067 116 GTEx DepMap Descartes 1.83 286.96
FN1 0.0014897 210 GTEx DepMap Descartes 8.83 595.20
COL3A1 0.0011973 301 GTEx DepMap Descartes 12.13 1295.73
GPC3 0.0004560 964 GTEx DepMap Descartes 0.72 199.23


Mesenchymal Fig 1D (Olsen)
Selected mesenchymal marker genes shown in Fig. 1D of Olsen et al. https://www.biorxiv.org/content/10.1101/2020.05.04.077057v1 - these are highly expressed in their mesenchymal cluster on their UMAP.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 2.86e-04
Mean rank of genes in gene set: 4617.15
Rank on gene expression program of genes in gene set:

Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
CALD1 0.0034248 42 GTEx DepMap Descartes 12.46 1676.00
COL6A2 0.0033889 46 GTEx DepMap Descartes 2.83 574.80
BGN 0.0021902 109 GTEx DepMap Descartes 1.48 408.48
PRRX1 0.0020963 117 GTEx DepMap Descartes 1.98 319.96
SPARC 0.0016324 185 GTEx DepMap Descartes 5.15 877.48
COL1A2 0.0013263 254 GTEx DepMap Descartes 13.52 1351.25
COL3A1 0.0011973 301 GTEx DepMap Descartes 12.13 1295.73
COL1A1 0.0010090 374 GTEx DepMap Descartes 13.32 1330.68
MGP 0.0008822 451 GTEx DepMap Descartes 4.91 1600.61
LUM 0.0000726 3898 GTEx DepMap Descartes 1.60 323.77
LEPR -0.0000898 15749 GTEx DepMap Descartes 0.75 47.33
PDGFRA -0.0002293 18894 GTEx DepMap Descartes 0.25 21.86
DCN -0.0003064 19603 GTEx DepMap Descartes 1.90 162.81




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: 17416.42
Median rank of genes in gene set: 19230
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
SLIT3 0.0019308 140 GTEx DepMap Descartes 7.80 501.55
RGS5 0.0012262 292 GTEx DepMap Descartes 2.08 228.40
ARHGEF7 0.0011440 318 GTEx DepMap Descartes 2.53 256.96
SYNPO2 0.0008543 475 GTEx DepMap Descartes 2.82 124.05
CYGB 0.0007093 599 GTEx DepMap Descartes 0.35 113.99
EML4 0.0004654 941 GTEx DepMap Descartes 3.10 326.76
RUFY3 0.0002753 1539 GTEx DepMap Descartes 2.41 307.51
KLF13 0.0002037 1989 GTEx DepMap Descartes 0.67 55.51
KLHL23 0.0002021 2002 GTEx DepMap Descartes 0.78 111.54
GNB1 0.0001683 2308 GTEx DepMap Descartes 2.86 518.11
KLC1 0.0001630 2355 GTEx DepMap Descartes 1.05 41.26
AKAP12 0.0001378 2661 GTEx DepMap Descartes 3.82 271.78
HEY1 0.0000917 3449 GTEx DepMap Descartes 0.06 8.70
GLRX 0.0000888 3502 GTEx DepMap Descartes 0.27 43.68
TENM4 0.0000699 3978 GTEx DepMap Descartes 2.91 NA
ZNF91 0.0000512 4535 GTEx DepMap Descartes 1.25 124.63
RBMS3 0.0000501 4576 GTEx DepMap Descartes 4.66 323.53
TMEM108 0.0000487 4626 GTEx DepMap Descartes 1.73 131.69
NAPB 0.0000354 5175 GTEx DepMap Descartes 0.45 64.46
ANP32A 0.0000303 5453 GTEx DepMap Descartes 0.40 63.48
PARP6 0.0000278 5589 GTEx DepMap Descartes 0.37 58.30
DNAJC9 0.0000224 5914 GTEx DepMap Descartes 0.42 102.15
ZNF22 0.0000200 6067 GTEx DepMap Descartes 0.13 35.02
DKK1 0.0000138 6507 GTEx DepMap Descartes 0.01 2.38
SETD7 0.0000112 6711 GTEx DepMap Descartes 0.45 33.47
PPP2R3C 0.0000038 7430 GTEx DepMap Descartes 0.53 164.71
NPTX2 0.0000002 7913 GTEx DepMap Descartes 0.06 10.03
HK2 -0.0000021 8897 GTEx DepMap Descartes 0.12 12.24
STRA6 -0.0000034 9115 GTEx DepMap Descartes 0.09 18.06
DIABLO -0.0000039 9220 GTEx DepMap Descartes 0.00 0.09


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: 8.62e-67
Mean rank of genes in gene set: 5626.02
Median rank of genes in gene set: 2116
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
EDNRA 0.0062143 8 GTEx DepMap Descartes 1.42 255.37
EPS8 0.0053155 13 GTEx DepMap Descartes 5.53 807.95
COL4A2 0.0042830 25 GTEx DepMap Descartes 9.48 1043.05
COL4A1 0.0040172 30 GTEx DepMap Descartes 10.82 1150.26
PEAK1 0.0038406 33 GTEx DepMap Descartes 5.84 NA
PDE3A 0.0037155 37 GTEx DepMap Descartes 7.15 621.34
CALD1 0.0034248 42 GTEx DepMap Descartes 12.46 1676.00
COL6A2 0.0033889 46 GTEx DepMap Descartes 2.83 574.80
COL6A3 0.0032111 55 GTEx DepMap Descartes 4.68 302.41
EPHA3 0.0029052 64 GTEx DepMap Descartes 2.52 316.83
OLFML2A 0.0026301 76 GTEx DepMap Descartes 0.24 27.49
SPARCL1 0.0026104 77 GTEx DepMap Descartes 1.33 286.23
PTPRG 0.0024051 90 GTEx DepMap Descartes 8.94 613.93
ID3 0.0023468 94 GTEx DepMap Descartes 0.72 455.07
COL5A1 0.0023439 95 GTEx DepMap Descartes 2.96 238.14
TNS1 0.0023239 96 GTEx DepMap Descartes 2.75 179.42
NID2 0.0023053 97 GTEx DepMap Descartes 0.54 73.31
MAML2 0.0022815 100 GTEx DepMap Descartes 7.63 715.82
TFPI 0.0022243 105 GTEx DepMap Descartes 1.98 170.61
DLC1 0.0022182 106 GTEx DepMap Descartes 16.17 1383.65
BGN 0.0021902 109 GTEx DepMap Descartes 1.48 408.48
OLFML2B 0.0021544 113 GTEx DepMap Descartes 0.85 187.75
COL6A1 0.0021067 116 GTEx DepMap Descartes 1.83 286.96
PRRX1 0.0020963 117 GTEx DepMap Descartes 1.98 319.96
KANK2 0.0020909 119 GTEx DepMap Descartes 0.53 78.03
MICAL2 0.0019451 137 GTEx DepMap Descartes 2.30 235.28
NID1 0.0019281 142 GTEx DepMap Descartes 1.38 166.74
SVIL 0.0019049 145 GTEx DepMap Descartes 6.13 475.87
YAP1 0.0018603 151 GTEx DepMap Descartes 1.86 229.04
SASH1 0.0018464 153 GTEx DepMap Descartes 3.01 282.72


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: 1.00e+00
Mean rank of genes in gene set: 16808.02
Median rank of genes in gene set: 18262
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
SH3PXD2B 0.0005851 734 GTEx DepMap Descartes 1.29 102.44
PDE10A 0.0000580 4309 GTEx DepMap Descartes 3.36 184.48
SLC2A14 0.0000132 6547 GTEx DepMap Descartes 0.05 5.79
NPC1 -0.0000062 9624 GTEx DepMap Descartes 0.66 72.52
APOC1 -0.0000328 12630 GTEx DepMap Descartes 0.41 367.94
PEG3 -0.0000438 13381 GTEx DepMap Descartes 0.01 NA
PAPSS2 -0.0000455 13484 GTEx DepMap Descartes 1.19 145.91
INHA -0.0000463 13532 GTEx DepMap Descartes 0.02 9.14
FREM2 -0.0000478 13617 GTEx DepMap Descartes 0.04 1.05
IGF1R -0.0000852 15569 GTEx DepMap Descartes 4.21 180.73
CYP11A1 -0.0001028 16215 GTEx DepMap Descartes 0.38 50.92
FDXR -0.0001180 16709 GTEx DepMap Descartes 0.08 16.97
SCAP -0.0001349 17195 GTEx DepMap Descartes 0.43 49.06
BAIAP2L1 -0.0001448 17439 GTEx DepMap Descartes 0.22 24.10
CYP11B1 -0.0001453 17449 GTEx DepMap Descartes 0.52 39.87
POR -0.0001518 17598 GTEx DepMap Descartes 0.86 147.57
MC2R -0.0001628 17838 GTEx DepMap Descartes 0.09 7.92
DHCR7 -0.0001629 17840 GTEx DepMap Descartes 0.06 11.57
CYP17A1 -0.0001656 17895 GTEx DepMap Descartes 0.15 30.94
GSTA4 -0.0001667 17925 GTEx DepMap Descartes 0.44 126.69
SCARB1 -0.0001715 17988 GTEx DepMap Descartes 2.08 106.96
SH3BP5 -0.0001830 18179 GTEx DepMap Descartes 1.59 219.22
GRAMD1B -0.0001885 18262 GTEx DepMap Descartes 1.58 66.98
FDX1 -0.0001942 18368 GTEx DepMap Descartes 1.20 132.72
HMGCS1 -0.0001974 18428 GTEx DepMap Descartes 0.54 46.45
FDPS -0.0001976 18431 GTEx DepMap Descartes 0.57 143.53
SULT2A1 -0.0002012 18489 GTEx DepMap Descartes 0.11 22.17
ERN1 -0.0002204 18784 GTEx DepMap Descartes 0.82 42.57
CYB5B -0.0002279 18873 GTEx DepMap Descartes 0.51 55.89
TM7SF2 -0.0002320 18920 GTEx DepMap Descartes 0.10 24.31


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: 18858.84
Median rank of genes in gene set: 19805
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
SYNPO2 0.0008543 475 GTEx DepMap Descartes 2.82 124.05
FAT3 0.0001362 2683 GTEx DepMap Descartes 0.65 22.05
RPH3A -0.0001295 17040 GTEx DepMap Descartes 0.14 7.97
NPY -0.0002004 18474 GTEx DepMap Descartes 1.99 2254.69
GREM1 -0.0002037 18535 GTEx DepMap Descartes 0.33 12.90
EYA4 -0.0002150 18706 GTEx DepMap Descartes 0.39 28.85
MAB21L1 -0.0002189 18761 GTEx DepMap Descartes 0.15 30.94
NTRK1 -0.0002293 18897 GTEx DepMap Descartes 0.25 31.28
TMEFF2 -0.0002314 18914 GTEx DepMap Descartes 0.68 85.98
GAL -0.0002492 19110 GTEx DepMap Descartes 0.57 520.87
SLC6A2 -0.0002536 19149 GTEx DepMap Descartes 0.18 25.20
RGMB -0.0002560 19184 GTEx DepMap Descartes 0.31 34.62
TUBB2A -0.0002662 19285 GTEx DepMap Descartes 0.98 345.28
MAP1B -0.0002728 19343 GTEx DepMap Descartes 6.32 285.99
PLXNA4 -0.0002771 19387 GTEx DepMap Descartes 1.10 32.97
ANKFN1 -0.0002843 19444 GTEx DepMap Descartes 0.69 65.35
CNTFR -0.0002961 19542 GTEx DepMap Descartes 0.24 47.62
PTCHD1 -0.0003047 19595 GTEx DepMap Descartes 0.35 9.42
HMX1 -0.0003144 19652 GTEx DepMap Descartes 0.31 65.38
REEP1 -0.0003151 19655 GTEx DepMap Descartes 0.66 64.50
IL7 -0.0003325 19751 GTEx DepMap Descartes 2.18 486.08
MAB21L2 -0.0003461 19805 GTEx DepMap Descartes 0.06 14.54
EPHA6 -0.0003954 20010 GTEx DepMap Descartes 1.55 142.15
PRPH -0.0003978 20019 GTEx DepMap Descartes 0.90 249.97
RYR2 -0.0004031 20036 GTEx DepMap Descartes 4.47 103.71
HS3ST5 -0.0004053 20042 GTEx DepMap Descartes 0.80 85.48
STMN4 -0.0004061 20045 GTEx DepMap Descartes 0.46 109.84
MLLT11 -0.0004413 20133 GTEx DepMap Descartes 0.57 129.65
SLC44A5 -0.0004611 20185 GTEx DepMap Descartes 0.99 82.67
GAP43 -0.0004777 20216 GTEx DepMap Descartes 1.57 392.44


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: 1.00e+00
Mean rank of genes in gene set: 14594.98
Median rank of genes in gene set: 17447
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
ARHGAP29 0.0007564 558 GTEx DepMap Descartes 1.16 76.22
CYP26B1 0.0007143 597 GTEx DepMap Descartes 0.04 6.50
CDH13 0.0004392 998 GTEx DepMap Descartes 2.23 159.46
APLNR 0.0003613 1190 GTEx DepMap Descartes 0.08 15.44
CALCRL 0.0001213 2898 GTEx DepMap Descartes 0.95 88.94
MMRN2 0.0000659 4084 GTEx DepMap Descartes 0.10 13.09
CLDN5 0.0000574 4334 GTEx DepMap Descartes 0.11 22.93
SOX18 0.0000171 6266 GTEx DepMap Descartes 0.08 23.20
EHD3 0.0000149 6415 GTEx DepMap Descartes 0.26 24.53
ID1 -0.0000051 9448 GTEx DepMap Descartes 0.21 85.03
ECSCR -0.0000215 11662 GTEx DepMap Descartes 0.00 0.10
F8 -0.0000400 13116 GTEx DepMap Descartes 0.14 7.84
ROBO4 -0.0000643 14545 GTEx DepMap Descartes 0.07 8.79
IRX3 -0.0000713 14913 GTEx DepMap Descartes 0.01 1.42
TM4SF18 -0.0000773 15177 GTEx DepMap Descartes 0.04 5.17
PLVAP -0.0000786 15242 GTEx DepMap Descartes 0.22 53.21
ESM1 -0.0000887 15708 GTEx DepMap Descartes 0.06 19.21
HYAL2 -0.0000952 15962 GTEx DepMap Descartes 0.13 16.64
TMEM88 -0.0001040 16246 GTEx DepMap Descartes 0.04 22.75
CRHBP -0.0001085 16407 GTEx DepMap Descartes 0.03 7.49
FCGR2B -0.0001356 17215 GTEx DepMap Descartes 0.02 1.54
BTNL9 -0.0001448 17440 GTEx DepMap Descartes 0.09 13.58
RASIP1 -0.0001455 17454 GTEx DepMap Descartes 0.09 13.09
KANK3 -0.0001460 17467 GTEx DepMap Descartes 0.08 13.75
NPR1 -0.0001778 18101 GTEx DepMap Descartes 0.03 3.52
SHE -0.0001810 18152 GTEx DepMap Descartes 0.08 5.44
RAMP2 -0.0001841 18196 GTEx DepMap Descartes 0.10 64.74
TIE1 -0.0002036 18530 GTEx DepMap Descartes 0.08 10.70
CDH5 -0.0002046 18547 GTEx DepMap Descartes 0.11 13.49
KDR -0.0002117 18651 GTEx DepMap Descartes 0.13 11.75


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: 3.85e-05
Mean rank of genes in gene set: 6941.24
Median rank of genes in gene set: 924
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
CCDC102B 0.0081381 2 GTEx DepMap Descartes 8.98 2569.01
EDNRA 0.0062143 8 GTEx DepMap Descartes 1.42 255.37
ABCC9 0.0053157 12 GTEx DepMap Descartes 0.74 69.71
COL6A3 0.0032111 55 GTEx DepMap Descartes 4.68 302.41
PRRX1 0.0020963 117 GTEx DepMap Descartes 1.98 319.96
ADAMTS2 0.0020557 126 GTEx DepMap Descartes 1.94 208.41
ITGA11 0.0020519 127 GTEx DepMap Descartes 1.36 97.31
ACTA2 0.0017911 158 GTEx DepMap Descartes 1.79 888.81
CDH11 0.0016807 181 GTEx DepMap Descartes 3.68 337.69
COL1A2 0.0013263 254 GTEx DepMap Descartes 13.52 1351.25
POSTN 0.0013185 257 GTEx DepMap Descartes 2.98 535.40
LAMC3 0.0013068 260 GTEx DepMap Descartes 0.25 23.70
CD248 0.0012884 268 GTEx DepMap Descartes 0.13 30.96
COL3A1 0.0011973 301 GTEx DepMap Descartes 12.13 1295.73
PCDH18 0.0011239 323 GTEx DepMap Descartes 0.17 18.22
GLI2 0.0010849 335 GTEx DepMap Descartes 1.09 110.21
PAMR1 0.0010196 369 GTEx DepMap Descartes 0.54 99.63
COL1A1 0.0010090 374 GTEx DepMap Descartes 13.32 1330.68
FNDC1 0.0009891 388 GTEx DepMap Descartes 0.51 50.01
COL27A1 0.0009331 416 GTEx DepMap Descartes 0.68 61.56
MGP 0.0008822 451 GTEx DepMap Descartes 4.91 1600.61
ADAMTSL3 0.0008789 453 GTEx DepMap Descartes 1.58 137.90
COL12A1 0.0008653 462 GTEx DepMap Descartes 2.57 137.47
LRRC17 0.0007489 564 GTEx DepMap Descartes 0.22 66.27
PCOLCE 0.0004728 924 GTEx DepMap Descartes 0.51 205.44
MXRA5 0.0004657 940 GTEx DepMap Descartes 0.22 13.75
C7 0.0002686 1574 GTEx DepMap Descartes 4.44 500.50
ELN 0.0001540 2457 GTEx DepMap Descartes 0.86 172.20
PRICKLE1 0.0001346 2704 GTEx DepMap Descartes 3.27 325.36
LUM 0.0000726 3898 GTEx DepMap Descartes 1.60 323.77


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: 18637.21
Median rank of genes in gene set: 19629
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
LAMA3 0.0013579 245 GTEx DepMap Descartes 0.65 44.03
PNMT -0.0000472 13588 GTEx DepMap Descartes 0.01 5.80
SLC24A2 -0.0000873 15648 GTEx DepMap Descartes 0.17 5.53
PENK -0.0000917 15824 GTEx DepMap Descartes 0.03 22.58
SCG2 -0.0001063 16328 GTEx DepMap Descartes 2.87 770.92
ARC -0.0001474 17505 GTEx DepMap Descartes 0.08 13.17
ST18 -0.0001543 17661 GTEx DepMap Descartes 0.09 6.05
HTATSF1 -0.0001545 17667 GTEx DepMap Descartes 0.21 42.14
SLC18A1 -0.0001562 17704 GTEx DepMap Descartes 0.10 14.13
DGKK -0.0001668 17927 GTEx DepMap Descartes 0.07 3.89
C1QL1 -0.0001729 18013 GTEx DepMap Descartes 0.06 23.92
CNTN3 -0.0001881 18257 GTEx DepMap Descartes 0.17 12.15
INSM1 -0.0001900 18292 GTEx DepMap Descartes 0.05 10.61
GRID2 -0.0002090 18618 GTEx DepMap Descartes 0.80 51.52
TMEM130 -0.0002204 18783 GTEx DepMap Descartes 0.34 38.70
SLC35F3 -0.0002788 19401 GTEx DepMap Descartes 0.59 44.95
SORCS3 -0.0002846 19447 GTEx DepMap Descartes 0.25 14.56
CDH18 -0.0002933 19524 GTEx DepMap Descartes 0.55 42.74
MGAT4C -0.0002989 19565 GTEx DepMap Descartes 1.65 40.56
PCSK2 -0.0002991 19566 GTEx DepMap Descartes 0.35 28.00
CNTNAP5 -0.0003094 19618 GTEx DepMap Descartes 0.46 25.33
TBX20 -0.0003109 19629 GTEx DepMap Descartes 0.20 53.66
CDH12 -0.0003194 19683 GTEx DepMap Descartes 0.91 91.25
KSR2 -0.0003378 19773 GTEx DepMap Descartes 0.42 7.57
CHGB -0.0003477 19809 GTEx DepMap Descartes 1.58 421.04
GRM7 -0.0003482 19812 GTEx DepMap Descartes 0.70 76.19
SPOCK3 -0.0003484 19814 GTEx DepMap Descartes 0.34 46.25
GALNTL6 -0.0003516 19839 GTEx DepMap Descartes 0.82 96.86
PACRG -0.0003575 19862 GTEx DepMap Descartes 0.68 147.49
PCSK1N -0.0003742 19930 GTEx DepMap Descartes 1.26 655.64


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-01
Mean rank of genes in gene set: 10384.78
Median rank of genes in gene set: 12510.5
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
SPECC1 0.0046175 19 GTEx DepMap Descartes 1.77 158.44
MICAL2 0.0019451 137 GTEx DepMap Descartes 2.30 235.28
RAPGEF2 0.0010087 375 GTEx DepMap Descartes 2.79 208.62
SELENBP1 0.0006230 681 GTEx DepMap Descartes 0.04 10.45
RGS6 0.0003997 1084 GTEx DepMap Descartes 0.87 94.36
GYPC 0.0003295 1315 GTEx DepMap Descartes 0.18 64.18
SLC25A21 0.0002236 1849 GTEx DepMap Descartes 0.11 16.24
SOX6 0.0001847 2140 GTEx DepMap Descartes 2.45 142.62
TSPAN5 0.0001459 2542 GTEx DepMap Descartes 1.76 239.32
ABCB10 0.0001384 2648 GTEx DepMap Descartes 0.30 43.87
GYPE 0.0001061 3176 GTEx DepMap Descartes 0.04 14.04
TRAK2 0.0001052 3197 GTEx DepMap Descartes 0.53 43.81
RHD 0.0000983 3326 GTEx DepMap Descartes 0.10 20.97
CPOX 0.0000628 4175 GTEx DepMap Descartes 0.04 8.37
SPTB 0.0000500 4581 GTEx DepMap Descartes 0.15 6.80
CAT 0.0000324 5349 GTEx DepMap Descartes 0.29 68.17
HBG2 0.0000000 8302 GTEx DepMap Descartes 0.00 0.00
HBG1 -0.0000124 10598 GTEx DepMap Descartes 0.00 0.00
GYPA -0.0000150 10937 GTEx DepMap Descartes 0.01 0.88
HEMGN -0.0000205 11557 GTEx DepMap Descartes 0.00 0.80
HBZ -0.0000253 12006 GTEx DepMap Descartes 0.00 3.21
EPB42 -0.0000269 12154 GTEx DepMap Descartes 0.00 0.33
HBB -0.0000304 12442 GTEx DepMap Descartes 0.15 143.42
SPTA1 -0.0000322 12579 GTEx DepMap Descartes 0.01 0.38
RHCE -0.0000378 12998 GTEx DepMap Descartes 0.04 8.94
ALAS2 -0.0000381 13016 GTEx DepMap Descartes 0.00 0.77
RHAG -0.0000407 13163 GTEx DepMap Descartes 0.01 0.99
GYPB -0.0000421 13259 GTEx DepMap Descartes 0.01 5.33
HBM -0.0000453 13466 GTEx DepMap Descartes 0.00 1.94
AHSP -0.0000468 13563 GTEx DepMap Descartes 0.00 0.47


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: 1.00e+00
Mean rank of genes in gene set: 14574.94
Median rank of genes in gene set: 17198
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
AXL 0.0009547 402 GTEx DepMap Descartes 0.98 141.94
PTPRE 0.0009410 411 GTEx DepMap Descartes 1.92 195.20
ADAP2 0.0008936 442 GTEx DepMap Descartes 0.26 63.96
TGFBI 0.0006508 651 GTEx DepMap Descartes 0.64 85.26
CSF1R 0.0004679 934 GTEx DepMap Descartes 0.17 28.07
CTSC 0.0002144 1903 GTEx DepMap Descartes 0.60 58.86
RGL1 0.0001512 2489 GTEx DepMap Descartes 1.10 120.55
ITPR2 0.0000655 4091 GTEx DepMap Descartes 2.75 116.37
CTSD -0.0000058 9570 GTEx DepMap Descartes 0.00 0.06
SLC9A9 -0.0000139 10802 GTEx DepMap Descartes 1.68 281.95
CST3 -0.0000203 11535 GTEx DepMap Descartes 1.01 178.12
IFNGR1 -0.0000215 11665 GTEx DepMap Descartes 0.42 94.51
CYBB -0.0000505 13802 GTEx DepMap Descartes 0.01 1.10
C1QA -0.0000678 14736 GTEx DepMap Descartes 0.14 93.59
C1QC -0.0000713 14910 GTEx DepMap Descartes 0.08 44.31
C1QB -0.0000738 15024 GTEx DepMap Descartes 0.12 77.73
VSIG4 -0.0000763 15129 GTEx DepMap Descartes 0.02 4.06
MS4A7 -0.0000824 15429 GTEx DepMap Descartes 0.01 2.33
CD14 -0.0000899 15752 GTEx DepMap Descartes 0.10 40.52
RNASE1 -0.0000900 15759 GTEx DepMap Descartes 0.08 46.05
MPEG1 -0.0001140 16579 GTEx DepMap Descartes 0.04 6.56
SPP1 -0.0001172 16679 GTEx DepMap Descartes 0.71 252.37
ABCA1 -0.0001301 17051 GTEx DepMap Descartes 1.41 76.06
WWP1 -0.0001309 17074 GTEx DepMap Descartes 1.00 108.10
HLA-DRB1 -0.0001350 17198 GTEx DepMap Descartes 0.10 45.69
LGMN -0.0001418 17370 GTEx DepMap Descartes 0.46 111.14
HLA-DPA1 -0.0001591 17770 GTEx DepMap Descartes 0.21 26.48
CTSS -0.0001856 18216 GTEx DepMap Descartes 0.22 33.66
HCK -0.0001920 18329 GTEx DepMap Descartes 0.07 16.45
FGL2 -0.0001921 18331 GTEx DepMap Descartes 0.09 13.44


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: 7.46e-01
Mean rank of genes in gene set: 10854.57
Median rank of genes in gene set: 13979
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
COL18A1 0.0055041 11 GTEx DepMap Descartes 3.67 411.97
OLFML2A 0.0026301 76 GTEx DepMap Descartes 0.24 27.49
LAMA4 0.0020313 129 GTEx DepMap Descartes 2.70 241.02
SOX5 0.0020065 131 GTEx DepMap Descartes 6.60 628.56
COL25A1 0.0019690 134 GTEx DepMap Descartes 0.68 61.61
NRXN3 0.0018029 157 GTEx DepMap Descartes 5.87 385.35
COL5A2 0.0016322 186 GTEx DepMap Descartes 3.98 374.57
EDNRB 0.0011958 302 GTEx DepMap Descartes 0.27 38.81
LAMC1 0.0010900 333 GTEx DepMap Descartes 1.84 145.69
EGFLAM 0.0010090 373 GTEx DepMap Descartes 0.56 69.35
HMGA2 0.0010050 377 GTEx DepMap Descartes 0.23 18.78
LAMB1 0.0009592 401 GTEx DepMap Descartes 2.42 274.86
STARD13 0.0009264 424 GTEx DepMap Descartes 3.48 349.69
PLCE1 0.0008942 441 GTEx DepMap Descartes 0.78 40.83
PAG1 0.0008308 496 GTEx DepMap Descartes 1.77 101.04
IL1RAPL1 0.0008258 504 GTEx DepMap Descartes 1.61 264.48
VIM 0.0008063 517 GTEx DepMap Descartes 3.00 682.79
ADAMTS5 0.0002443 1704 GTEx DepMap Descartes 0.17 11.93
SLC35F1 0.0001383 2649 GTEx DepMap Descartes 0.98 96.62
PMP22 -0.0000084 9996 GTEx DepMap Descartes 1.02 298.53
KCTD12 -0.0000151 10955 GTEx DepMap Descartes 0.30 24.58
PTN -0.0000322 12575 GTEx DepMap Descartes 0.33 110.56
FIGN -0.0000463 13533 GTEx DepMap Descartes 1.75 116.20
MPZ -0.0000517 13863 GTEx DepMap Descartes 0.08 19.86
TRPM3 -0.0000535 13979 GTEx DepMap Descartes 0.70 23.38
ERBB3 -0.0000761 15120 GTEx DepMap Descartes 0.06 4.51
GRIK3 -0.0000780 15218 GTEx DepMap Descartes 0.31 18.38
SOX10 -0.0000963 16004 GTEx DepMap Descartes 0.07 11.87
VCAN -0.0001079 16387 GTEx DepMap Descartes 4.91 224.70
MDGA2 -0.0001134 16567 GTEx DepMap Descartes 1.06 57.55


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: 1.91e-03
Mean rank of genes in gene set: 7840.41
Median rank of genes in gene set: 4542
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
TRPC6 0.0040030 31 GTEx DepMap Descartes 0.54 90.07
PDE3A 0.0037155 37 GTEx DepMap Descartes 7.15 621.34
ARHGAP6 0.0034017 45 GTEx DepMap Descartes 1.46 177.81
INPP4B 0.0032353 52 GTEx DepMap Descartes 2.94 231.80
ANGPT1 0.0026846 72 GTEx DepMap Descartes 0.59 98.39
MYH9 0.0017460 167 GTEx DepMap Descartes 2.86 244.84
MYLK 0.0017175 173 GTEx DepMap Descartes 1.06 71.15
FLNA 0.0012772 271 GTEx DepMap Descartes 1.08 81.67
DOK6 0.0010552 346 GTEx DepMap Descartes 1.56 101.06
HIPK2 0.0010378 360 GTEx DepMap Descartes 2.25 89.99
LIMS1 0.0010221 367 GTEx DepMap Descartes 2.76 370.43
VCL 0.0009316 419 GTEx DepMap Descartes 2.60 210.79
ACTN1 0.0008905 445 GTEx DepMap Descartes 2.40 325.33
GSN 0.0008729 458 GTEx DepMap Descartes 1.69 165.87
SLC24A3 0.0008063 516 GTEx DepMap Descartes 1.62 271.27
SLC2A3 0.0007768 537 GTEx DepMap Descartes 2.33 339.71
TLN1 0.0007347 575 GTEx DepMap Descartes 0.63 44.96
TGFB1 0.0006164 691 GTEx DepMap Descartes 0.63 149.58
LTBP1 0.0006048 708 GTEx DepMap Descartes 1.62 155.59
RAP1B 0.0005561 785 GTEx DepMap Descartes 2.02 88.56
STOM 0.0005106 857 GTEx DepMap Descartes 0.60 114.97
TPM4 0.0004315 1013 GTEx DepMap Descartes 2.23 289.19
ITGB3 0.0001195 2935 GTEx DepMap Descartes 0.00 0.08
ZYX 0.0001107 3093 GTEx DepMap Descartes 0.26 70.12
GP9 0.0000509 4542 GTEx DepMap Descartes 0.00 0.12
GP1BA 0.0000276 5603 GTEx DepMap Descartes 0.02 4.01
PPBP 0.0000068 7127 GTEx DepMap Descartes 0.00 0.72
SPN -0.0000023 8920 GTEx DepMap Descartes 0.00 0.01
THBS1 -0.0000087 10034 GTEx DepMap Descartes 3.83 308.94
PF4 -0.0000096 10177 GTEx DepMap Descartes 0.00 1.18


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: 6.34e-01
Mean rank of genes in gene set: 10589.23
Median rank of genes in gene set: 14997
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
DOCK10 0.0014324 224 GTEx DepMap Descartes 2.39 207.21
NCALD 0.0010546 347 GTEx DepMap Descartes 1.89 332.96
SP100 0.0008894 446 GTEx DepMap Descartes 1.36 163.11
ETS1 0.0008466 482 GTEx DepMap Descartes 1.23 152.94
PLEKHA2 0.0008393 485 GTEx DepMap Descartes 0.90 107.21
ARID5B 0.0008312 493 GTEx DepMap Descartes 2.37 201.45
IFI16 0.0008114 512 GTEx DepMap Descartes 0.99 154.31
ARHGAP15 0.0007431 570 GTEx DepMap Descartes 2.20 516.88
RCSD1 0.0006824 624 GTEx DepMap Descartes 0.32 42.04
ITPKB 0.0004508 972 GTEx DepMap Descartes 0.55 57.28
HLA-B 0.0004071 1059 GTEx DepMap Descartes 0.58 235.11
ARHGDIB 0.0003734 1152 GTEx DepMap Descartes 0.16 91.91
MSN 0.0003623 1185 GTEx DepMap Descartes 0.89 133.41
PRKCH 0.0003173 1363 GTEx DepMap Descartes 1.03 167.02
HLA-C 0.0002341 1777 GTEx DepMap Descartes 0.37 121.32
WIPF1 0.0002272 1822 GTEx DepMap Descartes 1.18 151.31
FOXP1 0.0001890 2104 GTEx DepMap Descartes 0.37 25.60
SAMD3 0.0001718 2278 GTEx DepMap Descartes 0.48 78.05
STK39 0.0001407 2622 GTEx DepMap Descartes 1.57 251.62
HLA-A 0.0001197 2932 GTEx DepMap Descartes 0.75 85.53
B2M 0.0001188 2948 GTEx DepMap Descartes 4.25 1112.82
LEF1 0.0001011 3276 GTEx DepMap Descartes 0.75 117.42
CCND3 0.0000074 7062 GTEx DepMap Descartes 1.02 274.84
NKG7 -0.0000732 14997 GTEx DepMap Descartes 0.01 7.56
EVL -0.0000823 15421 GTEx DepMap Descartes 2.08 310.45
CCL5 -0.0001233 16857 GTEx DepMap Descartes 0.04 15.43
MBNL1 -0.0001400 17329 GTEx DepMap Descartes 6.35 582.63
CD44 -0.0001636 17854 GTEx DepMap Descartes 2.11 202.87
ANKRD44 -0.0002249 18839 GTEx DepMap Descartes 2.06 147.80
GNG2 -0.0002464 19084 GTEx DepMap Descartes 1.08 144.97


Embryonic Pausing Signatures Up
Embryonic pausing signature upregulated genes from Supplementary Table 6 of Rehman et al. Cell 2021. These genes are upregulated in paused ESCs and diapaused embryos.
Wilcoxon ranksum test P-value for gene set overrepresentation: 2.70e-01
Mean rank of genes in gene set: 9331.79
Median rank of genes in gene set: 10737.5
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
YPEL2 0.0008580 470 GTEx DepMap Descartes 0.95 102.88
ACSS1 0.0005416 802 GTEx DepMap Descartes 0.16 22.83
SPRY1 0.0004579 961 GTEx DepMap Descartes 0.55 120.67
APOE 0.0002932 1458 GTEx DepMap Descartes 1.92 1037.61
HEXB 0.0000710 3939 GTEx DepMap Descartes 0.34 93.53
LY6G6E 0.0000000 8395 GTEx DepMap Descartes 0.00 0.00
PDCD4 -0.0000087 10040 GTEx DepMap Descartes 0.68 104.60
HEXA -0.0000194 11435 GTEx DepMap Descartes 0.04 3.35
RENBP -0.0000389 13064 GTEx DepMap Descartes 0.07 25.57
ALDH6A1 -0.0000761 15121 GTEx DepMap Descartes 0.11 11.37
CCNG2 -0.0000963 16008 GTEx DepMap Descartes 0.26 26.85
CTSL -0.0000996 16122 GTEx DepMap Descartes 0.45 NA
DPP7 -0.0001011 16157 GTEx DepMap Descartes 0.26 92.47
AUH -0.0001170 16673 GTEx DepMap Descartes 1.19 387.70


Embryonic Pausing Signatures Down
Embryonic pausing signature downregulated genes from Supplementary Table 6 of Rehman et al. Cell 2021. These genes are downregulated in paused ESCs and diapaused embryos.
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.00e+00
Mean rank of genes in gene set: 13799.19
Median rank of genes in gene set: 15085
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
ID3 0.0023468 94 GTEx DepMap Descartes 0.72 455.07
MGMT 0.0002798 1512 GTEx DepMap Descartes 0.99 118.96
DUSP14 0.0002334 1778 GTEx DepMap Descartes 0.11 28.34
FAM118B 0.0001996 2020 GTEx DepMap Descartes 0.19 55.26
SEC13 0.0001666 2328 GTEx DepMap Descartes 0.40 101.25
HDLBP 0.0001352 2698 GTEx DepMap Descartes 1.20 109.84
EIF2B2 0.0000994 3307 GTEx DepMap Descartes 0.11 14.25
MRPS11 0.0000993 3309 GTEx DepMap Descartes 0.17 27.80
TMEM109 0.0000700 3971 GTEx DepMap Descartes 0.09 24.29
DRG2 0.0000645 4134 GTEx DepMap Descartes 0.12 12.47
INO80E 0.0000630 4166 GTEx DepMap Descartes 0.15 20.28
TMEM39B 0.0000528 4480 GTEx DepMap Descartes 0.16 45.31
PELO 0.0000400 4974 GTEx DepMap Descartes 0.00 0.08
ANKRD37 0.0000326 5337 GTEx DepMap Descartes 0.07 24.72
PRADC1 0.0000232 5852 GTEx DepMap Descartes 0.05 23.21
MRPL12 0.0000204 6033 GTEx DepMap Descartes 0.00 0.02
ARPC1B 0.0000131 6562 GTEx DepMap Descartes 0.14 43.18
TIPIN 0.0000130 6571 GTEx DepMap Descartes 0.15 44.84
UBE2V1 0.0000104 6783 GTEx DepMap Descartes 0.02 3.47
RPS27L 0.0000065 7157 GTEx DepMap Descartes 0.51 50.37
PMF1 0.0000056 7243 GTEx DepMap Descartes 0.00 0.47
PHGDH 0.0000013 7748 GTEx DepMap Descartes 0.08 15.25
TOMM40 -0.0000021 8896 GTEx DepMap Descartes 0.15 25.42
NAA10 -0.0000040 9256 GTEx DepMap Descartes 0.05 16.05
PSMB10 -0.0000058 9554 GTEx DepMap Descartes 0.02 13.12
CITED1 -0.0000097 10192 GTEx DepMap Descartes 0.00 0.24
DPH3 -0.0000151 10952 GTEx DepMap Descartes 0.07 10.09
DGCR6 -0.0000202 11531 GTEx DepMap Descartes 0.00 0.06
TOMM40L -0.0000265 12097 GTEx DepMap Descartes 0.03 6.23
CCNE1 -0.0000283 12282 GTEx DepMap Descartes 0.03 8.57


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: 9.48e-03
Mean rank of genes in gene set: 5885.5
Rank on gene expression program of genes in gene set:
Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
EBF2 0.0037318 35 GTEx DepMap Descartes 1.87 272.71
PRRX1 0.0020963 117 GTEx DepMap Descartes 1.98 319.96
SMOC2 0.0019563 136 GTEx DepMap Descartes 1.34 308.13
OLFML1 0.0006505 652 GTEx DepMap Descartes 0.07 16.31
MXRA5 0.0004657 940 GTEx DepMap Descartes 0.22 13.75
NTRK2 0.0003649 1179 GTEx DepMap Descartes 0.93 63.78
F10 0.0000689 4005 GTEx DepMap Descartes 0.05 16.59
ANGPTL1 -0.0001029 16220 GTEx DepMap Descartes 0.16 25.74
SFRP1 -0.0001171 16677 GTEx DepMap Descartes 0.51 59.67
PDGFRA -0.0002293 18894 GTEx DepMap Descartes 0.25 21.86


Double-negative thymocytes: Double-negative thymocytes (curated markers)
the early immature thymocytes from the thymus in the double negative (co-receptors CD4- and CD8-) stage:
Wilcoxon ranksum test P-value for gene set overrepresentation: 9.52e-03
Mean rank of genes in gene set: 2249.33
Rank on gene expression program of genes in gene set:

Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
CD99 0.0007294 585 GTEx DepMap Descartes 0.81 399.26
HES1 0.0003612 1193 GTEx DepMap Descartes 0.21 71.25
FXYD2 0.0000401 4970 GTEx DepMap Descartes 0.00 0.78


T cells: Follicular helper T cells (model markers)
specialised CD4+ T cell subpopulation found in the periphery within B cell follicles and stimulating the cognate follicular B cells for class-switching:
Wilcoxon ranksum test P-value for gene set overrepresentation: 7.90e-02
Mean rank of genes in gene set: 7122.57
Rank on gene expression program of genes in gene set:

Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
CH25H 0.0001413 2605 GTEx DepMap Descartes 0.04 13.53
SOCS3 0.0000716 3925 GTEx DepMap Descartes 0.44 98.44
GPIHBP1 0.0000545 4423 GTEx DepMap Descartes 0.01 2.44
HOXB5 0.0000542 4434 GTEx DepMap Descartes 0.00 0.13
IGHV5-78 -0.0000024 8941 GTEx DepMap Descartes 0.00 0.00
FOXH1 -0.0000151 10950 GTEx DepMap Descartes 0.00 0.44
KLRB1 -0.0000648 14580 GTEx DepMap Descartes 0.02 5.78