Program: 6. Cancer Associated Fibroblast: Intermediate [Inf:AP].

Program: 6. Cancer Associated Fibroblast: Intermediate [Inf:AP].

Program description and justification of annotation: 6.
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 BICC1 0.0369479 BicC family RNA binding protein 1 GTEx DepMap Descartes 4.36 3517.55
2 PKHD1 0.0277657 PKHD1 ciliary IPT domain containing fibrocystin/polyductin GTEx DepMap Descartes 1.27 379.69
3 ANKRD1 0.0232933 ankyrin repeat domain 1 GTEx DepMap Descartes 0.38 1078.91
4 ELF3 0.0219177 E74 like ETS transcription factor 3 GTEx DepMap Descartes 0.73 723.61
5 SDR42E1 0.0188045 short chain dehydrogenase/reductase family 42E, member 1 GTEx DepMap Descartes 0.00 0.00
6 KRT18 0.0174844 keratin 18 GTEx DepMap Descartes 0.88 1669.47
7 CXCL2 0.0161554 C-X-C motif chemokine ligand 2 GTEx DepMap Descartes 0.42 1476.53
8 GLIS3 0.0144890 GLIS family zinc finger 3 GTEx DepMap Descartes 1.03 562.11
9 C3 0.0144585 complement C3 GTEx DepMap Descartes 2.28 1947.58
10 DEFB1 0.0143510 defensin beta 1 GTEx DepMap Descartes 0.26 2705.81
11 ABCC3 0.0142238 ATP binding cassette subfamily C member 3 GTEx DepMap Descartes 0.78 622.07
12 TM4SF4 0.0136228 transmembrane 4 L six family member 4 GTEx DepMap Descartes 0.57 1388.98
13 RASEF 0.0131801 RAS and EF-hand domain containing GTEx DepMap Descartes 0.18 130.50
14 KRT8 0.0130800 keratin 8 GTEx DepMap Descartes 0.56 791.55
15 ACSM3 0.0129766 acyl-CoA synthetase medium chain family member 3 GTEx DepMap Descartes 0.32 465.25
16 HNF1B 0.0116198 HNF1 homeobox B GTEx DepMap Descartes 0.12 143.96
17 CLDN1 0.0113368 claudin 1 GTEx DepMap Descartes 0.30 339.41
18 DOCK5 0.0110541 dedicator of cytokinesis 5 GTEx DepMap Descartes 0.52 225.31
19 KRT7 0.0108366 keratin 7 GTEx DepMap Descartes 0.11 277.66
20 IL1RAP 0.0106606 interleukin 1 receptor accessory protein GTEx DepMap Descartes 0.27 190.33
21 KIFC3 0.0104793 kinesin family member C3 GTEx DepMap Descartes 0.36 533.68
22 NNMT 0.0104140 nicotinamide N-methyltransferase GTEx DepMap Descartes 0.73 1529.76
23 SAMD12 0.0103534 sterile alpha motif domain containing 12 GTEx DepMap Descartes 0.24 110.35
24 COL27A1 0.0102972 collagen type XXVII alpha 1 chain GTEx DepMap Descartes 0.33 175.13
25 ANXA4 0.0100495 annexin A4 GTEx DepMap Descartes 0.43 390.31
26 DMKN 0.0099492 dermokine GTEx DepMap Descartes 0.06 116.16
27 RBPMS 0.0098590 RNA binding protein, mRNA processing factor GTEx DepMap Descartes 0.65 810.27
28 SLC4A4 0.0098357 solute carrier family 4 member 4 GTEx DepMap Descartes 0.20 120.86
29 VTCN1 0.0096389 V-set domain containing T cell activation inhibitor 1 GTEx DepMap Descartes 0.12 229.22
30 WWC1 0.0095233 WW and C2 domain containing 1 GTEx DepMap Descartes 0.65 387.85
31 LCN2 0.0094710 lipocalin 2 GTEx DepMap Descartes 0.15 1058.30
32 AGT 0.0093476 angiotensinogen GTEx DepMap Descartes 0.14 227.33
33 GRB7 0.0092268 growth factor receptor bound protein 7 GTEx DepMap Descartes 0.07 159.46
34 NR5A2 0.0088952 nuclear receptor subfamily 5 group A member 2 GTEx DepMap Descartes 0.35 235.02
35 LAD1 0.0088560 ladinin 1 GTEx DepMap Descartes 0.12 249.12
36 BCO2 0.0087978 beta-carotene oxygenase 2 GTEx DepMap Descartes 0.22 284.39
37 NEAT1 0.0083548 nuclear paraspeckle assembly transcript 1 GTEx DepMap Descartes 6.53 1096.73
38 RRAD 0.0083341 RRAD, Ras related glycolysis inhibitor and calcium channel regulator GTEx DepMap Descartes 0.14 597.14
39 BAIAP2L1 0.0080607 BAR/IMD domain containing adaptor protein 2 like 1 GTEx DepMap Descartes 0.26 276.16
40 LIF 0.0079466 LIF interleukin 6 family cytokine GTEx DepMap Descartes 0.19 225.14
41 SLC44A3 0.0078792 solute carrier family 44 member 3 GTEx DepMap Descartes 0.14 221.45
42 FGFR3 0.0078669 fibroblast growth factor receptor 3 GTEx DepMap Descartes 0.12 151.30
43 BACE2 0.0076422 beta-secretase 2 GTEx DepMap Descartes 0.24 NA
44 NFKBIZ 0.0076255 NFKB inhibitor zeta GTEx DepMap Descartes 0.29 323.74
45 DSG2 0.0076003 desmoglein 2 GTEx DepMap Descartes 0.06 29.88
46 TMC5 0.0074894 transmembrane channel like 5 GTEx DepMap Descartes 0.14 125.79
47 SLC12A2 0.0073958 solute carrier family 12 member 2 GTEx DepMap Descartes 0.41 303.61
48 YBX3 0.0072406 Y-box binding protein 3 GTEx DepMap Descartes 0.27 NA
49 COL18A1 0.0071853 collagen type XVIII alpha 1 chain GTEx DepMap Descartes 0.69 464.95
50 TNFAIP2 0.0071589 TNF alpha induced protein 2 GTEx DepMap Descartes 0.24 290.82


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UMAP plots showing activity of gene expression program identified in community:6. Cancer Associated Fibroblast: Intermediate [Inf:AP]

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
AIZARANI_LIVER_C7_EPCAM_POS_BILE_DUCT_CELLS_2 1.55e-31 64.40 34.82 1.04e-28 1.04e-28
25BICC1, PKHD1, ANKRD1, ELF3, KRT18, GLIS3, DEFB1, ABCC3, TM4SF4, KRT8, CLDN1, KRT7, KIFC3, COL27A1, ANXA4, RBPMS, SLC4A4, WWC1, AGT, LAD1, LIF, FGFR3, BACE2, DSG2, SLC12A2
 219
AIZARANI_LIVER_C4_EPCAM_POS_BILE_DUCT_CELLS_1 7.43e-26 53.20 28.25 1.66e-23 4.99e-23
21BICC1, PKHD1, ELF3, KRT18, GLIS3, C3, DEFB1, ABCC3, TM4SF4, KRT8, CLDN1, KRT7, COL27A1, ANXA4, RBPMS, SLC4A4, AGT, LAD1, FGFR3, BACE2, SLC12A2
 191
AIZARANI_LIVER_C24_EPCAM_POS_BILE_DUCT_CELLS_3 1.76e-19 38.31 19.60 2.96e-17 1.18e-16
17ELF3, KRT18, DEFB1, TM4SF4, KRT8, CLDN1, KRT7, ANXA4, SLC4A4, VTCN1, LCN2, LAD1, BACE2, DSG2, TMC5, SLC12A2, TNFAIP2
 185
AIZARANI_LIVER_C39_EPCAM_POS_BILE_DUCT_CELLS_4 6.00e-18 35.00 17.69 8.05e-16 4.03e-15
16BICC1, PKHD1, ANKRD1, ELF3, KRT18, DEFB1, TM4SF4, KRT8, CLDN1, KRT7, ANXA4, LAD1, LIF, DSG2, SLC12A2, TNFAIP2
 184
MURARO_PANCREAS_DUCTAL_CELL 3.44e-28 28.78 14.91 1.16e-25 2.31e-25
37BICC1, PKHD1, ANKRD1, ELF3, KRT18, CXCL2, GLIS3, C3, DEFB1, ABCC3, RASEF, KRT8, HNF1B, CLDN1, KRT7, SAMD12, ANXA4, RBPMS, SLC4A4, VTCN1, WWC1, LCN2, AGT, NR5A2, LAD1, NEAT1, BAIAP2L1, LIF, FGFR3, BACE2, NFKBIZ, DSG2, TMC5, SLC12A2, YBX3, COL18A1, TNFAIP2
 1276
CUI_DEVELOPING_HEART_C6_EPICARDIAL_CELL 8.57e-12 21.58 10.09 8.21e-10 5.75e-09
12BICC1, KRT18, C3, KRT8, CLDN1, KRT7, NNMT, ANXA4, SLC4A4, WWC1, BCO2, NFKBIZ
 195
DESCARTES_FETAL_PANCREAS_DUCTAL_CELLS 1.45e-09 23.05 9.63 1.18e-07 9.74e-07
9PKHD1, ELF3, DEFB1, ACSM3, ANXA4, SLC4A4, VTCN1, LAD1, FGFR3
 128
LAKE_ADULT_KIDNEY_C17_COLLECTING_SYSTEM_PCS_STRESSED_DISSOC_SUBSET 1.58e-09 15.40 7.02 1.18e-07 1.06e-06
11ELF3, GLIS3, DEFB1, SAMD12, RBPMS, WWC1, NEAT1, BACE2, NFKBIZ, YBX3, COL18A1
 240
MURARO_PANCREAS_ACINAR_CELL 4.02e-14 12.76 6.88 4.49e-12 2.70e-11
21ELF3, KRT18, CXCL2, C3, ABCC3, RASEF, KRT8, CLDN1, KRT7, ANXA4, RBPMS, LCN2, NR5A2, LAD1, NEAT1, BAIAP2L1, BACE2, NFKBIZ, TMC5, SLC12A2, YBX3
 731
TRAVAGLINI_LUNG_MUCOUS_CELL 5.39e-07 17.23 6.41 2.78e-05 3.61e-04
7C3, SLC4A4, LCN2, LIF, BACE2, TMC5, TNFAIP2
 125
DURANTE_ADULT_OLFACTORY_NEUROEPITHELIUM_SUSTENTACULAR_CELLS 3.46e-05 25.26 6.32 1.22e-03 2.32e-02
4ELF3, KRT18, KRT8, LCN2
 47
DURANTE_ADULT_OLFACTORY_NEUROEPITHELIUM_RESPIRATORY_COLUMNAR_CELLS 1.81e-04 31.85 5.95 5.05e-03 1.21e-01
3ELF3, KRT18, KRT8
 28
LAKE_ADULT_KIDNEY_C4_PROXIMAL_TUBULE_EPITHELIAL_CELLS_S2 3.74e-07 14.17 5.66 2.09e-05 2.51e-04
8BICC1, PKHD1, GLIS3, ACSM3, RBPMS, WWC1, NEAT1, COL18A1
 176
DURANTE_ADULT_OLFACTORY_NEUROEPITHELIUM_OLFACTORY_MICROVILLAR_CELLS 5.56e-05 22.15 5.58 1.78e-03 3.73e-02
4KRT18, KRT8, KRT7, ANXA4
 53
TRAVAGLINI_LUNG_GOBLET_CELL 1.67e-06 14.43 5.38 7.98e-05 1.12e-03
7C3, KRT7, SLC4A4, VTCN1, LCN2, BACE2, SLC12A2
 148
DURANTE_ADULT_OLFACTORY_NEUROEPITHELIUM_RESPIRATORY_HORIZONTAL_BASAL_CELLS 2.96e-04 26.56 5.01 7.65e-03 1.99e-01
3ELF3, KRT18, KRT8
 33
DESCARTES_FETAL_EYE_CORNEAL_AND_CONJUNCTIVAL_EPITHELIAL_CELLS 3.53e-07 11.73 4.95 2.09e-05 2.37e-04
9ELF3, KRT18, KRT8, ACSM3, CLDN1, KRT7, VTCN1, LCN2, TMC5
 243
HU_FETAL_RETINA_RPE 1.46e-07 11.08 4.89 9.78e-06 9.78e-05
10KRT18, KRT8, COL27A1, SLC4A4, WWC1, NEAT1, FGFR3, BACE2, DSG2, COL18A1
 292
DESCARTES_FETAL_PLACENTA_PAEP_MECOM_POSITIVE_CELLS 3.99e-06 12.56 4.70 1.78e-04 2.68e-03
7PKHD1, DEFB1, NNMT, SAMD12, VTCN1, LCN2, LIF
 169
DESCARTES_FETAL_SPLEEN_MESOTHELIAL_CELLS 1.01e-05 10.82 4.05 3.98e-04 6.77e-03
7KRT18, KRT8, KRT7, SLC4A4, WWC1, RRAD, DSG2
 195

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mSigDB Hallmark Gene Sets:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
HALLMARK_ESTROGEN_RESPONSE_EARLY 1.08e-03 7.12 2.18 5.40e-02 5.40e-02
5ELF3, KRT18, KRT8, WWC1, LAD1
 200
HALLMARK_IL2_STAT5_SIGNALING 4.30e-02 4.07 0.80 7.25e-01 1.00e+00
3ANXA4, LIF, NFKBIZ
 199
HALLMARK_TNFA_SIGNALING_VIA_NFKB 4.35e-02 4.05 0.80 7.25e-01 1.00e+00
3CXCL2, LIF, TNFAIP2
 200
HALLMARK_UV_RESPONSE_DN 1.10e-01 3.67 0.43 9.77e-01 1.00e+00
2ANXA4, RBPMS
 144
HALLMARK_UV_RESPONSE_UP 1.28e-01 3.34 0.39 9.77e-01 1.00e+00
2CXCL2, RRAD
 158
HALLMARK_INFLAMMATORY_RESPONSE 1.85e-01 2.63 0.31 9.77e-01 1.00e+00
2SLC4A4, LIF
 200
HALLMARK_P53_PATHWAY 1.85e-01 2.63 0.31 9.77e-01 1.00e+00
2RRAD, LIF
 200
HALLMARK_APICAL_SURFACE 1.61e-01 5.93 0.14 9.77e-01 1.00e+00
1PKHD1
 44
HALLMARK_PROTEIN_SECRETION 3.17e-01 2.68 0.07 9.77e-01 1.00e+00
1KRT18
 96
HALLMARK_ANDROGEN_RESPONSE 3.28e-01 2.58 0.06 9.77e-01 1.00e+00
1KRT8
 100
HALLMARK_SPERMATOGENESIS 4.15e-01 1.90 0.05 9.77e-01 1.00e+00
1SLC12A2
 135
HALLMARK_COAGULATION 4.22e-01 1.86 0.05 9.77e-01 1.00e+00
1C3
 138
HALLMARK_FATTY_ACID_METABOLISM 4.66e-01 1.62 0.04 9.77e-01 1.00e+00
1ACSM3
 158
HALLMARK_APOPTOSIS 4.72e-01 1.59 0.04 9.77e-01 1.00e+00
1KRT18
 161
HALLMARK_G2M_CHECKPOINT 5.47e-01 1.28 0.03 9.77e-01 1.00e+00
1SLC12A2
 200
HALLMARK_ADIPOGENESIS 5.47e-01 1.28 0.03 9.77e-01 1.00e+00
1C3
 200
HALLMARK_ESTROGEN_RESPONSE_LATE 5.47e-01 1.28 0.03 9.77e-01 1.00e+00
1FGFR3
 200
HALLMARK_MYOGENESIS 5.47e-01 1.28 0.03 9.77e-01 1.00e+00
1KIFC3
 200
HALLMARK_INTERFERON_GAMMA_RESPONSE 5.47e-01 1.28 0.03 9.77e-01 1.00e+00
1TNFAIP2
 200
HALLMARK_APICAL_JUNCTION 5.47e-01 1.28 0.03 9.77e-01 1.00e+00
1GRB7
 200

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KEGG Pathways:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
KEGG_MATURITY_ONSET_DIABETES_OF_THE_YOUNG 4.39e-03 22.60 2.52 8.16e-01 8.16e-01
2HNF1B, NR5A2
 25
KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION 2.07e-02 9.64 1.11 1.00e+00 1.00e+00
2KRT18, CLDN1
 56
KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION 8.44e-02 3.05 0.60 1.00e+00 1.00e+00
3CXCL2, IL1RAP, LIF
 265
KEGG_TIGHT_JUNCTION 9.54e-02 4.01 0.47 1.00e+00 1.00e+00
2CLDN1, YBX3
 132
KEGG_RENIN_ANGIOTENSIN_SYSTEM 6.56e-02 15.93 0.37 1.00e+00 1.00e+00
1AGT
 17
KEGG_PROXIMAL_TUBULE_BICARBONATE_RECLAMATION 8.77e-02 11.59 0.28 1.00e+00 1.00e+00
1SLC4A4
 23
KEGG_NICOTINATE_AND_NICOTINAMIDE_METABOLISM 9.13e-02 11.08 0.26 1.00e+00 1.00e+00
1NNMT
 24
KEGG_BUTANOATE_METABOLISM 1.27e-01 7.73 0.19 1.00e+00 1.00e+00
1ACSM3
 34
KEGG_BLADDER_CANCER 1.54e-01 6.22 0.15 1.00e+00 1.00e+00
1FGFR3
 42
KEGG_ABC_TRANSPORTERS 1.61e-01 5.93 0.14 1.00e+00 1.00e+00
1ABCC3
 44
KEGG_VIBRIO_CHOLERAE_INFECTION 1.94e-01 4.81 0.12 1.00e+00 1.00e+00
1SLC12A2
 54
KEGG_NOD_LIKE_RECEPTOR_SIGNALING_PATHWAY 2.19e-01 4.18 0.10 1.00e+00 1.00e+00
1CXCL2
 62
KEGG_COMPLEMENT_AND_COAGULATION_CASCADES 2.40e-01 3.75 0.09 1.00e+00 1.00e+00
1C3
 69
KEGG_LEISHMANIA_INFECTION 2.49e-01 3.59 0.09 1.00e+00 1.00e+00
1C3
 72
KEGG_ARRHYTHMOGENIC_RIGHT_VENTRICULAR_CARDIOMYOPATHY_ARVC 2.55e-01 3.49 0.09 1.00e+00 1.00e+00
1DSG2
 74
KEGG_APOPTOSIS 2.93e-01 2.97 0.07 1.00e+00 1.00e+00
1IL1RAP
 87
KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION 3.69e-01 2.22 0.05 1.00e+00 1.00e+00
1CLDN1
 116
KEGG_CELL_ADHESION_MOLECULES_CAMS 4.10e-01 1.93 0.05 1.00e+00 1.00e+00
1CLDN1
 133
KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS 4.24e-01 1.85 0.05 1.00e+00 1.00e+00
1C3
 139
KEGG_JAK_STAT_SIGNALING_PATHWAY 4.59e-01 1.66 0.04 1.00e+00 1.00e+00
1LIF
 155

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CHR Positional Gene Sets:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
chr3q28 6.27e-03 18.58 2.09 1.00e+00 1.00e+00
2CLDN1, IL1RAP
 30
chr1q32 8.51e-02 3.03 0.60 1.00e+00 1.00e+00
3ELF3, NR5A2, LAD1
 266
chr17q12 1.09e-01 3.69 0.43 1.00e+00 1.00e+00
2HNF1B, GRB7
 143
chr12q13 2.07e-01 1.98 0.39 1.00e+00 1.00e+00
3KRT18, KRT8, KRT7
 407
chr16p12 1.36e-01 3.21 0.38 1.00e+00 1.00e+00
2ACSM3, TMC5
 164
chr11q23 1.92e-01 2.57 0.30 1.00e+00 1.00e+00
2NNMT, BCO2
 205
chr21q22 3.99e-01 1.48 0.17 1.00e+00 1.00e+00
2BACE2, COL18A1
 353
chr5q34 1.41e-01 6.89 0.17 1.00e+00 1.00e+00
1WWC1
 38
chr3q12 1.67e-01 5.67 0.14 1.00e+00 1.00e+00
1NFKBIZ
 46
chr9q32 1.71e-01 5.54 0.13 1.00e+00 1.00e+00
1COL27A1
 47
chr1p12 1.77e-01 5.31 0.13 1.00e+00 1.00e+00
1VTCN1
 49
chr8p12 2.34e-01 3.86 0.09 1.00e+00 1.00e+00
1RBPMS
 67
chr16q21 2.55e-01 3.49 0.09 1.00e+00 1.00e+00
1KIFC3
 74
chr18q12 3.17e-01 2.68 0.07 1.00e+00 1.00e+00
1DSG2
 96
chr1p21 3.25e-01 2.60 0.06 1.00e+00 1.00e+00
1SLC44A3
 99
chr9p24 3.31e-01 2.55 0.06 1.00e+00 1.00e+00
1GLIS3
 101
chr16q23 3.39e-01 2.48 0.06 1.00e+00 1.00e+00
1SDR42E1
 104
chr5q23 3.57e-01 2.32 0.06 1.00e+00 1.00e+00
1SLC12A2
 111
chr10q21 3.69e-01 2.22 0.05 1.00e+00 1.00e+00
1BICC1
 116
chr8p21 3.99e-01 2.01 0.05 1.00e+00 1.00e+00
1DOCK5
 128

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Transcription Factor Targets:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
RGTTAMWNATT_HNF1_01 1.04e-05 20.11 6.05 1.18e-02 1.18e-02
5HNF1B, AGT, GRB7, NR5A2, SLC12A2
 74
HNF1_Q6 4.58e-04 6.82 2.35 1.73e-01 5.19e-01
6PKHD1, TM4SF4, HNF1B, SLC4A4, SLC44A3, SLC12A2
 256
HNF1_01 2.64e-03 5.76 1.77 4.84e-01 1.00e+00
5PKHD1, TM4SF4, HNF1B, SLC4A4, NR5A2
 246
HES2_TARGET_GENES 3.28e-04 3.46 1.72 1.73e-01 3.72e-01
14ANKRD1, CXCL2, C3, ABCC3, TM4SF4, KRT8, KRT7, IL1RAP, KIFC3, NNMT, LCN2, BCO2, NEAT1, NFKBIZ
 1420
ZNF318_TARGET_GENES 2.64e-03 4.17 1.57 4.84e-01 1.00e+00
7ANKRD1, KRT18, ABCC3, KRT8, KIFC3, NEAT1, YBX3
 495
TBX1_TARGET_GENES 6.24e-03 5.91 1.53 7.85e-01 1.00e+00
4C3, KRT7, IL1RAP, LCN2
 188
MED25_TARGET_GENES 9.53e-03 7.39 1.45 9.00e-01 1.00e+00
3KRT8, KRT7, NEAT1
 111
HNF1_C 1.60e-02 4.44 1.15 1.00e+00 1.00e+00
4PKHD1, HNF1B, BACE2, SLC12A2
 249
E12_Q6 1.96e-02 4.16 1.08 1.00e+00 1.00e+00
4KRT8, HNF1B, WWC1, GRB7
 265
HNF4_Q6 2.10e-02 4.07 1.06 1.00e+00 1.00e+00
4KIFC3, GRB7, NR5A2, LAD1
 271
AREB6_01 2.18e-02 4.03 1.05 1.00e+00 1.00e+00
4ANKRD1, KRT8, SAMD12, RRAD
 274
HMG20B_TARGET_GENES 3.48e-02 2.07 0.98 1.00e+00 1.00e+00
12ANKRD1, C3, KRT8, ACSM3, KIFC3, COL27A1, ANXA4, AGT, GRB7, BCO2, NEAT1, NFKBIZ
 1922
NR1H4_TARGET_GENES 3.36e-02 3.50 0.91 1.00e+00 1.00e+00
4ELF3, C3, TM4SF4, AGT
 315
ZNF85_TARGET_GENES 3.77e-02 3.37 0.87 1.00e+00 1.00e+00
4ACSM3, DOCK5, BCO2, NFKBIZ
 327
LHX2_TARGET_GENES 7.22e-02 2.04 0.82 1.00e+00 1.00e+00
8CXCL2, ABCC3, TM4SF4, KRT8, DMKN, NR5A2, LAD1, NEAT1
 1177
STAT5A_04 5.12e-02 3.78 0.75 1.00e+00 1.00e+00
3ANKRD1, GRB7, NR5A2
 214
TATAAA_TATA_01 1.40e-01 1.82 0.74 1.00e+00 1.00e+00
8GLIS3, DEFB1, TM4SF4, KRT8, AGT, NR5A2, BCO2, LIF
 1317
TGACCTY_ERR1_Q2 1.09e-01 1.93 0.73 1.00e+00 1.00e+00
7ELF3, HNF1B, RBPMS, WWC1, LCN2, NR5A2, FGFR3
 1064
TEF1_Q6 5.90e-02 3.56 0.70 1.00e+00 1.00e+00
3ANKRD1, ELF3, NNMT
 227
GCM_Q2 7.05e-02 3.30 0.65 1.00e+00 1.00e+00
3ANKRD1, WWC1, GRB7
 245

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GO Biological Processes:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
GOBP_RESPONSE_TO_HYDROSTATIC_PRESSURE 2.31e-04 129.66 11.45 4.32e-01 1.00e+00
2KRT8, COL18A1
 6
GOBP_HYPEROSMOTIC_RESPONSE 1.44e-04 34.58 6.44 3.60e-01 1.00e+00
3CLDN1, SLC12A2, YBX3
 26
GOBP_RESPONSE_TO_WATER 1.37e-03 43.30 4.59 1.00e+00 1.00e+00
2KRT8, COL18A1
 14
GOBP_HEPATOCYTE_APOPTOTIC_PROCESS 1.37e-03 43.30 4.59 1.00e+00 1.00e+00
2KRT18, KRT8
 14
GOBP_HEPATOCYTE_DIFFERENTIATION 1.80e-03 37.11 3.99 1.00e+00 1.00e+00
2KRT18, HNF1B
 16
GOBP_CELL_DIFFERENTIATION_INVOLVED_IN_EMBRYONIC_PLACENTA_DEVELOPMENT 3.72e-03 24.78 2.74 1.00e+00 1.00e+00
2KRT8, LIF
 23
GOBP_CORNIFICATION 1.01e-03 9.97 2.56 1.00e+00 1.00e+00
4KRT18, KRT8, KRT7, DSG2
 113
GOBP_EPITHELIAL_CELL_DIFFERENTIATION 2.15e-05 5.18 2.45 1.61e-01 1.61e-01
12PKHD1, ELF3, KRT18, KRT8, HNF1B, CLDN1, KRT7, ANXA4, NR5A2, LIF, DSG2, COL18A1
 775
GOBP_BONE_GROWTH 4.74e-03 21.66 2.42 1.00e+00 1.00e+00
2COL27A1, FGFR3
 26
GOBP_POSITIVE_REGULATION_OF_INFLAMMATORY_RESPONSE 1.83e-03 8.43 2.17 1.00e+00 1.00e+00
4C3, AGT, NEAT1, NFKBIZ
 133
GOBP_CELL_CELL_JUNCTION_ORGANIZATION 1.31e-03 6.81 2.09 1.00e+00 1.00e+00
5PKHD1, CLDN1, KIFC3, AGT, DSG2
 209
GOBP_EPITHELIAL_CELL_MORPHOGENESIS 6.69e-03 17.94 2.02 1.00e+00 1.00e+00
2PKHD1, COL18A1
 31
GOBP_RESPONSE_TO_OSMOTIC_STRESS 4.15e-03 10.09 1.97 1.00e+00 1.00e+00
3CLDN1, SLC12A2, YBX3
 82
GOBP_CELL_JUNCTION_MAINTENANCE 7.12e-03 17.34 1.95 1.00e+00 1.00e+00
2CLDN1, KIFC3
 32
GOBP_EPITHELIUM_DEVELOPMENT 1.17e-04 3.86 1.92 3.60e-01 8.79e-01
14PKHD1, ELF3, KRT18, C3, KRT8, HNF1B, CLDN1, KRT7, ANXA4, AGT, NR5A2, LIF, DSG2, COL18A1
 1275
GOBP_MAINTENANCE_OF_BLOOD_BRAIN_BARRIER 7.55e-03 16.78 1.89 1.00e+00 1.00e+00
2CLDN1, SLC12A2
 33
GOBP_POSITIVE_REGULATION_OF_MORPHOGENESIS_OF_AN_EPITHELIUM 7.55e-03 16.78 1.89 1.00e+00 1.00e+00
2AGT, LIF
 33
GOBP_VASCULAR_TRANSPORT 5.05e-03 9.38 1.83 1.00e+00 1.00e+00
3ABCC3, SLC4A4, SLC12A2
 88
GOBP_KIDNEY_MORPHOGENESIS 5.05e-03 9.38 1.83 1.00e+00 1.00e+00
3HNF1B, AGT, LIF
 88
GOBP_RENAL_TUBULE_DEVELOPMENT 5.37e-03 9.17 1.79 1.00e+00 1.00e+00
3HNF1B, AGT, LIF
 90

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Immunological Gene Sets:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
GSE20715_0H_VS_24H_OZONE_LUNG_DN 1.19e-05 10.54 3.95 1.45e-02 5.79e-02
7ELF3, KRT18, C3, ABCC3, KRT8, DOCK5, LCN2
 200
GSE21774_CD62L_POS_CD56_BRIGHT_VS_CD62L_NEG_CD56_DIM_NK_CELL_UP 1.19e-05 10.54 3.95 1.45e-02 5.79e-02
7GLIS3, C3, KIFC3, DMKN, LCN2, BAIAP2L1, SLC44A3
 200
GSE21379_WT_VS_SAP_KO_TFH_CD4_TCELL_UP 1.19e-05 10.54 3.95 1.45e-02 5.79e-02
7KRT18, C3, ABCC3, DOCK5, DMKN, LCN2, DSG2
 200
GSE27670_CTRL_VS_BLIMP1_TRANSDUCED_GC_BCELL_DN 1.19e-05 10.54 3.95 1.45e-02 5.79e-02
7PKHD1, CXCL2, SLC4A4, WWC1, BAIAP2L1, NFKBIZ, DSG2
 200
GSE21360_SECONDARY_VS_QUATERNARY_MEMORY_CD8_TCELL_UP 7.41e-05 9.68 3.33 7.22e-02 3.61e-01
6CXCL2, DMKN, RBPMS, LCN2, NFKBIZ, TNFAIP2
 182
GSE34179_THPOK_KO_VS_WT_VA14I_NKTCELL_DN 1.20e-04 8.83 3.04 8.61e-02 5.86e-01
6C3, TM4SF4, ANXA4, WWC1, LAD1, LIF
 199
GSE20715_0H_VS_48H_OZONE_TLR4_KO_LUNG_DN 1.24e-04 8.78 3.02 8.61e-02 6.03e-01
6ELF3, KRT18, CXCL2, KRT8, DMKN, LCN2
 200
GSE1112_HY_CD8AB_VS_HY_CD8AA_THYMOCYTE_RTOC_CULTURE_DN 9.02e-04 7.43 2.27 3.29e-01 1.00e+00
5CXCL2, GLIS3, C3, DEFB1, NFKBIZ
 192
GSE9509_LPS_VS_LPS_AND_IL10_STIM_IL10_KO_MACROPHAGE_20MIN_UP 9.44e-04 7.35 2.25 3.29e-01 1.00e+00
5C3, RBPMS, NEAT1, BACE2, NFKBIZ
 194
GSE19888_ADENOSINE_A3R_ACT_VS_TCELL_MEMBRANES_ACT_AND_A3R_INH_PRETREAT_IN_MAST_CELL_DN 1.03e-03 7.19 2.20 3.29e-01 1.00e+00
5GRB7, LAD1, NEAT1, BAIAP2L1, FGFR3
 198
GSE20715_0H_VS_24H_OZONE_TLR4_KO_LUNG_DN 1.08e-03 7.12 2.18 3.29e-01 1.00e+00
5ELF3, KRT18, CXCL2, IL1RAP, LCN2
 200
GSE3982_NEUTROPHIL_VS_CENT_MEMORY_CD4_TCELL_UP 1.08e-03 7.12 2.18 3.29e-01 1.00e+00
5DOCK5, IL1RAP, LCN2, YBX3, TNFAIP2
 200
GSE9316_IL6_KO_VS_IFNG_KO_INVIVO_EXPANDED_CD4_TCELL_DN 1.08e-03 7.12 2.18 3.29e-01 1.00e+00
5CXCL2, NNMT, LIF, NFKBIZ, TNFAIP2
 200
GSE12392_IFNAR_KO_VS_IFNB_KO_CD8_NEG_SPLEEN_DC_DN 1.08e-03 7.12 2.18 3.29e-01 1.00e+00
5ELF3, CXCL2, RRAD, FGFR3, NFKBIZ
 200
GSE22443_NAIVE_VS_ACT_AND_IL2_TREATED_CD8_TCELL_DN 1.08e-03 7.12 2.18 3.29e-01 1.00e+00
5ANKRD1, ELF3, KRT18, C3, COL18A1
 200
GSE46606_UNSTIM_VS_CD40L_IL2_IL5_1DAY_STIMULATED_IRF4HIGH_SORTED_BCELL_DN 1.08e-03 7.12 2.18 3.29e-01 1.00e+00
5RASEF, RRAD, LIF, NFKBIZ, TNFAIP2
 200
GSE36891_UNSTIM_VS_POLYIC_TLR3_STIM_PERITONEAL_MACROPHAGE_UP 2.76e-03 7.50 1.93 6.06e-01 1.00e+00
4CXCL2, LIF, NFKBIZ, TNFAIP2
 149
GSE4590_SMALL_VS_LARGE_PRE_BCELL_DN 3.55e-03 6.97 1.80 6.06e-01 1.00e+00
4ELF3, DOCK5, RBPMS, GRB7
 160
GSE32255_WT_UNSTIM_VS_JMJD2D_KNOCKDOWN_4H_LPS_STIM_DC_DN 4.67e-03 6.43 1.66 6.06e-01 1.00e+00
4SAMD12, ANXA4, BCO2, BACE2
 173
GSE21360_TERTIARY_VS_QUATERNARY_MEMORY_CD8_TCELL_DN 5.06e-03 6.28 1.62 6.06e-01 1.00e+00
4C3, RBPMS, LCN2, LAD1
 177

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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
PKHD1 2 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None The TIG domain is potentially DNA-binding but there is no literature evidence to suggest that PKHD1 is a TF. Membrane protein that operates upstream in the signaling cascade leading to NFKB (PMID: 21300060)
ELF3 4 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
GLIS3 8 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
HNF1B 16 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
IL1RAP 20 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None None
ANXA4 25 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None None
AGT 32 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None None
NR5A2 34 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
NFKBIZ 44 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None None
YBX3 48 Yes Known motif Monomer or homomultimer 100 perc ID - in vitro None Identical DBD to YBX1. Might also bind RNA.
MYRF 64 Yes Known motif Monomer or homomultimer High-throughput in vitro None Mouse ortholog binds a highly similar motif.
ANXA3 72 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None Protein operates far upstream on the signaling cascade.
PLXNB1 81 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None Protein is a semaphorin receptor that operates far upstream on the signaling cascade.
BHLHE40 96 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
SMAD3 99 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
ZFP36 100 No ssDNA/RNA binding Not a DNA binding protein No motif None RNA binding protein (PMID: 10330172).
MLXIPL 102 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
ATF3 103 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
MET 117 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None Its a cell surface receptor and kinase - included only because Vasquerizas 2009 included it with an x.
RUNX1 118 Yes Known motif Monomer or homomultimer In vivo/Misc source Only known motifs are from Transfac or HocoMoco - origin is uncertain 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
NB02_ACGATGTGTGCCTGCA-1 Hepatocytes 0.12 1258.14
Raw ScoresHepatocytes: 0.26, iPS_cells:CRL2097_foreskin-derived:d20_hepatic_diff: 0.2, Epithelial_cells:bronchial: 0.2, Smooth_muscle_cells:vascular: 0.2, Smooth_muscle_cells:vascular:IL-17: 0.2, Chondrocytes:MSC-derived: 0.2, Fibroblasts:breast: 0.19, Tissue_stem_cells:BM_MSC:TGFb3: 0.19, Endothelial_cells:lymphatic:TNFa_48h: 0.19, Endothelial_cells:lymphatic: 0.19
NB02_GTCAAGTAGAATTGTG-1 iPS_cells:CRL2097_foreskin-derived:d20_hepatic_diff 0.07 755.74
Raw ScoresTissue_stem_cells:BM_MSC:TGFb3: 0.25, Smooth_muscle_cells:vascular:IL-17: 0.25, Smooth_muscle_cells:vascular: 0.25, Osteoblasts: 0.24, Tissue_stem_cells:BM_MSC:BMP2: 0.24, Fibroblasts:breast: 0.24, Tissue_stem_cells:BM_MSC: 0.24, iPS_cells:adipose_stem_cells: 0.24, Tissue_stem_cells:BM_MSC:osteogenic: 0.24, Chondrocytes:MSC-derived: 0.24
NB02_CGAGAAGGTCGCATAT-1 iPS_cells:CRL2097_foreskin-derived:d20_hepatic_diff 0.05 631.81
Raw ScoresiPS_cells:CRL2097_foreskin: 0.15, Fibroblasts:breast: 0.14, Smooth_muscle_cells:vascular: 0.14, Smooth_muscle_cells:vascular:IL-17: 0.14, Tissue_stem_cells:BM_MSC:TGFb3: 0.14, Osteoblasts: 0.14, Tissue_stem_cells:BM_MSC: 0.13, Osteoblasts:BMP2: 0.13, iPS_cells:adipose_stem_cells: 0.13, Smooth_muscle_cells:bronchial: 0.13
NB02_GTACTTTGTATTCTCT-1 iPS_cells:CRL2097_foreskin-derived:d20_hepatic_diff 0.06 617.59
Raw ScoresHepatocytes: 0.16, Fibroblasts:breast: 0.16, iPS_cells:adipose_stem_cells: 0.15, Smooth_muscle_cells:vascular: 0.15, Osteoblasts: 0.15, Osteoblasts:BMP2: 0.15, iPS_cells:CRL2097_foreskin: 0.15, Smooth_muscle_cells:vascular:IL-17: 0.14, iPS_cells:skin_fibroblast: 0.14, Smooth_muscle_cells:bronchial: 0.14
NB02_GGACAGACACAACGTT-1 Hepatocytes 0.11 579.18
Raw ScoresHepatocytes: 0.24, Smooth_muscle_cells:vascular:IL-17: 0.2, Fibroblasts:breast: 0.2, Smooth_muscle_cells:vascular: 0.2, Tissue_stem_cells:BM_MSC:TGFb3: 0.2, Osteoblasts: 0.2, Smooth_muscle_cells:bronchial: 0.2, Osteoblasts:BMP2: 0.2, Smooth_muscle_cells:bronchial:vit_D: 0.19, Tissue_stem_cells:BM_MSC: 0.19
NB02_CTTAGGACAAGTCTGT-1 Smooth_muscle_cells:vascular:IL-17 0.06 520.28
Raw ScoresHepatocytes: 0.15, Fibroblasts:breast: 0.15, iPS_cells:adipose_stem_cells: 0.15, Smooth_muscle_cells:vascular:IL-17: 0.14, Chondrocytes:MSC-derived: 0.14, Tissue_stem_cells:BM_MSC:TGFb3: 0.14, Smooth_muscle_cells:vascular: 0.14, iPS_cells:CRL2097_foreskin: 0.14, iPS_cells:skin_fibroblast: 0.14, Smooth_muscle_cells:bronchial: 0.14
NB02_CGAATGTCATGGTCAT-1 Fibroblasts:breast 0.06 477.00
Raw ScoresFibroblasts:breast: 0.13, Smooth_muscle_cells:vascular: 0.13, Smooth_muscle_cells:bronchial: 0.13, Smooth_muscle_cells:bronchial:vit_D: 0.13, Tissue_stem_cells:iliac_MSC: 0.13, iPS_cells:CRL2097_foreskin: 0.13, Tissue_stem_cells:BM_MSC:TGFb3: 0.13, Osteoblasts: 0.13, Tissue_stem_cells:BM_MSC:BMP2: 0.12, Smooth_muscle_cells:vascular:IL-17: 0.12
NB02_TCAGCAACAGCTTAAC-1 iPS_cells:CRL2097_foreskin-derived:d20_hepatic_diff 0.03 431.82
Raw ScoresHepatocytes: 0.11, iPS_cells:CRL2097_foreskin-derived:d20_hepatic_diff: 0.1, Osteoblasts:BMP2: 0.09, Chondrocytes:MSC-derived: 0.09, Epithelial_cells:bladder: 0.09, Osteoblasts: 0.09, Tissue_stem_cells:BM_MSC:TGFb3: 0.09, iPS_cells:CRL2097_foreskin: 0.09, Fibroblasts:breast: 0.09, Smooth_muscle_cells:vascular: 0.09
NB02_TTGGAACCAAGTCTAC-1 Neurons:Schwann_cell 0.06 422.45
Raw ScoresSmooth_muscle_cells:vascular: 0.16, Smooth_muscle_cells:vascular:IL-17: 0.16, Fibroblasts:breast: 0.15, Osteoblasts:BMP2: 0.15, Hepatocytes: 0.15, iPS_cells:CRL2097_foreskin: 0.15, Osteoblasts: 0.15, Smooth_muscle_cells:bronchial: 0.15, Tissue_stem_cells:BM_MSC: 0.14, Smooth_muscle_cells:bronchial:vit_D: 0.14
NB02_ACTGTCCCATGTCGAT-1 iPS_cells:CRL2097_foreskin-derived:d20_hepatic_diff 0.04 410.20
Raw ScoresOsteoblasts: 0.12, Hepatocytes: 0.12, Smooth_muscle_cells:vascular: 0.12, Smooth_muscle_cells:vascular:IL-17: 0.11, Fibroblasts:breast: 0.11, Endothelial_cells:lymphatic:TNFa_48h: 0.11, Osteoblasts:BMP2: 0.11, Chondrocytes:MSC-derived: 0.11, Tissue_stem_cells:BM_MSC:TGFb3: 0.11, Tissue_stem_cells:iliac_MSC: 0.11
NB02_GGGTCTGCAAGTAATG-1 Hepatocytes 0.09 401.06
Raw ScoresHepatocytes: 0.17, Smooth_muscle_cells:vascular: 0.14, Osteoblasts:BMP2: 0.14, Osteoblasts: 0.13, Smooth_muscle_cells:vascular:IL-17: 0.13, Smooth_muscle_cells:bronchial: 0.13, Fibroblasts:breast: 0.13, Smooth_muscle_cells:bronchial:vit_D: 0.13, Tissue_stem_cells:iliac_MSC: 0.13, iPS_cells:CRL2097_foreskin: 0.13
NB02_GCATGCGTCACTCCTG-1 Tissue_stem_cells:BM_MSC:osteogenic 0.04 382.13
Raw ScoresHepatocytes: 0.13, Smooth_muscle_cells:vascular:IL-17: 0.13, Chondrocytes:MSC-derived: 0.13, Smooth_muscle_cells:vascular: 0.13, Osteoblasts:BMP2: 0.12, Tissue_stem_cells:BM_MSC:osteogenic: 0.12, Endothelial_cells:lymphatic:TNFa_48h: 0.12, Tissue_stem_cells:BM_MSC:BMP2: 0.12, Osteoblasts: 0.12, Smooth_muscle_cells:bronchial: 0.12
NB02_GGTGAAGAGGCATGGT-1 Hepatocytes 0.11 367.52
Raw ScoresHepatocytes: 0.21, Smooth_muscle_cells:vascular: 0.17, Smooth_muscle_cells:vascular:IL-17: 0.16, Tissue_stem_cells:BM_MSC:TGFb3: 0.16, Tissue_stem_cells:BM_MSC:BMP2: 0.16, Fibroblasts:breast: 0.15, Smooth_muscle_cells:bronchial: 0.15, Smooth_muscle_cells:bronchial:vit_D: 0.15, Osteoblasts: 0.15, Chondrocytes:MSC-derived: 0.15
NB02_CTCGAGGAGGAACTGC-1 iPS_cells:CRL2097_foreskin-derived:d20_hepatic_diff 0.04 355.70
Raw ScoresHepatocytes: 0.13, Fibroblasts:breast: 0.13, Smooth_muscle_cells:bronchial: 0.13, iPS_cells:CRL2097_foreskin: 0.13, Smooth_muscle_cells:bronchial:vit_D: 0.12, Chondrocytes:MSC-derived: 0.12, Osteoblasts:BMP2: 0.12, Osteoblasts: 0.12, Smooth_muscle_cells:vascular:IL-17: 0.12, Smooth_muscle_cells:vascular: 0.12
NB02_CGAGAAGTCAGCATGT-1 Chondrocytes:MSC-derived 0.11 353.52
Raw ScoresChondrocytes:MSC-derived: 0.2, Fibroblasts:breast: 0.2, Osteoblasts: 0.2, Tissue_stem_cells:BM_MSC:TGFb3: 0.19, Tissue_stem_cells:BM_MSC: 0.19, Tissue_stem_cells:BM_MSC:BMP2: 0.19, Tissue_stem_cells:BM_MSC:osteogenic: 0.19, Smooth_muscle_cells:vascular:IL-17: 0.19, iPS_cells:adipose_stem_cells: 0.19, Smooth_muscle_cells:vascular: 0.18
NB02_ATGGGAGTCACGAAGG-1 Fibroblasts:breast 0.06 311.61
Raw ScoresFibroblasts:breast: 0.14, Smooth_muscle_cells:vascular: 0.13, Tissue_stem_cells:BM_MSC:TGFb3: 0.13, Tissue_stem_cells:BM_MSC:BMP2: 0.13, Smooth_muscle_cells:vascular:IL-17: 0.13, Osteoblasts: 0.13, Tissue_stem_cells:BM_MSC: 0.13, iPS_cells:adipose_stem_cells: 0.12, Tissue_stem_cells:BM_MSC:osteogenic: 0.12, Chondrocytes:MSC-derived: 0.12
NB02_CCGTTCAAGACTGTAA-1 Hepatocytes 0.05 307.08
Raw ScoresHepatocytes: 0.13, Tissue_stem_cells:BM_MSC:TGFb3: 0.11, Endothelial_cells:lymphatic:TNFa_48h: 0.11, Tissue_stem_cells:BM_MSC:BMP2: 0.11, Endothelial_cells:lymphatic: 0.11, Chondrocytes:MSC-derived: 0.11, Smooth_muscle_cells:bronchial: 0.11, iPS_cells:CRL2097_foreskin: 0.1, Smooth_muscle_cells:bronchial:vit_D: 0.1, Osteoblasts: 0.1
NB02_TGGCCAGTCTTGCAAG-1 Hepatocytes 0.08 301.88
Raw ScoresHepatocytes: 0.18, Tissue_stem_cells:BM_MSC:TGFb3: 0.15, Smooth_muscle_cells:vascular:IL-17: 0.15, Osteoblasts: 0.15, Smooth_muscle_cells:vascular: 0.15, Chondrocytes:MSC-derived: 0.15, Osteoblasts:BMP2: 0.15, Smooth_muscle_cells:bronchial: 0.14, Tissue_stem_cells:BM_MSC: 0.14, Smooth_muscle_cells:bronchial:vit_D: 0.14
NB02_GCGAGAATCTTCGGTC-1 iPS_cells:CRL2097_foreskin-derived:d20_hepatic_diff 0.04 301.64
Raw ScoresHepatocytes: 0.13, Tissue_stem_cells:BM_MSC:TGFb3: 0.12, Tissue_stem_cells:BM_MSC:BMP2: 0.12, Tissue_stem_cells:BM_MSC: 0.12, Osteoblasts:BMP2: 0.12, Osteoblasts: 0.11, Smooth_muscle_cells:vascular:IL-17: 0.11, Tissue_stem_cells:BM_MSC:osteogenic: 0.11, Smooth_muscle_cells:bronchial: 0.11, Smooth_muscle_cells:vascular: 0.11
NB02_TACTCGCTCTGATACG-1 iPS_cells:CRL2097_foreskin-derived:d20_hepatic_diff 0.04 286.11
Raw ScoresEndothelial_cells:lymphatic:TNFa_48h: 0.13, Smooth_muscle_cells:vascular: 0.13, Hepatocytes: 0.13, Smooth_muscle_cells:vascular:IL-17: 0.13, Tissue_stem_cells:BM_MSC: 0.13, Fibroblasts:breast: 0.12, Endothelial_cells:HUVEC:VEGF: 0.12, Endothelial_cells:lymphatic: 0.12, Tissue_stem_cells:BM_MSC:BMP2: 0.12, Osteoblasts: 0.12
NB02_ATGCGATGTCCTGCTT-1 Hepatocytes 0.05 283.88
Raw ScoresSmooth_muscle_cells:vascular: 0.12, Smooth_muscle_cells:vascular:IL-17: 0.12, Chondrocytes:MSC-derived: 0.12, Osteoblasts:BMP2: 0.12, Osteoblasts: 0.12, Tissue_stem_cells:BM_MSC: 0.12, Fibroblasts:breast: 0.11, iPS_cells:CRL2097_foreskin: 0.11, Tissue_stem_cells:BM_MSC:osteogenic: 0.11, Hepatocytes: 0.11
NB02_GTCTTCGTCTTAACCT-1 iPS_cells:CRL2097_foreskin-derived:d20_hepatic_diff 0.05 277.56
Raw ScoresiPS_cells:CRL2097_foreskin-derived:d20_hepatic_diff: 0.11, Hepatocytes: 0.1, Tissue_stem_cells:BM_MSC:TGFb3: 0.1, Smooth_muscle_cells:vascular:IL-17: 0.1, Tissue_stem_cells:BM_MSC:BMP2: 0.1, Osteoblasts: 0.1, Chondrocytes:MSC-derived: 0.1, Smooth_muscle_cells:vascular: 0.1, iPS_cells:adipose_stem_cells: 0.1, Osteoblasts:BMP2: 0.09
NB02_CCGGTAGCATGATCCA-1 Smooth_muscle_cells:vascular:IL-17 0.05 273.24
Raw ScoresTissue_stem_cells:BM_MSC:TGFb3: 0.14, Smooth_muscle_cells:vascular: 0.14, Smooth_muscle_cells:vascular:IL-17: 0.13, Tissue_stem_cells:BM_MSC:BMP2: 0.13, Fibroblasts:breast: 0.13, Smooth_muscle_cells:bronchial: 0.13, Osteoblasts:BMP2: 0.13, Endothelial_cells:lymphatic:TNFa_48h: 0.13, Tissue_stem_cells:BM_MSC: 0.13, Smooth_muscle_cells:bronchial:vit_D: 0.13
NB02_TGAGGGACAGCTGCTG-1 iPS_cells:CRL2097_foreskin-derived:d20_hepatic_diff 0.07 270.43
Raw ScoresHepatocytes: 0.15, Fibroblasts:breast: 0.15, Smooth_muscle_cells:vascular: 0.15, Smooth_muscle_cells:bronchial: 0.15, Smooth_muscle_cells:vascular:IL-17: 0.14, Osteoblasts: 0.14, iPS_cells:CRL2097_foreskin: 0.14, iPS_cells:CRL2097_foreskin-derived:d20_hepatic_diff: 0.14, Smooth_muscle_cells:bronchial:vit_D: 0.14, Osteoblasts:BMP2: 0.14
NB02_CGTCAGGTCAACACAC-1 Hepatocytes 0.04 265.57
Raw ScoresOsteoblasts: 0.1, Osteoblasts:BMP2: 0.1, Tissue_stem_cells:BM_MSC:TGFb3: 0.1, Fibroblasts:breast: 0.1, Neurons:Schwann_cell: 0.1, Smooth_muscle_cells:vascular:IL-17: 0.1, Tissue_stem_cells:BM_MSC:BMP2: 0.1, iPS_cells:CRL2097_foreskin-derived:d20_hepatic_diff: 0.1, Smooth_muscle_cells:vascular: 0.1, iPS_cells:CRL2097_foreskin: 0.1
NB02_ATTCTACCAAACTGTC-1 Tissue_stem_cells:BM_MSC 0.13 260.47
Raw ScoresFibroblasts:breast: 0.2, Chondrocytes:MSC-derived: 0.19, Tissue_stem_cells:BM_MSC: 0.19, Smooth_muscle_cells:vascular:IL-17: 0.19, iPS_cells:adipose_stem_cells: 0.19, Smooth_muscle_cells:vascular: 0.19, Osteoblasts: 0.19, Tissue_stem_cells:BM_MSC:osteogenic: 0.19, Tissue_stem_cells:BM_MSC:BMP2: 0.19, Tissue_stem_cells:BM_MSC:TGFb3: 0.18
NB02_CGTGTAACATCACAAC-1 Hepatocytes 0.07 252.71
Raw ScoresHepatocytes: 0.11, Fibroblasts:breast: 0.11, Smooth_muscle_cells:vascular:IL-17: 0.11, Smooth_muscle_cells:vascular: 0.11, Osteoblasts:BMP2: 0.1, iPS_cells:CRL2097_foreskin: 0.1, Epithelial_cells:bladder: 0.1, iPS_cells:adipose_stem_cells: 0.1, Smooth_muscle_cells:bronchial: 0.1, Osteoblasts: 0.1
NB02_TTCTTAGCAATCACAC-1 Smooth_muscle_cells:vascular:IL-17 0.08 239.27
Raw ScoresSmooth_muscle_cells:vascular: 0.13, Smooth_muscle_cells:bronchial: 0.13, Osteoblasts: 0.13, Smooth_muscle_cells:vascular:IL-17: 0.13, Smooth_muscle_cells:bronchial:vit_D: 0.13, Fibroblasts:breast: 0.13, iPS_cells:CRL2097_foreskin: 0.13, Chondrocytes:MSC-derived: 0.12, Tissue_stem_cells:BM_MSC:TGFb3: 0.12, Tissue_stem_cells:BM_MSC: 0.12
NB02_AGATCTGCATTATCTC-1 iPS_cells:CRL2097_foreskin-derived:d20_hepatic_diff 0.04 234.93
Raw ScoresSmooth_muscle_cells:vascular: 0.1, Smooth_muscle_cells:vascular:IL-17: 0.1, Smooth_muscle_cells:bronchial: 0.1, Fibroblasts:breast: 0.1, Tissue_stem_cells:BM_MSC:TGFb3: 0.1, Smooth_muscle_cells:bronchial:vit_D: 0.09, Hepatocytes: 0.09, Osteoblasts: 0.09, Osteoblasts:BMP2: 0.09, Chondrocytes:MSC-derived: 0.09
NB02_ATAAGAGAGATTACCC-1 Smooth_muscle_cells:vascular:IL-17 0.07 228.95
Raw ScoresHepatocytes: 0.14, Smooth_muscle_cells:vascular:IL-17: 0.14, Tissue_stem_cells:BM_MSC:BMP2: 0.14, Smooth_muscle_cells:vascular: 0.14, iPS_cells:adipose_stem_cells: 0.13, Osteoblasts:BMP2: 0.13, Fibroblasts:breast: 0.13, Tissue_stem_cells:BM_MSC:TGFb3: 0.13, Tissue_stem_cells:BM_MSC:osteogenic: 0.13, Smooth_muscle_cells:bronchial:vit_D: 0.13
NB02_CACATTTTCAAGCCTA-1 Tissue_stem_cells:BM_MSC:TGFb3 0.04 224.38
Raw ScoresHepatocytes: 0.11, Smooth_muscle_cells:vascular: 0.11, Fibroblasts:breast: 0.11, Tissue_stem_cells:BM_MSC:TGFb3: 0.1, Smooth_muscle_cells:vascular:IL-17: 0.1, Endothelial_cells:lymphatic:TNFa_48h: 0.1, Tissue_stem_cells:BM_MSC:BMP2: 0.1, Neuroepithelial_cell:ESC-derived: 0.1, Epithelial_cells:bronchial: 0.1, Tissue_stem_cells:BM_MSC: 0.09
NB02_GATCGCGAGGACGAAA-1 Tissue_stem_cells:BM_MSC:osteogenic 0.05 222.47
Raw ScoresOsteoblasts: 0.09, Tissue_stem_cells:BM_MSC: 0.09, Tissue_stem_cells:BM_MSC:osteogenic: 0.09, Fibroblasts:breast: 0.09, Chondrocytes:MSC-derived: 0.09, Osteoblasts:BMP2: 0.09, Smooth_muscle_cells:vascular: 0.09, Smooth_muscle_cells:vascular:IL-17: 0.09, Tissue_stem_cells:BM_MSC:BMP2: 0.09, iPS_cells:adipose_stem_cells: 0.08
NB02_CTAAGACTCTATGTGG-1 Fibroblasts:breast 0.07 220.76
Raw ScoresFibroblasts:breast: 0.13, Tissue_stem_cells:BM_MSC:TGFb3: 0.12, Chondrocytes:MSC-derived: 0.12, iPS_cells:adipose_stem_cells: 0.12, Osteoblasts: 0.12, Tissue_stem_cells:BM_MSC:BMP2: 0.12, iPS_cells:CRL2097_foreskin: 0.12, Osteoblasts:BMP2: 0.12, Tissue_stem_cells:iliac_MSC: 0.11, Smooth_muscle_cells:vascular: 0.11
NB02_GCGCAACGTTGGTAAA-1 iPS_cells:adipose_stem_cells 0.04 219.28
Raw ScoresSmooth_muscle_cells:vascular:IL-17: 0.11, Epithelial_cells:bladder: 0.11, Osteoblasts:BMP2: 0.11, Smooth_muscle_cells:vascular: 0.11, Tissue_stem_cells:BM_MSC: 0.11, iPS_cells:adipose_stem_cells: 0.1, Osteoblasts: 0.1, Tissue_stem_cells:BM_MSC:TGFb3: 0.1, iPS_cells:PDB_fibroblasts: 0.1, Fibroblasts:breast: 0.1
NB02_ATCTGCCAGCTAACTC-1 Tissue_stem_cells:BM_MSC 0.07 214.69
Raw ScoresOsteoblasts: 0.12, Osteoblasts:BMP2: 0.12, Tissue_stem_cells:BM_MSC: 0.12, Smooth_muscle_cells:vascular:IL-17: 0.12, Tissue_stem_cells:BM_MSC:TGFb3: 0.12, Chondrocytes:MSC-derived: 0.12, Fibroblasts:breast: 0.12, Smooth_muscle_cells:vascular: 0.12, iPS_cells:adipose_stem_cells: 0.12, iPS_cells:CRL2097_foreskin: 0.12
NB02_GATCGCGCAATGGACG-1 Hepatocytes 0.05 213.39
Raw ScoresOsteoblasts: 0.09, Smooth_muscle_cells:bronchial: 0.09, Smooth_muscle_cells:vascular:IL-17: 0.08, Tissue_stem_cells:BM_MSC:osteogenic: 0.08, Tissue_stem_cells:BM_MSC:BMP2: 0.08, Hepatocytes: 0.08, Chondrocytes:MSC-derived: 0.08, Tissue_stem_cells:BM_MSC: 0.08, Smooth_muscle_cells:vascular: 0.08, Smooth_muscle_cells:bronchial:vit_D: 0.08
NB02_TCACGAAGTAGCACGA-1 iPS_cells:adipose_stem_cells 0.07 209.37
Raw ScoresSmooth_muscle_cells:vascular:IL-17: 0.15, Fibroblasts:breast: 0.14, Tissue_stem_cells:BM_MSC:TGFb3: 0.14, Smooth_muscle_cells:vascular: 0.14, iPS_cells:adipose_stem_cells: 0.14, Tissue_stem_cells:BM_MSC:BMP2: 0.14, Smooth_muscle_cells:bronchial: 0.14, Chondrocytes:MSC-derived: 0.14, Smooth_muscle_cells:bronchial:vit_D: 0.14, Hepatocytes: 0.13
NB02_AATCCAGGTTTACTCT-1 Hepatocytes 0.07 207.98
Raw ScoresHepatocytes: 0.11, iPS_cells:CRL2097_foreskin-derived:d20_hepatic_diff: 0.09, Smooth_muscle_cells:vascular: 0.09, Tissue_stem_cells:BM_MSC:BMP2: 0.09, Tissue_stem_cells:BM_MSC:TGFb3: 0.09, Smooth_muscle_cells:vascular:IL-17: 0.09, Tissue_stem_cells:BM_MSC: 0.08, Tissue_stem_cells:iliac_MSC: 0.08, Chondrocytes:MSC-derived: 0.08, Fibroblasts:breast: 0.08
NB02_AGCGGTCAGCTCCTTC-1 iPS_cells:adipose_stem_cells 0.05 207.16
Raw ScoresSmooth_muscle_cells:bronchial: 0.13, Smooth_muscle_cells:bronchial:vit_D: 0.13, Fibroblasts:breast: 0.13, iPS_cells:CRL2097_foreskin: 0.12, Osteoblasts: 0.12, Tissue_stem_cells:iliac_MSC: 0.12, iPS_cells:adipose_stem_cells: 0.12, Chondrocytes:MSC-derived: 0.12, Hepatocytes: 0.12, iPS_cells:CRL2097_foreskin-derived:d20_hepatic_diff: 0.12
NB02_TAGTGGTCAGGGAGAG-1 Hepatocytes 0.05 204.01
Raw ScoresHepatocytes: 0.11, Neurons:Schwann_cell: 0.1, Fibroblasts:breast: 0.1, Astrocyte:Embryonic_stem_cell-derived: 0.1, Osteoblasts:BMP2: 0.09, Smooth_muscle_cells:vascular: 0.09, Neuroepithelial_cell:ESC-derived: 0.09, Epithelial_cells:bladder: 0.09, iPS_cells:adipose_stem_cells: 0.09, Smooth_muscle_cells:vascular:IL-17: 0.09
NB02_ACGAGCCCAGACACTT-1 Hepatocytes 0.03 203.74
Raw ScoresSmooth_muscle_cells:bronchial:vit_D: 0.08, Hepatocytes: 0.07, Smooth_muscle_cells:bronchial: 0.07, iPS_cells:CRL2097_foreskin-derived:d20_hepatic_diff: 0.07, Neurons:Schwann_cell: 0.07, Smooth_muscle_cells:vascular:IL-17: 0.07, Smooth_muscle_cells:vascular: 0.07, Embryonic_stem_cells: 0.07, Tissue_stem_cells:BM_MSC:BMP2: 0.07, Tissue_stem_cells:BM_MSC: 0.07
NB02_ACGCAGCCATCTCGCT-1 iPS_cells:CRL2097_foreskin-derived:d20_hepatic_diff 0.04 201.45
Raw ScoresSmooth_muscle_cells:vascular: 0.12, Smooth_muscle_cells:vascular:IL-17: 0.12, Fibroblasts:breast: 0.11, iPS_cells:adipose_stem_cells: 0.1, Smooth_muscle_cells:bronchial: 0.1, Smooth_muscle_cells:bronchial:vit_D: 0.1, Hepatocytes: 0.1, iPS_cells:CRL2097_foreskin: 0.1, Chondrocytes:MSC-derived: 0.1, Tissue_stem_cells:BM_MSC:TGFb3: 0.1
NB02_TGTTCCGAGATCCTGT-1 Tissue_stem_cells:BM_MSC:BMP2 0.05 200.11
Raw ScoresOsteoblasts: 0.1, Tissue_stem_cells:BM_MSC:BMP2: 0.1, Chondrocytes:MSC-derived: 0.1, Smooth_muscle_cells:bronchial: 0.1, Tissue_stem_cells:BM_MSC: 0.1, Tissue_stem_cells:BM_MSC:TGFb3: 0.1, Tissue_stem_cells:BM_MSC:osteogenic: 0.1, Smooth_muscle_cells:bronchial:vit_D: 0.1, iPS_cells:CRL2097_foreskin: 0.09, Smooth_muscle_cells:vascular: 0.09
NB02_CATATGGCAGGGTATG-1 iPS_cells:CRL2097_foreskin-derived:d20_hepatic_diff 0.03 199.39
Raw ScoresHepatocytes: 0.1, iPS_cells:CRL2097_foreskin-derived:d20_hepatic_diff: 0.1, Tissue_stem_cells:BM_MSC:TGFb3: 0.1, Epithelial_cells:bladder: 0.1, Fibroblasts:breast: 0.1, Tissue_stem_cells:BM_MSC:BMP2: 0.1, Chondrocytes:MSC-derived: 0.09, Smooth_muscle_cells:vascular:IL-17: 0.09, Smooth_muscle_cells:bronchial: 0.09, Smooth_muscle_cells:vascular: 0.09
NB02_TTGCGTCAGATGTCGG-1 Hepatocytes 0.15 198.60
Raw ScoresHepatocytes: 0.24, Smooth_muscle_cells:vascular: 0.17, Osteoblasts: 0.16, Smooth_muscle_cells:vascular:IL-17: 0.16, Fibroblasts:breast: 0.16, Tissue_stem_cells:iliac_MSC: 0.16, iPS_cells:CRL2097_foreskin-derived:d20_hepatic_diff: 0.16, Tissue_stem_cells:BM_MSC:TGFb3: 0.16, Osteoblasts:BMP2: 0.16, Tissue_stem_cells:BM_MSC:BMP2: 0.16
NB02_AATCCAGAGATATGGT-1 Tissue_stem_cells:BM_MSC:BMP2 0.05 197.81
Raw ScoresSmooth_muscle_cells:vascular:IL-17: 0.11, Tissue_stem_cells:BM_MSC:TGFb3: 0.11, Fibroblasts:breast: 0.11, Tissue_stem_cells:BM_MSC:BMP2: 0.1, Smooth_muscle_cells:vascular: 0.1, Osteoblasts: 0.1, Tissue_stem_cells:BM_MSC: 0.1, iPS_cells:adipose_stem_cells: 0.1, Tissue_stem_cells:BM_MSC:osteogenic: 0.1, Osteoblasts:BMP2: 0.1
NB02_GCATGTAGTAGCGATG-1 Hepatocytes 0.04 194.07
Raw ScoresHepatocytes: 0.08, Epithelial_cells:bladder: 0.07, Fibroblasts:breast: 0.07, Osteoblasts: 0.07, Smooth_muscle_cells:vascular:IL-17: 0.07, Tissue_stem_cells:iliac_MSC: 0.07, Tissue_stem_cells:BM_MSC:TGFb3: 0.07, Smooth_muscle_cells:bronchial: 0.07, Tissue_stem_cells:BM_MSC:BMP2: 0.07, Endothelial_cells:lymphatic:TNFa_48h: 0.07
NB02_AACTTTCAGATGAGAG-1 Tissue_stem_cells:BM_MSC:BMP2 0.03 192.43
Raw ScoresTissue_stem_cells:BM_MSC:BMP2: 0.1, Tissue_stem_cells:BM_MSC:TGFb3: 0.1, Tissue_stem_cells:BM_MSC:osteogenic: 0.09, Osteoblasts: 0.09, Tissue_stem_cells:iliac_MSC: 0.09, Smooth_muscle_cells:vascular:IL-17: 0.09, Fibroblasts:breast: 0.09, Tissue_stem_cells:BM_MSC: 0.09, Endothelial_cells:HUVEC:IL-1b: 0.09, Monocyte:F._tularensis_novicida: 0.09
NB02_TGTTCCGCATACGCTA-1 Tissue_stem_cells:BM_MSC:BMP2 0.07 188.47
Raw ScoresTissue_stem_cells:BM_MSC:TGFb3: 0.12, Tissue_stem_cells:BM_MSC:BMP2: 0.12, Fibroblasts:breast: 0.12, Smooth_muscle_cells:vascular: 0.12, Tissue_stem_cells:iliac_MSC: 0.12, Osteoblasts: 0.12, Chondrocytes:MSC-derived: 0.12, Smooth_muscle_cells:vascular:IL-17: 0.12, Smooth_muscle_cells:bronchial:vit_D: 0.11, Smooth_muscle_cells:bronchial: 0.11
NB02_CATGGCGTCGCTTGTC-1 Fibroblasts:breast 0.07 185.74
Raw ScoresSmooth_muscle_cells:vascular:IL-17: 0.13, Fibroblasts:breast: 0.13, Smooth_muscle_cells:vascular: 0.12, Osteoblasts:BMP2: 0.12, Smooth_muscle_cells:bronchial:vit_D: 0.12, Smooth_muscle_cells:bronchial: 0.12, Osteoblasts: 0.12, Tissue_stem_cells:BM_MSC: 0.12, Chondrocytes:MSC-derived: 0.12, Tissue_stem_cells:BM_MSC:TGFb3: 0.12


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: 1.75e-10
Mean rank of genes in gene set: 3033.73
Rank on gene expression program of genes in gene set:
Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
TGFB2 0.0048325 115 GTEx DepMap Descartes 0.12 77.17
BGN 0.0034096 223 GTEx DepMap Descartes 0.31 671.94
THBS1 0.0033280 233 GTEx DepMap Descartes 0.61 339.33
COL1A2 0.0028187 309 GTEx DepMap Descartes 1.78 1420.98
VEGFA 0.0027814 313 GTEx DepMap Descartes 0.30 111.29
FN1 0.0025784 345 GTEx DepMap Descartes 0.99 480.80
MMP2 0.0025679 348 GTEx DepMap Descartes 0.24 330.82
TPM1 0.0025006 362 GTEx DepMap Descartes 0.39 397.38
COL3A1 0.0019599 503 GTEx DepMap Descartes 0.94 729.03
COL5A1 0.0018619 543 GTEx DepMap Descartes 0.22 97.43
TPM2 0.0018465 551 GTEx DepMap Descartes 0.26 638.33
TGFBR2 0.0018162 563 GTEx DepMap Descartes 0.13 82.51
COL5A2 0.0017802 580 GTEx DepMap Descartes 0.43 243.54
VCAN 0.0017611 587 GTEx DepMap Descartes 0.39 136.25
COL4A1 0.0017567 590 GTEx DepMap Descartes 0.25 195.24
MYL9 0.0016481 641 GTEx DepMap Descartes 0.12 198.70
DCN 0.0013891 785 GTEx DepMap Descartes 0.11 62.79
MYLK 0.0013139 854 GTEx DepMap Descartes 0.05 29.71
CNN2 0.0012835 875 GTEx DepMap Descartes 0.06 137.73
LUM 0.0012420 919 GTEx DepMap Descartes 0.12 191.85
CNN3 0.0012062 953 GTEx DepMap Descartes 0.21 432.64
COL13A1 0.0011573 992 GTEx DepMap Descartes 0.01 14.53
COL1A1 0.0011264 1019 GTEx DepMap Descartes 0.90 662.84
TNC 0.0010420 1096 GTEx DepMap Descartes 0.18 60.36
COL8A1 0.0010307 1107 GTEx DepMap Descartes 0.17 165.26
TAGLN 0.0009342 1216 GTEx DepMap Descartes 0.14 162.21
IGFBP7 0.0009300 1222 GTEx DepMap Descartes 0.27 799.59
THY1 0.0008955 1275 GTEx DepMap Descartes 0.12 141.55
COL12A1 0.0008790 1301 GTEx DepMap Descartes 0.06 22.31
THBS2 0.0006857 1697 GTEx DepMap Descartes 0.27 211.22
MMP11 0.0005423 2112 GTEx DepMap Descartes 0.03 39.60
COL14A1 0.0005129 2209 GTEx DepMap Descartes 0.12 63.82
TGFB1 0.0004587 2442 GTEx DepMap Descartes 0.10 99.90
IGFBP3 0.0004329 2565 GTEx DepMap Descartes 0.05 71.02
ACTA2 0.0003921 2733 GTEx DepMap Descartes 0.09 289.91
WNT5A 0.0003087 3192 GTEx DepMap Descartes 0.01 4.11
HOPX 0.0002189 3822 GTEx DepMap Descartes 0.01 12.31
ACTG2 0.0001640 4252 GTEx DepMap Descartes 0.00 0.00
TGFBR1 0.0000399 5484 GTEx DepMap Descartes 0.06 38.50
COL10A1 -0.0000337 6517 GTEx DepMap Descartes 0.00 0.00
ITGA7 -0.0000692 7184 GTEx DepMap Descartes 0.02 10.50
COL15A1 -0.0001736 9010 GTEx DepMap Descartes 0.01 13.30
TMEM119 -0.0001816 9138 GTEx DepMap Descartes 0.01 10.55
PGF -0.0001970 9362 GTEx DepMap Descartes 0.01 6.74
MYH11 -0.0002218 9710 GTEx DepMap Descartes 0.01 3.29
MEF2C -0.0003029 10618 GTEx DepMap Descartes 0.02 15.20
COL11A1 -0.0004516 11645 GTEx DepMap Descartes 0.10 23.36
POSTN -0.0006491 12131 GTEx DepMap Descartes 0.16 141.78
RGS5 -0.0010384 12410 GTEx DepMap Descartes 0.07 21.91


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: 2.44e-08
Mean rank of genes in gene set: 796.38
Rank on gene expression program of genes in gene set:

Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
BGN 0.0034096 223 GTEx DepMap Descartes 0.31 671.94
COL1A2 0.0028187 309 GTEx DepMap Descartes 1.78 1420.98
SPARC 0.0022476 416 GTEx DepMap Descartes 0.60 805.70
COL3A1 0.0019599 503 GTEx DepMap Descartes 0.94 729.03
CALD1 0.0016992 618 GTEx DepMap Descartes 1.04 829.41
MGP 0.0015521 692 GTEx DepMap Descartes 0.21 547.57
DCN 0.0013891 785 GTEx DepMap Descartes 0.11 62.79
LEPR 0.0013694 803 GTEx DepMap Descartes 0.09 43.28
COL6A2 0.0013346 837 GTEx DepMap Descartes 0.36 425.35
LUM 0.0012420 919 GTEx DepMap Descartes 0.12 191.85
COL1A1 0.0011264 1019 GTEx DepMap Descartes 0.90 662.84
PRRX1 0.0010039 1134 GTEx DepMap Descartes 0.07 67.89
PDGFRA 0.0005471 2095 GTEx DepMap Descartes 0.03 12.91


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: 3.37e-07
Mean rank of genes in gene set: 2678.44
Rank on gene expression program of genes in gene set:

Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
CXCL2 0.0161554 7 GTEx DepMap Descartes 0.42 1476.53
C3 0.0144585 9 GTEx DepMap Descartes 2.28 1947.58
LIF 0.0079466 40 GTEx DepMap Descartes 0.19 225.14
CCL2 0.0064337 58 GTEx DepMap Descartes 0.28 1153.43
SERPING1 0.0059012 69 GTEx DepMap Descartes 0.39 687.85
SOD2 0.0034501 217 GTEx DepMap Descartes 0.53 155.02
CFB 0.0033713 228 GTEx DepMap Descartes 0.11 209.93
IL1R1 0.0029962 278 GTEx DepMap Descartes 0.23 184.56
PDGFD 0.0024281 374 GTEx DepMap Descartes 0.12 159.26
C7 0.0016964 621 GTEx DepMap Descartes 0.12 99.80
CXCL12 0.0013094 858 GTEx DepMap Descartes 0.08 127.46
GPX3 0.0009484 1191 GTEx DepMap Descartes 0.08 156.77
RGMA 0.0009165 1243 GTEx DepMap Descartes 0.01 6.72
PDGFRB 0.0005663 2037 GTEx DepMap Descartes 0.07 59.83
PDGFRA 0.0005471 2095 GTEx DepMap Descartes 0.03 12.91
IGF1 0.0004678 2390 GTEx DepMap Descartes 0.11 86.86
IL33 0.0003286 3087 GTEx DepMap Descartes 0.03 40.42
HGF 0.0003154 3160 GTEx DepMap Descartes 0.02 14.04
IGFBP6 0.0002349 3709 GTEx DepMap Descartes 0.04 136.08
IL10 -0.0000359 6571 GTEx DepMap Descartes 0.00 0.00
SCARA3 -0.0000404 6651 GTEx DepMap Descartes 0.00 0.00
CXCL14 -0.0000426 6684 GTEx DepMap Descartes 0.01 21.83
SCARA5 -0.0000465 6766 GTEx DepMap Descartes 0.00 0.00
PDPN -0.0001913 9286 GTEx DepMap Descartes 0.03 33.58
CFD -0.0001945 9332 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: 10032.11
Median rank of genes in gene set: 11333
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
GRB10 0.0032227 248 GTEx DepMap Descartes 0.21 177.96
GLDC 0.0028187 308 GTEx DepMap Descartes 0.07 62.17
ABLIM1 0.0024378 371 GTEx DepMap Descartes 0.39 172.98
MYRIP 0.0011246 1020 GTEx DepMap Descartes 0.19 117.65
DAPK1 0.0010420 1097 GTEx DepMap Descartes 0.14 84.96
EML4 0.0010129 1122 GTEx DepMap Descartes 0.42 282.46
PRSS12 0.0009461 1197 GTEx DepMap Descartes 0.20 117.13
PTS 0.0007098 1642 GTEx DepMap Descartes 0.12 445.13
FAM107B 0.0006136 1893 GTEx DepMap Descartes 0.20 217.85
LYN 0.0005270 2169 GTEx DepMap Descartes 0.06 29.69
TUBB4B 0.0005207 2185 GTEx DepMap Descartes 0.09 188.43
PARP6 0.0005157 2199 GTEx DepMap Descartes 0.10 102.64
DUSP4 0.0004978 2273 GTEx DepMap Descartes 0.03 24.40
NFIL3 0.0004677 2391 GTEx DepMap Descartes 0.05 96.98
TDG 0.0004647 2411 GTEx DepMap Descartes 0.08 85.07
NCS1 0.0004308 2569 GTEx DepMap Descartes 0.08 49.17
AKAP12 0.0004301 2574 GTEx DepMap Descartes 0.40 150.12
FAM169A 0.0004115 2648 GTEx DepMap Descartes 0.03 16.96
NCOA7 0.0003864 2759 GTEx DepMap Descartes 0.31 NA
CAMSAP1 0.0003793 2811 GTEx DepMap Descartes 0.13 61.79
SYT4 0.0003670 2884 GTEx DepMap Descartes 0.07 101.98
MAPK8 0.0003205 3125 GTEx DepMap Descartes 0.26 119.65
IGSF3 0.0003168 3149 GTEx DepMap Descartes 0.05 28.10
SNAP25 0.0002842 3355 GTEx DepMap Descartes 0.19 336.53
MMD 0.0002825 3372 GTEx DepMap Descartes 0.09 92.50
NEFL 0.0002809 3383 GTEx DepMap Descartes 0.07 51.81
EIF1B 0.0002624 3518 GTEx DepMap Descartes 0.05 220.99
NAPB 0.0002408 3666 GTEx DepMap Descartes 0.05 75.75
RUFY3 0.0001659 4239 GTEx DepMap Descartes 0.24 197.76
PHPT1 0.0001626 4261 GTEx DepMap Descartes 0.10 321.26


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: 6.97e-43
Mean rank of genes in gene set: 3940.9
Median rank of genes in gene set: 2876
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
COL27A1 0.0102972 24 GTEx DepMap Descartes 0.33 175.13
PDGFC 0.0063208 62 GTEx DepMap Descartes 0.19 186.54
EGFR 0.0060274 68 GTEx DepMap Descartes 0.24 87.89
GDF15 0.0058818 70 GTEx DepMap Descartes 0.25 1060.48
CFH 0.0058378 71 GTEx DepMap Descartes 0.46 303.94
FNDC3B 0.0056456 76 GTEx DepMap Descartes 0.78 374.15
SEL1L3 0.0054724 82 GTEx DepMap Descartes 0.18 185.52
SDC4 0.0054624 83 GTEx DepMap Descartes 0.21 331.97
TNFRSF12A 0.0052849 86 GTEx DepMap Descartes 0.27 693.56
PDLIM1 0.0051945 91 GTEx DepMap Descartes 0.18 627.03
SMAD3 0.0050826 99 GTEx DepMap Descartes 0.22 131.84
PHLDB2 0.0049211 104 GTEx DepMap Descartes 0.19 142.42
EXT1 0.0048677 110 GTEx DepMap Descartes 1.49 646.78
YAP1 0.0047758 120 GTEx DepMap Descartes 0.22 169.81
KLF6 0.0046303 129 GTEx DepMap Descartes 0.60 567.84
CFI 0.0046250 131 GTEx DepMap Descartes 0.08 151.13
MGST1 0.0045280 141 GTEx DepMap Descartes 0.21 375.85
PLOD2 0.0044270 143 GTEx DepMap Descartes 0.44 412.63
ANXA2 0.0043579 148 GTEx DepMap Descartes 0.44 526.43
PROM1 0.0043054 151 GTEx DepMap Descartes 0.05 24.89
EPS8 0.0043027 153 GTEx DepMap Descartes 0.27 246.00
SHROOM3 0.0042180 158 GTEx DepMap Descartes 0.14 43.57
ITGAV 0.0041119 162 GTEx DepMap Descartes 0.59 354.07
HES1 0.0040673 164 GTEx DepMap Descartes 0.19 512.70
MAML2 0.0040450 167 GTEx DepMap Descartes 0.48 283.58
ACADVL 0.0040055 171 GTEx DepMap Descartes 0.58 995.67
NFIA 0.0038866 180 GTEx DepMap Descartes 0.36 33.70
ZFP36L1 0.0037899 187 GTEx DepMap Descartes 0.52 726.09
SYNJ2 0.0037698 189 GTEx DepMap Descartes 0.24 124.37
LPP 0.0036715 194 GTEx DepMap Descartes 0.87 168.56


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: 9.02e-01
Mean rank of genes in gene set: 7053.44
Median rank of genes in gene set: 7687.5
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
BAIAP2L1 0.0080607 39 GTEx DepMap Descartes 0.26 276.16
LDLR 0.0051980 90 GTEx DepMap Descartes 0.32 243.30
APOC1 0.0010833 1058 GTEx DepMap Descartes 0.51 3237.30
ERN1 0.0009299 1223 GTEx DepMap Descartes 0.05 27.49
FREM2 0.0007980 1461 GTEx DepMap Descartes 0.01 2.38
DHCR24 0.0006475 1794 GTEx DepMap Descartes 0.12 116.03
SCAP 0.0004455 2497 GTEx DepMap Descartes 0.08 73.73
PAPSS2 0.0004347 2552 GTEx DepMap Descartes 0.09 65.66
SH3PXD2B 0.0004167 2629 GTEx DepMap Descartes 0.10 52.71
NPC1 0.0003787 2816 GTEx DepMap Descartes 0.08 72.66
DHCR7 0.0002659 3490 GTEx DepMap Descartes 0.04 50.24
CLU 0.0001366 4501 GTEx DepMap Descartes 0.22 306.08
FDPS 0.0001176 4663 GTEx DepMap Descartes 0.15 210.86
HMGCS1 0.0000887 4927 GTEx DepMap Descartes 0.07 60.24
SCARB1 0.0000133 5821 GTEx DepMap Descartes 0.03 9.86
STAR -0.0000051 6072 GTEx DepMap Descartes 0.00 0.00
SH3BP5 -0.0000066 6097 GTEx DepMap Descartes 0.03 23.83
TM7SF2 -0.0000657 7130 GTEx DepMap Descartes 0.03 45.61
MSMO1 -0.0001258 8245 GTEx DepMap Descartes 0.05 121.38
FDXR -0.0001272 8267 GTEx DepMap Descartes 0.00 0.00
HMGCR -0.0001318 8338 GTEx DepMap Descartes 0.05 28.70
FDX1 -0.0001828 9154 GTEx DepMap Descartes 0.02 14.54
GRAMD1B -0.0002011 9429 GTEx DepMap Descartes 0.03 10.06
INHA -0.0002808 10405 GTEx DepMap Descartes 0.01 3.03
DNER -0.0003235 10802 GTEx DepMap Descartes 0.04 18.40
CYB5B -0.0003636 11094 GTEx DepMap Descartes 0.02 13.85
POR -0.0003680 11137 GTEx DepMap Descartes 0.04 64.87
SGCZ -0.0004066 11398 GTEx DepMap Descartes 0.18 40.51
SLC16A9 -0.0004301 11538 GTEx DepMap Descartes 0.01 2.28
GSTA4 -0.0004538 11661 GTEx DepMap Descartes 0.02 17.03


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: 11330.54
Median rank of genes in gene set: 12267
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
GREM1 0.0008604 1335 GTEx DepMap Descartes 0.09 26.15
RPH3A 0.0000856 4957 GTEx DepMap Descartes 0.01 0.83
MAB21L1 -0.0000433 6700 GTEx DepMap Descartes 0.02 40.83
FAT3 -0.0000450 6738 GTEx DepMap Descartes 0.06 10.83
TUBB2A -0.0001944 9331 GTEx DepMap Descartes 0.22 410.17
GAP43 -0.0003030 10623 GTEx DepMap Descartes 0.19 268.05
GAL -0.0003668 11126 GTEx DepMap Descartes 0.11 791.73
REEP1 -0.0003799 11232 GTEx DepMap Descartes 0.05 37.37
EPHA6 -0.0004038 11385 GTEx DepMap Descartes 0.20 121.62
PTCHD1 -0.0004229 11493 GTEx DepMap Descartes 0.05 3.96
CNTFR -0.0004365 11568 GTEx DepMap Descartes 0.02 27.44
MAB21L2 -0.0004425 11601 GTEx DepMap Descartes 0.01 5.62
SYNPO2 -0.0004584 11680 GTEx DepMap Descartes 0.10 26.13
NTRK1 -0.0004667 11713 GTEx DepMap Descartes 0.06 41.54
RGMB -0.0005151 11870 GTEx DepMap Descartes 0.04 33.02
TMEFF2 -0.0005297 11913 GTEx DepMap Descartes 0.02 6.52
SLC44A5 -0.0005392 11931 GTEx DepMap Descartes 0.10 59.29
SLC6A2 -0.0005718 12004 GTEx DepMap Descartes 0.02 16.66
PLXNA4 -0.0006188 12073 GTEx DepMap Descartes 0.04 6.94
MLLT11 -0.0006639 12158 GTEx DepMap Descartes 0.08 145.02
ANKFN1 -0.0007697 12267 GTEx DepMap Descartes 0.01 7.34
BASP1 -0.0008192 12311 GTEx DepMap Descartes 0.17 406.04
CNKSR2 -0.0008287 12327 GTEx DepMap Descartes 0.06 14.39
HS3ST5 -0.0008600 12344 GTEx DepMap Descartes 0.07 34.88
MARCH11 -0.0009117 12366 GTEx DepMap Descartes 0.09 NA
CCND1 -0.0009328 12372 GTEx DepMap Descartes 0.10 105.99
MAP1B -0.0009467 12377 GTEx DepMap Descartes 0.44 103.24
ISL1 -0.0010445 12413 GTEx DepMap Descartes 0.03 27.19
ELAVL2 -0.0010608 12416 GTEx DepMap Descartes 0.09 34.72
EYA1 -0.0011218 12445 GTEx DepMap Descartes 0.02 8.48


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: 3.99e-01
Mean rank of genes in gene set: 6124.29
Median rank of genes in gene set: 5803
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
NR5A2 0.0088952 34 GTEx DepMap Descartes 0.35 235.02
ARHGAP29 0.0040209 169 GTEx DepMap Descartes 0.20 100.61
NPR1 0.0012182 942 GTEx DepMap Descartes 0.01 11.34
MYRIP 0.0011246 1020 GTEx DepMap Descartes 0.19 117.65
CDH5 0.0009500 1190 GTEx DepMap Descartes 0.02 15.14
FLT4 0.0008777 1303 GTEx DepMap Descartes 0.00 0.00
CALCRL 0.0008649 1327 GTEx DepMap Descartes 0.02 21.72
CEACAM1 0.0006934 1684 GTEx DepMap Descartes 0.05 67.16
SHE 0.0004974 2274 GTEx DepMap Descartes 0.01 1.76
KANK3 0.0004971 2276 GTEx DepMap Descartes 0.01 13.10
ID1 0.0004226 2607 GTEx DepMap Descartes 0.14 526.28
CYP26B1 0.0002660 3489 GTEx DepMap Descartes 0.01 2.95
IRX3 0.0002453 3628 GTEx DepMap Descartes 0.01 20.79
ROBO4 0.0002271 3769 GTEx DepMap Descartes 0.01 16.02
EHD3 0.0002263 3779 GTEx DepMap Descartes 0.01 16.99
TMEM88 0.0001343 4525 GTEx DepMap Descartes 0.03 209.41
TIE1 0.0000795 5018 GTEx DepMap Descartes 0.01 9.03
GALNT15 0.0000325 5580 GTEx DepMap Descartes 0.01 NA
KDR 0.0000276 5643 GTEx DepMap Descartes 0.01 1.12
SLCO2A1 0.0000029 5963 GTEx DepMap Descartes 0.01 5.61
SHANK3 -0.0000092 6135 GTEx DepMap Descartes 0.03 18.83
F8 -0.0000269 6392 GTEx DepMap Descartes 0.00 0.00
CRHBP -0.0000811 7418 GTEx DepMap Descartes 0.00 0.00
PLVAP -0.0001560 8778 GTEx DepMap Descartes 0.00 0.00
RASIP1 -0.0001615 8849 GTEx DepMap Descartes 0.00 0.00
MMRN2 -0.0001756 9039 GTEx DepMap Descartes 0.01 1.47
NOTCH4 -0.0001799 9109 GTEx DepMap Descartes 0.00 0.00
HYAL2 -0.0001910 9284 GTEx DepMap Descartes 0.02 28.62
TEK -0.0002140 9606 GTEx DepMap Descartes 0.01 5.38
BTNL9 -0.0002790 10387 GTEx DepMap Descartes 0.00 0.00


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: 5.82e-05
Mean rank of genes in gene set: 4174.11
Median rank of genes in gene set: 2635
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
BICC1 0.0369479 1 GTEx DepMap Descartes 4.36 3517.55
COL27A1 0.0102972 24 GTEx DepMap Descartes 0.33 175.13
COL1A2 0.0028187 309 GTEx DepMap Descartes 1.78 1420.98
COL3A1 0.0019599 503 GTEx DepMap Descartes 0.94 729.03
LOX 0.0017168 611 GTEx DepMap Descartes 0.03 28.43
C7 0.0016964 621 GTEx DepMap Descartes 0.12 99.80
MGP 0.0015521 692 GTEx DepMap Descartes 0.21 547.57
ADAMTSL3 0.0014046 776 GTEx DepMap Descartes 0.07 43.87
DCN 0.0013891 785 GTEx DepMap Descartes 0.11 62.79
LUM 0.0012420 919 GTEx DepMap Descartes 0.12 191.85
COL1A1 0.0011264 1019 GTEx DepMap Descartes 0.90 662.84
ELN 0.0011105 1034 GTEx DepMap Descartes 0.12 145.94
ITGA11 0.0011079 1036 GTEx DepMap Descartes 0.07 21.86
PRRX1 0.0010039 1134 GTEx DepMap Descartes 0.07 67.89
COL12A1 0.0008790 1301 GTEx DepMap Descartes 0.06 22.31
SFRP2 0.0005594 2065 GTEx DepMap Descartes 0.07 124.57
PDGFRA 0.0005471 2095 GTEx DepMap Descartes 0.03 12.91
ABCA6 0.0005142 2204 GTEx DepMap Descartes 0.05 15.60
ABCC9 0.0005060 2234 GTEx DepMap Descartes 0.02 6.60
ADAMTS2 0.0004761 2349 GTEx DepMap Descartes 0.10 58.78
CDH11 0.0004538 2457 GTEx DepMap Descartes 0.18 95.64
IGFBP3 0.0004329 2565 GTEx DepMap Descartes 0.05 71.02
PRICKLE1 0.0003979 2705 GTEx DepMap Descartes 0.15 110.76
ACTA2 0.0003921 2733 GTEx DepMap Descartes 0.09 289.91
COL6A3 0.0003679 2876 GTEx DepMap Descartes 0.18 78.17
ISLR 0.0003180 3142 GTEx DepMap Descartes 0.04 81.05
EDNRA 0.0002659 3491 GTEx DepMap Descartes 0.05 24.49
PCDH18 0.0001198 4642 GTEx DepMap Descartes 0.02 15.10
LAMC3 0.0000821 4987 GTEx DepMap Descartes 0.01 4.43
GLI2 0.0000610 5220 GTEx DepMap Descartes 0.05 29.91


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: 10268.97
Median rank of genes in gene set: 11978
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
SLC35F3 0.0043981 144 GTEx DepMap Descartes 0.30 352.21
LAMA3 0.0017848 575 GTEx DepMap Descartes 0.08 36.42
PENK 0.0004908 2301 GTEx DepMap Descartes 0.08 292.74
CNTN3 0.0003836 2779 GTEx DepMap Descartes 0.02 23.94
SORCS3 0.0003564 2946 GTEx DepMap Descartes 0.03 21.94
DGKK 0.0001228 4620 GTEx DepMap Descartes 0.01 0.43
SLC24A2 -0.0000455 6744 GTEx DepMap Descartes 0.00 0.00
HTATSF1 -0.0001642 8884 GTEx DepMap Descartes 0.04 66.58
CDH12 -0.0003477 10991 GTEx DepMap Descartes 0.07 34.03
GRM7 -0.0003668 11127 GTEx DepMap Descartes 0.11 51.31
PACRG -0.0004261 11510 GTEx DepMap Descartes 0.05 119.56
ARC -0.0004277 11522 GTEx DepMap Descartes 0.01 4.85
TBX20 -0.0004428 11605 GTEx DepMap Descartes 0.01 3.51
ST18 -0.0004549 11671 GTEx DepMap Descartes 0.01 0.86
SPOCK3 -0.0004588 11684 GTEx DepMap Descartes 0.08 54.16
MGAT4C -0.0004833 11772 GTEx DepMap Descartes 0.08 9.66
C1QL1 -0.0004950 11813 GTEx DepMap Descartes 0.01 8.81
CDH18 -0.0005284 11908 GTEx DepMap Descartes 0.06 28.70
NTNG1 -0.0005567 11972 GTEx DepMap Descartes 0.03 7.01
EML6 -0.0005617 11984 GTEx DepMap Descartes 0.19 33.24
GRID2 -0.0005630 11988 GTEx DepMap Descartes 0.05 13.19
PCSK2 -0.0005657 11994 GTEx DepMap Descartes 0.01 10.20
KSR2 -0.0006369 12111 GTEx DepMap Descartes 0.01 1.98
GCH1 -0.0006556 12148 GTEx DepMap Descartes 0.02 13.05
TENM1 -0.0007052 12208 GTEx DepMap Descartes 0.11 NA
SLC18A1 -0.0007071 12211 GTEx DepMap Descartes 0.00 0.00
TIAM1 -0.0007553 12256 GTEx DepMap Descartes 0.08 40.66
ROBO1 -0.0007608 12261 GTEx DepMap Descartes 0.24 107.06
GALNTL6 -0.0008141 12306 GTEx DepMap Descartes 0.05 26.15
KCTD16 -0.0010363 12409 GTEx DepMap Descartes 0.09 17.15


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: 1.78e-01
Mean rank of genes in gene set: 5655.69
Median rank of genes in gene set: 5431
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
BLVRB 0.0022470 417 GTEx DepMap Descartes 0.05 125.06
SLC25A21 0.0017973 570 GTEx DepMap Descartes 0.01 7.10
DENND4A 0.0017600 589 GTEx DepMap Descartes 0.43 198.74
MARCH3 0.0015686 681 GTEx DepMap Descartes 0.11 NA
GCLC 0.0007735 1508 GTEx DepMap Descartes 0.14 168.28
SLC25A37 0.0007533 1547 GTEx DepMap Descartes 0.11 91.53
GYPC 0.0007515 1550 GTEx DepMap Descartes 0.01 21.46
SOX6 0.0006144 1891 GTEx DepMap Descartes 0.16 71.31
MICAL2 0.0005911 1956 GTEx DepMap Descartes 0.14 64.63
EPB41 0.0001767 4144 GTEx DepMap Descartes 0.14 94.51
SPECC1 0.0001524 4351 GTEx DepMap Descartes 0.02 4.88
TRAK2 0.0001448 4422 GTEx DepMap Descartes 0.06 37.24
FECH 0.0000844 4969 GTEx DepMap Descartes 0.02 9.33
ABCB10 0.0000550 5307 GTEx DepMap Descartes 0.05 48.98
TMCC2 0.0000440 5431 GTEx DepMap Descartes 0.00 0.00
RGS6 -0.0000088 6130 GTEx DepMap Descartes 0.01 5.77
SLC4A1 -0.0000291 6439 GTEx DepMap Descartes 0.00 0.00
ALAS2 -0.0000382 6609 GTEx DepMap Descartes 0.00 0.00
TFR2 -0.0001123 8005 GTEx DepMap Descartes 0.09 104.04
CAT -0.0001193 8132 GTEx DepMap Descartes 0.02 42.63
RHD -0.0001327 8356 GTEx DepMap Descartes 0.00 0.00
XPO7 -0.0001513 8689 GTEx DepMap Descartes 0.03 24.18
CPOX -0.0001751 9032 GTEx DepMap Descartes 0.01 1.51
RAPGEF2 -0.0001889 9256 GTEx DepMap Descartes 0.16 77.50
SPTB -0.0002088 9538 GTEx DepMap Descartes 0.02 3.96
ANK1 -0.0002543 10101 GTEx DepMap Descartes 0.01 6.41
SNCA -0.0002649 10236 GTEx DepMap Descartes 0.05 44.89
SELENBP1 -0.0004985 11820 GTEx DepMap Descartes 0.03 33.85
TSPAN5 -0.0008536 12339 GTEx DepMap Descartes 0.10 72.32
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: 3.18e-02
Mean rank of genes in gene set: 5186.82
Median rank of genes in gene set: 4097
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
PTPRE 0.0023869 381 GTEx DepMap Descartes 0.19 125.01
WWP1 0.0017921 572 GTEx DepMap Descartes 0.20 182.37
CTSB 0.0014870 730 GTEx DepMap Descartes 0.35 475.39
TGFBI 0.0013807 794 GTEx DepMap Descartes 0.11 113.52
CTSD 0.0010118 1123 GTEx DepMap Descartes 0.40 819.41
ITPR2 0.0008284 1411 GTEx DepMap Descartes 0.18 54.44
SLCO2B1 0.0007393 1575 GTEx DepMap Descartes 0.05 34.94
MSR1 0.0007206 1608 GTEx DepMap Descartes 0.04 77.07
SPP1 0.0006796 1710 GTEx DepMap Descartes 0.59 1437.10
AXL 0.0005139 2205 GTEx DepMap Descartes 0.05 45.07
CTSS 0.0004352 2549 GTEx DepMap Descartes 0.03 46.74
HRH1 0.0003820 2795 GTEx DepMap Descartes 0.09 48.44
CPVL 0.0003620 2908 GTEx DepMap Descartes 0.01 7.49
ABCA1 0.0003273 3092 GTEx DepMap Descartes 0.12 41.07
CST3 0.0002994 3257 GTEx DepMap Descartes 0.08 99.83
HCK 0.0002966 3275 GTEx DepMap Descartes 0.01 21.43
LGMN 0.0002716 3459 GTEx DepMap Descartes 0.09 202.54
MERTK 0.0002189 3820 GTEx DepMap Descartes 0.01 4.70
CD163 0.0001857 4060 GTEx DepMap Descartes 0.01 3.73
CTSC 0.0001778 4134 GTEx DepMap Descartes 0.03 23.75
IFNGR1 0.0001636 4255 GTEx DepMap Descartes 0.06 92.32
RGL1 0.0001129 4710 GTEx DepMap Descartes 0.07 70.47
CD74 0.0001032 4796 GTEx DepMap Descartes 0.09 133.50
CD14 0.0000885 4930 GTEx DepMap Descartes 0.04 141.44
ATP8B4 0.0000544 5314 GTEx DepMap Descartes 0.02 13.69
MS4A4A 0.0000169 5767 GTEx DepMap Descartes 0.01 16.66
SLC9A9 -0.0000388 6618 GTEx DepMap Descartes 0.10 85.47
CSF1R -0.0000805 7400 GTEx DepMap Descartes 0.02 19.50
FGL2 -0.0002091 9544 GTEx DepMap Descartes 0.00 0.00
CYBB -0.0002125 9593 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: 8.15e-01
Mean rank of genes in gene set: 6763
Median rank of genes in gene set: 6354.5
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
COL18A1 0.0071853 49 GTEx DepMap Descartes 0.69 464.95
LAMC1 0.0036300 200 GTEx DepMap Descartes 0.35 184.25
ERBB3 0.0019448 508 GTEx DepMap Descartes 0.06 51.88
COL5A2 0.0017802 580 GTEx DepMap Descartes 0.43 243.54
VCAN 0.0017611 587 GTEx DepMap Descartes 0.39 136.25
DST 0.0015832 671 GTEx DepMap Descartes 1.11 194.21
STARD13 0.0011991 958 GTEx DepMap Descartes 0.17 125.40
VIM 0.0010740 1072 GTEx DepMap Descartes 0.52 931.12
PLCE1 0.0007947 1470 GTEx DepMap Descartes 0.15 30.53
GAS7 0.0007862 1487 GTEx DepMap Descartes 0.08 39.63
IL1RAPL2 0.0003970 2709 GTEx DepMap Descartes 0.06 54.78
ADAMTS5 0.0002646 3501 GTEx DepMap Descartes 0.00 0.00
LAMA4 0.0001587 4299 GTEx DepMap Descartes 0.02 12.85
SLC35F1 0.0001088 4743 GTEx DepMap Descartes 0.01 13.79
MPZ 0.0000883 4933 GTEx DepMap Descartes 0.00 0.00
PLP1 0.0000497 5371 GTEx DepMap Descartes 0.01 4.88
HMGA2 0.0000485 5382 GTEx DepMap Descartes 0.06 8.89
COL25A1 0.0000478 5397 GTEx DepMap Descartes 0.05 14.63
IL1RAPL1 0.0000325 5579 GTEx DepMap Descartes 0.23 119.03
EDNRB 0.0000288 5626 GTEx DepMap Descartes 0.01 3.71
NRXN3 0.0000087 5885 GTEx DepMap Descartes 0.18 60.47
PTPRZ1 -0.0000200 6276 GTEx DepMap Descartes 0.01 2.87
SFRP1 -0.0000288 6433 GTEx DepMap Descartes 0.05 39.16
OLFML2A -0.0000330 6501 GTEx DepMap Descartes 0.00 0.00
MDGA2 -0.0000943 7654 GTEx DepMap Descartes 0.00 0.00
FIGN -0.0001017 7802 GTEx DepMap Descartes 0.06 18.25
TRPM3 -0.0001568 8793 GTEx DepMap Descartes 0.05 17.48
SCN7A -0.0001625 8856 GTEx DepMap Descartes 0.02 15.93
GRIK3 -0.0001893 9264 GTEx DepMap Descartes 0.02 4.83
KCTD12 -0.0002378 9899 GTEx DepMap Descartes 0.01 8.20


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: 1.26e-01
Mean rank of genes in gene set: 5656.29
Median rank of genes in gene set: 5723
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
UBASH3B 0.0068963 52 GTEx DepMap Descartes 0.24 165.86
MYH9 0.0042632 155 GTEx DepMap Descartes 0.40 259.05
THBS1 0.0033280 233 GTEx DepMap Descartes 0.61 339.33
FLNA 0.0021984 432 GTEx DepMap Descartes 0.42 195.87
LTBP1 0.0018719 537 GTEx DepMap Descartes 0.18 104.40
ACTN1 0.0018292 556 GTEx DepMap Descartes 0.37 327.61
GSN 0.0017113 616 GTEx DepMap Descartes 0.20 149.44
STOM 0.0013786 797 GTEx DepMap Descartes 0.09 109.52
MYLK 0.0013139 854 GTEx DepMap Descartes 0.05 29.71
VCL 0.0012725 892 GTEx DepMap Descartes 0.13 55.82
ARHGAP6 0.0009516 1189 GTEx DepMap Descartes 0.04 28.90
TRPC6 0.0007118 1635 GTEx DepMap Descartes 0.01 16.05
TPM4 0.0006767 1713 GTEx DepMap Descartes 0.15 100.32
P2RX1 0.0006614 1750 GTEx DepMap Descartes 0.01 10.00
FLI1 0.0005632 2054 GTEx DepMap Descartes 0.03 42.52
ZYX 0.0004809 2331 GTEx DepMap Descartes 0.07 154.33
TGFB1 0.0004587 2442 GTEx DepMap Descartes 0.10 99.90
RAP1B 0.0004454 2500 GTEx DepMap Descartes 0.16 43.75
PSTPIP2 0.0002348 3710 GTEx DepMap Descartes 0.02 30.36
CD9 0.0002236 3790 GTEx DepMap Descartes 0.16 161.65
ITGB3 0.0001473 4396 GTEx DepMap Descartes 0.00 0.00
SLC24A3 0.0001115 4723 GTEx DepMap Descartes 0.04 40.19
FERMT3 0.0000205 5723 GTEx DepMap Descartes 0.02 49.23
SLC2A3 0.0000204 5725 GTEx DepMap Descartes 0.10 66.18
TLN1 0.0000115 5844 GTEx DepMap Descartes 0.04 21.97
LIMS1 0.0000037 5949 GTEx DepMap Descartes 0.13 112.16
ANGPT1 0.0000004 5997 GTEx DepMap Descartes 0.01 13.16
TUBB1 -0.0000652 7119 GTEx DepMap Descartes 0.00 0.00
MMRN1 -0.0000942 7652 GTEx DepMap Descartes 0.00 0.00
DOK6 -0.0001040 7843 GTEx DepMap Descartes 0.10 40.28


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: 9.56e-01
Mean rank of genes in gene set: 7227.88
Median rank of genes in gene set: 8387
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
ABLIM1 0.0024378 371 GTEx DepMap Descartes 0.39 172.98
CCND3 0.0023765 383 GTEx DepMap Descartes 0.14 229.81
MSN 0.0015514 694 GTEx DepMap Descartes 0.11 108.36
ARID5B 0.0013044 863 GTEx DepMap Descartes 0.27 110.38
MCTP2 0.0012648 897 GTEx DepMap Descartes 0.07 37.85
ETS1 0.0012504 911 GTEx DepMap Descartes 0.11 73.86
SP100 0.0010634 1086 GTEx DepMap Descartes 0.12 110.60
MBNL1 0.0009906 1154 GTEx DepMap Descartes 0.41 223.14
FOXP1 0.0005591 2066 GTEx DepMap Descartes 0.77 318.76
BACH2 0.0005499 2087 GTEx DepMap Descartes 0.42 156.22
ITPKB 0.0005392 2123 GTEx DepMap Descartes 0.02 11.70
PLEKHA2 0.0004908 2300 GTEx DepMap Descartes 0.06 37.52
ANKRD44 0.0000689 5131 GTEx DepMap Descartes 0.13 70.71
PRKCH 0.0000658 5167 GTEx DepMap Descartes 0.02 25.65
B2M 0.0000656 5169 GTEx DepMap Descartes 0.48 700.19
CCL5 0.0000301 5607 GTEx DepMap Descartes 0.00 0.00
ARHGDIB 0.0000131 5823 GTEx DepMap Descartes 0.01 22.50
LCP1 -0.0000018 6032 GTEx DepMap Descartes 0.01 11.07
CD44 -0.0000473 6781 GTEx DepMap Descartes 0.09 100.77
STK39 -0.0000833 7465 GTEx DepMap Descartes 0.15 197.19
SAMD3 -0.0001202 8150 GTEx DepMap Descartes 0.01 5.19
RCSD1 -0.0001479 8624 GTEx DepMap Descartes 0.01 2.20
LEF1 -0.0001759 9045 GTEx DepMap Descartes 0.01 9.86
IKZF1 -0.0002068 9507 GTEx DepMap Descartes 0.00 0.00
RAP1GAP2 -0.0002306 9812 GTEx DepMap Descartes 0.32 152.16
SKAP1 -0.0002579 10153 GTEx DepMap Descartes 0.02 6.51
SORL1 -0.0002702 10288 GTEx DepMap Descartes 0.09 24.28
PTPRC -0.0002734 10327 GTEx DepMap Descartes 0.01 7.99
SCML4 -0.0002847 10437 GTEx DepMap Descartes 0.06 34.14
WIPF1 -0.0003735 11181 GTEx DepMap Descartes 0.05 41.10


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 (curated 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: 3.87e-03
Mean rank of genes in gene set: 704.33
Rank on gene expression program of genes in gene set:
Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
COL1A2 0.0028187 309 GTEx DepMap Descartes 1.78 1420.98
DCN 0.0013891 785 GTEx DepMap Descartes 0.11 62.79
COL1A1 0.0011264 1019 GTEx DepMap Descartes 0.90 662.84


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: 8.03e-03
Mean rank of genes in gene set: 108.5
Rank on gene expression program of genes in gene set:

Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
FXYD2 0.0067950 53 GTEx DepMap Descartes 0.06 82.01
HES1 0.0040673 164 GTEx DepMap Descartes 0.19 512.70


pDC precursor: pDC precursor (curated markers)
precursors of plasmacytoid dendritic cells which have intermixed lymphoid and myeloid origins and give rise to plasmacytoid dendritic cells:
Wilcoxon ranksum test P-value for gene set overrepresentation: 2.69e-02
Mean rank of genes in gene set: 1333.5
Rank on gene expression program of genes in gene set:

Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
CCDC50 0.0009240 1230 GTEx DepMap Descartes 0.10 50.57
IRF7 0.0008144 1437 GTEx DepMap Descartes 0.05 125.24