Program: 7. Hepatocyte-like Cells.

Program: 7. Hepatocyte-like Cells.


Program description and justification of annotation generated by GPT5: Hepatocytes/Liver parenchyma with acute-phase complement-coagulation and xenobiotic metabolism (non-malignant liver tissue admixture).

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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 TTR 0.0178884 transthyretin GTEx DepMap Descartes 2.23 1552.58
2 APOC3 0.0166959 apolipoprotein C3 GTEx DepMap Descartes 6.56 8028.29
3 APOA2 0.0160086 apolipoprotein A2 GTEx DepMap Descartes 6.86 5323.87
4 APOA1 0.0158184 apolipoprotein A1 GTEx DepMap Descartes 9.94 6362.97
5 ALB 0.0156337 albumin GTEx DepMap Descartes 65.43 22211.27
6 APOC1 0.0155098 apolipoprotein C1 GTEx DepMap Descartes 6.17 6328.76
7 AMBP 0.0154460 alpha-1-microglobulin/bikunin precursor GTEx DepMap Descartes 3.09 1706.35
8 RBP4 0.0152068 retinol binding protein 4 GTEx DepMap Descartes 3.19 1652.31
9 ORM1 0.0137252 orosomucoid 1 GTEx DepMap Descartes 0.97 833.89
10 TF 0.0133573 transferrin GTEx DepMap Descartes 5.13 181.22
11 MT1G 0.0132070 metallothionein 1G GTEx DepMap Descartes 1.72 1933.33
12 ORM2 0.0128501 orosomucoid 2 GTEx DepMap Descartes 0.56 508.66
13 FABP1 0.0127124 fatty acid binding protein 1 GTEx DepMap Descartes 2.01 693.92
14 SERPINC1 0.0125430 serpin family C member 1 GTEx DepMap Descartes 0.87 424.55
15 SERPINA1 0.0124490 serpin family A member 1 GTEx DepMap Descartes 9.24 1689.58
16 APOH 0.0123889 apolipoprotein H GTEx DepMap Descartes 2.74 1589.06
17 HP 0.0118195 haptoglobin GTEx DepMap Descartes 2.60 575.11
18 HRG 0.0117758 histidine rich glycoprotein GTEx DepMap Descartes 1.58 261.88
19 GC 0.0109686 GC vitamin D binding protein GTEx DepMap Descartes 1.32 554.33
20 ALDOB 0.0108179 aldolase, fructose-bisphosphate B GTEx DepMap Descartes 2.71 744.29
21 APOB 0.0105415 apolipoprotein B GTEx DepMap Descartes 8.78 357.33
22 AHSG 0.0103227 alpha 2-HS glycoprotein GTEx DepMap Descartes 5.64 2000.95
23 FGA 0.0100699 fibrinogen alpha chain GTEx DepMap Descartes 8.10 1260.14
24 CES1 0.0098968 carboxylesterase 1 GTEx DepMap Descartes 0.86 290.11
25 MT1E 0.0096892 metallothionein 1E GTEx DepMap Descartes 1.95 1572.31
26 KNG1 0.0096380 kininogen 1 GTEx DepMap Descartes 1.58 261.20
27 A1BG 0.0094293 alpha-1-B glycoprotein GTEx DepMap Descartes 1.74 335.32
28 IGFBP1 0.0091676 insulin like growth factor binding protein 1 GTEx DepMap Descartes 5.92 2044.25
29 AGT 0.0090146 angiotensinogen GTEx DepMap Descartes 1.37 437.06
30 ADH1B 0.0085518 alcohol dehydrogenase 1B (class I), beta polypeptide GTEx DepMap Descartes 3.42 376.23
31 MT2A 0.0085217 metallothionein 2A GTEx DepMap Descartes 10.62 6102.94
32 FGB 0.0083576 fibrinogen beta chain GTEx DepMap Descartes 10.38 2714.10
33 MT1H 0.0083026 metallothionein 1H GTEx DepMap Descartes 0.67 569.26
34 CYP2E1 0.0081639 cytochrome P450 family 2 subfamily E member 1 GTEx DepMap Descartes 3.32 251.93
35 VTN 0.0080599 vitronectin GTEx DepMap Descartes 0.46 197.98
36 TAT 0.0080485 tyrosine aminotransferase GTEx DepMap Descartes 0.70 118.78
37 HPX 0.0079439 hemopexin GTEx DepMap Descartes 1.46 532.67
38 PLG 0.0079146 plasminogen GTEx DepMap Descartes 2.19 446.13
39 HAMP 0.0078801 hepcidin antimicrobial peptide GTEx DepMap Descartes 0.85 197.20
40 ADH1A 0.0074989 alcohol dehydrogenase 1A (class I), alpha polypeptide GTEx DepMap Descartes 0.59 304.00
41 AGXT 0.0074805 alanine–glyoxylate aminotransferase GTEx DepMap Descartes 1.42 268.49
42 ITIH1 0.0074593 inter-alpha-trypsin inhibitor heavy chain 1 GTEx DepMap Descartes 0.66 137.49
43 SPP2 0.0074142 secreted phosphoprotein 2 GTEx DepMap Descartes 1.45 812.62
44 CFHR2 0.0073599 complement factor H related 2 GTEx DepMap Descartes 0.60 293.10
45 ITIH2 0.0072864 inter-alpha-trypsin inhibitor heavy chain 2 GTEx DepMap Descartes 0.85 196.69
46 APCS 0.0072276 amyloid P component, serum GTEx DepMap Descartes 0.87 595.29
47 ISG15 0.0071035 ISG15 ubiquitin like modifier GTEx DepMap Descartes 0.75 698.87
48 ANGPTL3 0.0069669 angiopoietin like 3 GTEx DepMap Descartes 0.92 176.41
49 AZGP1 0.0067667 alpha-2-glycoprotein 1, zinc-binding GTEx DepMap Descartes 1.23 338.46
50 MT1M 0.0067411 metallothionein 1M GTEx DepMap Descartes 0.32 500.73


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UMAP plots showing activity of gene expression program identified in GEP 7. Hepatocyte-like Cells:

Interactive UMAP Plot
Interactive UMAP Plot
Interactive UMAP Plot

Boxlot showing activity of gene expression program identified in GEP 7. Hepatocyte-like Cells:
Interactive Boxplot
Interactive Boxplot
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
AIZARANI_LIVER_C11_HEPATOCYTES_1 7.79e-85 1251.71 405.35 5.23e-82 5.23e-82
47TTR, APOC3, APOA2, APOA1, ALB, APOC1, AMBP, RBP4, ORM1, TF, MT1G, ORM2, FABP1, SERPINC1, SERPINA1, APOH, HP, HRG, GC, ALDOB, APOB, AHSG, FGA, CES1, MT1E, KNG1, A1BG, IGFBP1, AGT, ADH1B, MT2A, FGB, CYP2E1, VTN, TAT, HPX, PLG, HAMP, ADH1A, AGXT, ITIH1, SPP2, ITIH2, APCS, ANGPTL3, AZGP1, MT1M
 298
AIZARANI_LIVER_C14_HEPATOCYTES_2 6.70e-82 841.20 342.17 2.25e-79 4.50e-79
44TTR, APOC3, APOA2, APOA1, APOC1, AMBP, RBP4, ORM1, TF, MT1G, ORM2, FABP1, SERPINC1, SERPINA1, APOH, HP, HRG, GC, ALDOB, APOB, AHSG, FGA, CES1, MT1E, KNG1, A1BG, IGFBP1, ADH1B, MT2A, FGB, MT1H, CYP2E1, VTN, TAT, HPX, PLG, HAMP, ADH1A, AGXT, ITIH1, SPP2, APCS, ANGPTL3, AZGP1
 226
AIZARANI_LIVER_C17_HEPATOCYTES_3 1.10e-63 516.94 266.84 1.85e-61 7.40e-61
32APOC3, APOA2, APOA1, APOC1, AMBP, RBP4, ORM1, TF, ORM2, SERPINC1, SERPINA1, APOH, HP, HRG, APOB, AHSG, FGA, CES1, KNG1, A1BG, IGFBP1, ADH1B, MT2A, FGB, CYP2E1, VTN, HPX, PLG, ADH1A, AGXT, ITIH1, AZGP1
 102
DESCARTES_FETAL_SPLEEN_AFP_ALB_POSITIVE_CELLS 4.68e-69 430.27 215.94 1.05e-66 3.14e-66
38TTR, APOC3, APOA2, APOA1, ALB, APOC1, AMBP, RBP4, TF, MT1G, FABP1, SERPINC1, SERPINA1, APOH, HRG, GC, ALDOB, APOB, AHSG, FGA, MT1E, KNG1, IGFBP1, AGT, MT2A, FGB, MT1H, VTN, HPX, PLG, HAMP, ADH1A, AGXT, ITIH1, SPP2, ITIH2, ANGPTL3, AZGP1
 188
DESCARTES_FETAL_PLACENTA_AFP_ALB_POSITIVE_CELLS 5.54e-58 287.00 151.69 6.20e-56 3.72e-55
33TTR, APOC3, APOA2, APOA1, ALB, AMBP, RBP4, TF, MT1G, FABP1, SERPINC1, SERPINA1, APOH, HRG, GC, ALDOB, APOB, AHSG, FGA, MT1E, KNG1, AGT, MT2A, FGB, MT1H, VTN, HPX, PLG, ADH1A, AGXT, ITIH1, ITIH2, ANGPTL3
 171
DESCARTES_FETAL_LIVER_HEPATOBLASTS 1.02e-58 202.89 96.72 1.37e-56 6.86e-56
41TTR, APOC3, APOA2, APOA1, ALB, APOC1, AMBP, RBP4, TF, MT1G, FABP1, SERPINC1, SERPINA1, APOH, HRG, GC, ALDOB, APOB, AHSG, FGA, MT1E, KNG1, A1BG, IGFBP1, AGT, MT2A, FGB, MT1H, VTN, TAT, HPX, PLG, HAMP, ADH1A, AGXT, ITIH1, SPP2, ITIH2, ANGPTL3, AZGP1, MT1M
 501
DESCARTES_MAIN_FETAL_AFP_ALB_POSITIVE_CELLS 4.43e-20 69.95 33.90 4.25e-18 2.97e-17
14ALB, MT1G, FABP1, SERPINC1, SERPINA1, HRG, AHSG, FGA, KNG1, FGB, VTN, ANGPTL3, AZGP1, MT1M
 128
DESCARTES_FETAL_PANCREAS_ACINAR_CELLS 6.55e-13 56.99 23.54 5.49e-11 4.39e-10
9ALB, AMBP, MT1G, FABP1, APOB, MT1E, MT2A, MT1H, MT1M
 88
GAO_SMALL_INTESTINE_24W_C4_ENTEROCYTE_PROGENITOR_SUBTYPE_2 3.39e-09 37.15 13.71 2.07e-07 2.28e-06
7APOC3, APOA1, RBP4, ALDOB, APOB, AGT, VTN
 97
DESCARTES_FETAL_STOMACH_MUC13_DMBT1_POSITIVE_CELLS 3.39e-09 37.15 13.71 2.07e-07 2.28e-06
7APOC3, APOA1, MT1G, ALDOB, APOB, MT2A, MT1H
 97
DESCARTES_FETAL_STOMACH_PARIETAL_AND_CHIEF_CELLS 3.19e-06 46.89 11.69 1.65e-04 2.14e-03
4ALB, FGA, FGB, ANGPTL3
 42
DESCARTES_FETAL_INTESTINE_INTESTINAL_EPITHELIAL_CELLS 1.76e-12 24.56 11.55 1.31e-10 1.18e-09
12APOC3, APOA2, APOA1, RBP4, MT1G, FABP1, ALDOB, APOB, FGA, MT1E, AGT, MT1H
 276
BUSSLINGER_DUODENAL_BCHE_CELLS 3.51e-06 45.69 11.41 1.68e-04 2.36e-03
4MT1G, MT1E, MT2A, MT1H
 43
BUSSLINGER_DUODENAL_EC_CELLS 5.75e-05 46.70 8.79 2.03e-03 3.86e-02
3TTR, GC, CES1
 31
BUSSLINGER_GASTRIC_METALLOTHIONEIN_CELLS 4.26e-06 23.98 7.28 1.90e-04 2.86e-03
5ALB, MT1G, MT1E, MT2A, MT1H
 100
MURARO_PANCREAS_EPSILON_CELL 1.65e-04 31.93 6.11 4.99e-03 1.11e-01
3SERPINA1, AGT, VTN
 44
BUSSLINGER_DUODENAL_TUFT_CELLS 4.40e-05 23.19 5.91 1.64e-03 2.95e-02
4MT1G, SERPINA1, MT2A, AZGP1
 81
AIZARANI_LIVER_C4_EPCAM_POS_BILE_DUCT_CELLS_1 6.33e-06 15.13 5.20 2.66e-04 4.25e-03
6AMBP, GC, APOB, AGT, VTN, ITIH2
 191
TRAVAGLINI_LUNG_MACROPHAGE_CELL 8.46e-06 14.36 4.94 3.34e-04 5.68e-03
6APOC1, RBP4, SERPINA1, MT1E, ISG15, MT1M
 201
BUSSLINGER_GASTRIC_CHIEF_CELLS 3.39e-04 24.72 4.77 9.09e-03 2.27e-01
3MT1G, MT2A, AZGP1
 56

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mSigDB Hallmark Gene Sets:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
HALLMARK_COAGULATION 1.01e-12 40.07 17.48 2.52e-11 5.04e-11
10APOC3, APOA1, APOC1, TF, SERPINC1, SERPINA1, HRG, FGA, PLG, ITIH1
 138
HALLMARK_XENOBIOTIC_METABOLISM 3.98e-14 34.48 16.13 1.99e-12 1.99e-12
12RBP4, FABP1, HRG, CES1, IGFBP1, MT2A, CYP2E1, VTN, TAT, PLG, ITIH1, ANGPTL3
 200
HALLMARK_BILE_ACID_METABOLISM 1.54e-04 16.53 4.25 1.93e-03 7.72e-03
4TTR, APOA1, GC, AGXT
 112
HALLMARK_COMPLEMENT 1.17e-04 11.70 3.59 1.93e-03 5.85e-03
5APOC1, SERPINC1, SERPINA1, PLG, ITIH1
 200
HALLMARK_ANGIOGENESIS 3.44e-03 25.16 2.85 2.87e-02 1.72e-01
2APOH, VTN
 36
HALLMARK_HYPOXIA 1.36e-03 9.11 2.36 1.36e-02 6.78e-02
4ALDOB, MT1E, IGFBP1, MT2A
 200
HALLMARK_PEROXISOME 2.62e-02 8.39 0.97 1.87e-01 1.00e+00
2TTR, ALB
 104
HALLMARK_INTERFERON_GAMMA_RESPONSE 8.36e-02 4.32 0.51 4.19e-01 1.00e+00
2MT2A, ISG15
 200
HALLMARK_KRAS_SIGNALING_UP 8.36e-02 4.32 0.51 4.19e-01 1.00e+00
2RBP4, CFHR2
 200
HALLMARK_HEDGEHOG_SIGNALING 8.37e-02 11.97 0.29 4.19e-01 1.00e+00
1PLG
 36
HALLMARK_INTERFERON_ALPHA_RESPONSE 2.10e-01 4.37 0.11 8.98e-01 1.00e+00
1ISG15
 97
HALLMARK_ANDROGEN_RESPONSE 2.15e-01 4.23 0.10 8.98e-01 1.00e+00
1AZGP1
 100
HALLMARK_UNFOLDED_PROTEIN_RESPONSE 2.40e-01 3.74 0.09 9.22e-01 1.00e+00
1IGFBP1
 113
HALLMARK_UV_RESPONSE_DN 2.95e-01 2.93 0.07 9.59e-01 1.00e+00
1MT1E
 144
HALLMARK_FATTY_ACID_METABOLISM 3.18e-01 2.67 0.07 9.59e-01 1.00e+00
1FABP1
 158
HALLMARK_IL2_STAT5_SIGNALING 3.82e-01 2.12 0.05 9.59e-01 1.00e+00
1SERPINC1
 199
HALLMARK_G2M_CHECKPOINT 3.84e-01 2.11 0.05 9.59e-01 1.00e+00
1MT2A
 200
HALLMARK_ADIPOGENESIS 3.84e-01 2.11 0.05 9.59e-01 1.00e+00
1ORM1
 200
HALLMARK_ESTROGEN_RESPONSE_LATE 3.84e-01 2.11 0.05 9.59e-01 1.00e+00
1SERPINA1
 200
HALLMARK_GLYCOLYSIS 3.84e-01 2.11 0.05 9.59e-01 1.00e+00
1ALDOB
 200

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KEGG Pathways:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
KEGG_COMPLEMENT_AND_COAGULATION_CASCADES 1.58e-08 44.33 14.93 2.93e-06 2.93e-06
6SERPINC1, SERPINA1, FGA, KNG1, FGB, PLG
 69
KEGG_PPAR_SIGNALING_PATHWAY 2.34e-05 27.46 6.97 2.18e-03 4.35e-03
4APOC3, APOA2, APOA1, FABP1
 69
KEGG_TYROSINE_METABOLISM 1.44e-04 33.55 6.42 8.92e-03 2.68e-02
3ADH1B, TAT, ADH1A
 42
KEGG_GLYCOLYSIS_GLUCONEOGENESIS 4.57e-04 22.21 4.30 2.12e-02 8.50e-02
3ALDOB, ADH1B, ADH1A
 62
KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450 6.52e-04 19.56 3.80 2.19e-02 1.21e-01
3ADH1B, CYP2E1, ADH1A
 70
KEGG_DRUG_METABOLISM_CYTOCHROME_P450 7.07e-04 18.99 3.69 2.19e-02 1.32e-01
3ADH1B, CYP2E1, ADH1A
 72
KEGG_FATTY_ACID_METABOLISM 4.66e-03 21.38 2.43 1.24e-01 8.67e-01
2ADH1B, ADH1A
 42
KEGG_RETINOL_METABOLISM 1.05e-02 13.80 1.59 2.45e-01 1.00e+00
2ADH1B, ADH1A
 64
KEGG_RENIN_ANGIOTENSIN_SYSTEM 4.05e-02 26.18 0.61 7.96e-01 1.00e+00
1AGT
 17
KEGG_PHENYLALANINE_METABOLISM 4.28e-02 24.63 0.58 7.96e-01 1.00e+00
1TAT
 18
KEGG_PENTOSE_PHOSPHATE_PATHWAY 6.35e-02 16.11 0.39 9.22e-01 1.00e+00
1ALDOB
 27
KEGG_LINOLEIC_ACID_METABOLISM 6.80e-02 14.96 0.36 9.22e-01 1.00e+00
1CYP2E1
 29
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 7.26e-02 13.97 0.34 9.22e-01 1.00e+00
1AGXT
 31
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM 7.48e-02 13.52 0.33 9.22e-01 1.00e+00
1AGXT
 32
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 7.93e-02 12.69 0.31 9.22e-01 1.00e+00
1ALDOB
 34
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 7.93e-02 12.69 0.31 9.22e-01 1.00e+00
1TAT
 34
KEGG_DRUG_METABOLISM_OTHER_ENZYMES 1.17e-01 8.38 0.20 1.00e+00 1.00e+00
1CES1
 51
KEGG_ARACHIDONIC_ACID_METABOLISM 1.31e-01 7.35 0.18 1.00e+00 1.00e+00
1CYP2E1
 58
KEGG_RIG_I_LIKE_RECEPTOR_SIGNALING_PATHWAY 1.58e-01 5.99 0.15 1.00e+00 1.00e+00
1ISG15
 71
KEGG_PEROXISOME 1.72e-01 5.44 0.13 1.00e+00 1.00e+00
1AGXT
 78

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CHR Positional Gene Sets:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
chr16q13 4.21e-08 65.05 19.02 1.17e-05 1.17e-05
5MT1G, MT1E, MT2A, MT1H, MT1M
 40
chr9q32 2.01e-04 29.76 5.71 2.80e-02 5.60e-02
3AMBP, ORM1, ORM2
 47
chr3q27 2.71e-03 11.70 2.30 2.51e-01 7.53e-01
3HRG, AHSG, KNG1
 115
chr6q26 3.35e-02 32.20 0.74 1.00e+00 1.00e+00
1PLG
 14
chr4q31 5.51e-02 5.52 0.64 1.00e+00 1.00e+00
2FGA, FGB
 157
chr16q22 6.92e-02 4.83 0.56 1.00e+00 1.00e+00
2HP, TAT
 179
chr11q23 8.71e-02 4.21 0.49 1.00e+00 1.00e+00
2APOC3, APOA1
 205
chr1q23 9.58e-02 3.98 0.47 1.00e+00 1.00e+00
2APOA2, APCS
 217
chr19q13 7.50e-01 1.13 0.22 1.00e+00 1.00e+00
3APOC1, A1BG, HAMP
 1165
chr10p14 1.08e-01 9.11 0.22 1.00e+00 1.00e+00
1ITIH2
 47
chr7p12 1.31e-01 7.35 0.18 1.00e+00 1.00e+00
1IGFBP1
 58
chr1q31 1.58e-01 5.99 0.15 1.00e+00 1.00e+00
1CFHR2
 71
chr2p24 1.64e-01 5.74 0.14 1.00e+00 1.00e+00
1APOB
 74
chr17q24 2.04e-01 4.51 0.11 1.00e+00 1.00e+00
1APOH
 94
chr16q12 2.08e-01 4.41 0.11 1.00e+00 1.00e+00
1CES1
 96
chr18q12 2.08e-01 4.41 0.11 1.00e+00 1.00e+00
1TTR
 96
chr3q22 2.47e-01 3.61 0.09 1.00e+00 1.00e+00
1TF
 117
chr9q31 2.67e-01 3.30 0.08 1.00e+00 1.00e+00
1ALDOB
 128
chr1q25 3.21e-01 2.64 0.07 1.00e+00 1.00e+00
1SERPINC1
 160
chr17q11 3.23e-01 2.62 0.06 1.00e+00 1.00e+00
1VTN
 161

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Transcription Factor Targets:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
NR1H4_TARGET_GENES 8.11e-12 21.39 10.08 9.19e-09 9.19e-09
12AMBP, RBP4, SERPINC1, SERPINA1, HRG, KNG1, AGT, ADH1B, CYP2E1, TAT, ADH1A, AGXT
 315
RGTTAMWNATT_HNF1_01 9.60e-07 33.03 9.94 2.72e-04 1.09e-03
5TTR, GC, IGFBP1, AGT, PLG
 74
HNF1_Q6 1.60e-07 15.77 6.33 6.03e-05 1.81e-04
8ALB, GC, FGA, IGFBP1, FGB, CYP2E1, PLG, ANGPTL3
 256
HNF1_01 1.91e-06 13.99 5.25 4.22e-04 2.16e-03
7ALB, GC, FGA, IGFBP1, CYP2E1, PLG, APCS
 246
ZSCAN2_TARGET_GENES 1.18e-08 8.94 4.44 6.70e-06 1.34e-05
14APOC3, APOA2, APOA1, AMBP, TF, FABP1, SERPINA1, APOH, HP, AHSG, FGA, CES1, AGT, VTN
 908
HHEX_TARGET_GENES 3.05e-06 6.34 3.01 4.94e-04 3.46e-03
12TTR, APOC3, APOA2, APOA1, AMBP, TF, HRG, AHSG, FGA, AGT, VTN, PLG
 1035
HNF1_C 3.20e-04 9.35 2.87 3.63e-02 3.63e-01
5RBP4, GC, FGA, FGB, APCS
 249
CDP_01 1.57e-03 14.24 2.79 1.49e-01 1.00e+00
3TTR, ALB, GC
 95
HMG20B_TARGET_GENES 2.23e-06 5.07 2.61 4.22e-04 2.53e-03
16APOC3, APOA2, APOA1, AMBP, RBP4, TF, SERPINA1, APOB, AHSG, FGA, MT1E, KNG1, AGT, HPX, PLG, AZGP1
 1922
TGTTTGY_HNF3_Q6 3.21e-04 5.29 2.14 3.63e-02 3.63e-01
8TF, FABP1, SERPINA1, AHSG, FGA, A1BG, IGFBP1, ITIH1
 748
TTCYNRGAA_STAT5B_01 1.30e-03 6.79 2.09 1.33e-01 1.00e+00
5FGA, A1BG, AGT, VTN, HAMP
 341
TCF7_TARGET_GENES 7.19e-05 4.05 2.01 1.02e-02 8.15e-02
14APOA2, RBP4, TF, FABP1, SERPINA1, APOB, AHSG, FGA, CES1, A1BG, IGFBP1, MT2A, AGXT, ITIH2
 1987
TGCCAAR_NF1_Q6 6.84e-03 3.88 1.35 5.96e-01 1.00e+00
6APOA2, ALB, RBP4, AHSG, ITIH2, ISG15
 727
STAT5B_01 2.33e-02 5.20 1.03 1.00e+00 1.00e+00
3FGA, VTN, HAMP
 255
STAT_01 2.40e-02 5.14 1.02 1.00e+00 1.00e+00
3FGA, AGT, VTN
 258
STAT5A_01 2.42e-02 5.12 1.01 1.00e+00 1.00e+00
3FGA, VTN, HAMP
 259
DBP_Q6 2.57e-02 5.00 0.99 1.00e+00 1.00e+00
3FABP1, SERPINA1, ITIH1
 265
CDP_02 2.95e-02 7.85 0.91 1.00e+00 1.00e+00
2GC, A1BG
 111
TATAAA_TATA_01 1.23e-01 2.14 0.74 1.00e+00 1.00e+00
6RBP4, ORM2, FABP1, ALDOB, AGT, CYP2E1
 1317
ARP1_01 6.13e-02 5.19 0.61 1.00e+00 1.00e+00
2SERPINC1, CYP2E1
 167

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GO Biological Processes:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
GOBP_POSITIVE_REGULATION_OF_CHOLESTEROL_ESTERIFICATION 3.84e-09 350.91 68.02 6.68e-07 2.87e-05
4APOA2, APOA1, APOC1, AGT
 9
GOBP_CHYLOMICRON_REMODELING 3.84e-09 350.91 68.02 6.68e-07 2.87e-05
4APOC3, APOA2, APOA1, APOB
 9
GOBP_REGULATION_OF_VERY_LOW_DENSITY_LIPOPROTEIN_PARTICLE_REMODELING 2.68e-07 430.78 56.44 2.42e-05 2.01e-03
3APOC3, APOA2, APOA1
 6
GOBP_CHYLOMICRON_ASSEMBLY 1.00e-08 252.63 52.52 1.36e-06 7.49e-05
4APOC3, APOA2, APOA1, APOB
 11
GOBP_NEGATIVE_REGULATION_OF_LIPASE_ACTIVITY 4.15e-10 188.92 50.06 1.11e-07 3.10e-06
5APOC3, APOA2, APOA1, APOC1, ANGPTL3
 17
GOBP_DETOXIFICATION_OF_INORGANIC_COMPOUND 4.15e-10 188.92 50.06 1.11e-07 3.10e-06
5MT1G, MT1E, MT2A, MT1H, MT1M
 17
GOBP_HIGH_DENSITY_LIPOPROTEIN_PARTICLE_REMODELING 5.73e-10 173.11 46.73 1.34e-07 4.29e-06
5APOC3, APOA2, APOA1, ALB, APOC1
 18
GOBP_STRESS_RESPONSE_TO_METAL_ION 5.73e-10 173.11 46.73 1.34e-07 4.29e-06
5MT1G, MT1E, MT2A, MT1H, MT1M
 18
GOBP_NEGATIVE_REGULATION_OF_LIPOPROTEIN_LIPASE_ACTIVITY 4.68e-07 327.81 46.27 3.78e-05 3.50e-03
3APOC3, APOC1, ANGPTL3
 7
GOBP_PHOSPHOLIPID_EFFLUX 2.16e-08 196.88 42.85 2.79e-06 1.62e-04
4APOC3, APOA2, APOA1, APOC1
 13
GOBP_PROTEIN_CONTAINING_COMPLEX_REMODELING 2.03e-12 118.97 41.61 1.76e-09 1.52e-08
7APOC3, APOA2, APOA1, ALB, APOC1, APOB, AGT
 35
GOBP_TRIGLYCERIDE_RICH_LIPOPROTEIN_PARTICLE_CLEARANCE 7.48e-07 259.50 39.26 5.71e-05 5.59e-03
3APOC3, APOC1, APOB
 8
GOBP_REGULATION_OF_CHOLESTEROL_ESTERIFICATION 3.02e-08 176.78 39.22 3.58e-06 2.26e-04
4APOA2, APOA1, APOC1, AGT
 14
GOBP_TRIGLYCERIDE_RICH_LIPOPROTEIN_PARTICLE_REMODELING 3.02e-08 176.78 39.22 3.58e-06 2.26e-04
4APOC3, APOA2, APOA1, APOB
 14
GOBP_PLATELET_DEGRANULATION 5.89e-22 77.76 38.30 4.41e-18 4.41e-18
15APOA1, ALB, ORM1, TF, ORM2, SERPINA1, APOH, HRG, AHSG, FGA, KNG1, A1BG, FGB, PLG, SPP2
 128
GOBP_REGULATION_OF_LIPOPROTEIN_LIPASE_ACTIVITY 2.81e-09 119.64 33.45 5.53e-07 2.10e-05
5APOC3, APOA1, APOC1, APOH, ANGPTL3
 24
GOBP_CELLULAR_RESPONSE_TO_ZINC_ION 2.81e-09 119.64 33.45 5.53e-07 2.10e-05
5MT1G, MT1E, MT2A, MT1H, MT1M
 24
GOBP_FIBRINOLYSIS 3.50e-09 113.57 31.93 6.68e-07 2.62e-05
5APOH, HRG, FGA, FGB, PLG
 25
GOBP_ACUTE_PHASE_RESPONSE 1.58e-11 85.40 30.57 8.43e-09 1.18e-07
7ORM1, ORM2, SERPINA1, HP, AHSG, HAMP, APCS
 46
GOBP_VERY_LOW_DENSITY_LIPOPROTEIN_PARTICLE_CLEARANCE 1.60e-06 185.92 30.16 1.15e-04 1.19e-02
3APOC3, APOC1, APOB
 10

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Immunological Gene Sets:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
GSE37301_RAG2_KO_VS_RAG2_AND_ETS1_KO_NK_CELL_UP 4.84e-07 17.32 6.49 2.36e-03 2.36e-03
7AMBP, ORM1, HRG, GC, FGB, ITIH1, CFHR2
 200
GSE41176_UNSTIM_VS_ANTI_IGM_STIM_TAK1_KO_BCELL_24H_DN 7.99e-06 14.51 4.99 1.34e-02 3.89e-02
6ORM1, MT1G, MT1E, MT2A, MT1H, MT1M
 199
GSE13484_UNSTIM_VS_YF17D_VACCINE_STIM_PBMC_DN 8.22e-06 14.43 4.97 1.34e-02 4.01e-02
6MT1G, CES1, MT1E, MT2A, MT1H, ISG15
 200
GSE24634_IL4_VS_CTRL_TREATED_NAIVE_CD4_TCELL_DAY5_DN 1.14e-04 11.76 3.60 5.70e-02 5.57e-01
5ORM1, MT1G, KNG1, MT2A, MT1H
 199
GSE41176_UNSTIM_VS_ANTI_IGM_STIM_BCELL_3H_UP 1.14e-04 11.76 3.60 5.70e-02 5.57e-01
5ALB, MT1G, MT1E, MT2A, MT1H
 199
GSE360_HIGH_DOSE_B_MALAYI_VS_M_TUBERCULOSIS_DC_DN 1.17e-04 11.70 3.59 5.70e-02 5.70e-01
5MT1G, SERPINA1, MT1E, MT2A, MT1H
 200
GSE37301_GRANULOCYTE_MONOCYTE_PROGENITOR_VS_RAG2_KO_NK_CELL_DN 1.17e-04 11.70 3.59 5.70e-02 5.70e-01
5TTR, AMBP, VTN, HPX, ITIH1
 200
GSE43955_TH0_VS_TGFB_IL6_TH17_ACT_CD4_TCELL_1H_UP 1.17e-04 11.70 3.59 5.70e-02 5.70e-01
5AMBP, MT1E, IGFBP1, MT2A, TAT
 200
GSE43955_TH0_VS_TGFB_IL6_TH17_ACT_CD4_TCELL_30H_UP 1.17e-04 11.70 3.59 5.70e-02 5.70e-01
5AMBP, FABP1, APOB, MT1E, MT2A
 200
GSE42088_UNINF_VS_LEISHMANIA_INF_DC_8H_UP 1.17e-04 11.70 3.59 5.70e-02 5.70e-01
5MT1G, MT1E, MT2A, MT1H, MT1M
 200
GSE43863_NAIVE_VS_TH1_EFF_CD4_TCELL_D6_LCMV_DN 1.04e-03 9.81 2.54 1.78e-01 1.00e+00
4MT1G, MT2A, MT1H, MT1M
 186
GSE10325_MYELOID_VS_LUPUS_MYELOID_UP 1.26e-03 9.30 2.41 1.78e-01 1.00e+00
4APOA1, APOH, APOB, AGXT
 196
GSE21546_WT_VS_SAP1A_KO_DP_THYMOCYTES_UP 1.26e-03 9.30 2.41 1.78e-01 1.00e+00
4MT1G, MT2A, MT1H, ISG15
 196
GSE28130_ACTIVATED_VS_INDUCEED_TREG_UP 1.26e-03 9.30 2.41 1.78e-01 1.00e+00
4ALB, SERPINC1, GC, APCS
 196
GSE9988_ANTI_TREM1_VS_LOW_LPS_MONOCYTE_UP 1.31e-03 9.20 2.38 1.78e-01 1.00e+00
4MT1G, MT1E, MT2A, MT1H
 198
GSE24574_BCL6_HIGH_TFH_VS_TCONV_CD4_TCELL_DN 1.31e-03 9.20 2.38 1.78e-01 1.00e+00
4ALB, SERPINC1, GC, APCS
 198
GSE10325_CD4_TCELL_VS_LUPUS_CD4_TCELL_DN 1.33e-03 9.16 2.37 1.78e-01 1.00e+00
4MT1E, MT2A, MT1H, ISG15
 199
GSE17721_CPG_VS_GARDIQUIMOD_6H_BMDC_UP 1.33e-03 9.16 2.37 1.78e-01 1.00e+00
4SERPINC1, CES1, FGB, SPP2
 199
GSE360_L_DONOVANI_VS_B_MALAYI_LOW_DOSE_DC_UP 1.33e-03 9.16 2.37 1.78e-01 1.00e+00
4MT1G, MT1E, MT2A, ISG15
 199
GSE360_LOW_DOSE_B_MALAYI_VS_M_TUBERCULOSIS_DC_DN 1.33e-03 9.16 2.37 1.78e-01 1.00e+00
4MT1G, SERPINA1, MT1E, MT2A
 199

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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
AGT 29 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None None
PRAP1 84 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None None
DSP 127 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None None
KLF6 142 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
FOS 150 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
ZFP36 151 No ssDNA/RNA binding Not a DNA binding protein No motif None RNA binding protein (PMID: 10330172).
ATF5 165 Yes Known motif Obligate heteromer In vivo/Misc source Only known motifs are from Transfac or HocoMoco - origin is uncertain Transfac motifs dont correspond to canonical bZIP binding sites. Annotated as obligate heteromer based on peptide array studies (PMID:12805554).
FOSB 173 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
ANXA4 180 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None None
FOXA3 184 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
NR0B2 192 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None Transcription cofactor - lacks a conventional DNA binding domain and represses the transcriptional activity of various nuclear receptors (PMID: 14752053)
ONECUT1 193 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
TRIB1 199 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None Associates with CEBPB and CEBPA and inhibits their activities (PMID: 17724128). This is probably achieved through control of their proteosomal degradation (PMID: 17576771)
PKHD1 205 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)
CEBPA 211 Yes Known motif Monomer or homomultimer 100 perc ID - in vitro None None
ID2 214 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
EGR1 216 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
LSR 219 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None Cell plasma membrane resident protein that functions in cell-cell junctions (PMID: 25753034)
HNF4G 220 Yes Known motif Monomer or homomultimer In vivo/Misc source None None
CEBPB 221 Yes Known motif Monomer or homomultimer High-throughput in vitro None None

Druggable Genes for this Gene Expression Program:

Gene Symbol Gene Loading Rank Drug Names Drug Category GTEx DepMap
ADH1B 30
1FOMEPIZOLE
 Small molecule GTEx DepMap
PLG 38
2TRANEXAMIC ACID, AMINOCAPROIC ACID
 Small molecule GTEx DepMap
ADH1A 40
1FOMEPIZOLE
 Small molecule GTEx DepMap
F2 61
2DABIGATRAN ETEXILATE, ARGATROBAN
 Small molecule GTEx DepMap
CYP3A4 70
1COBICISTAT
 Small molecule GTEx DepMap
HPD 77
1NITISINONE
 Small molecule GTEx DepMap
MTTP 98
1LOMITAPIDE
 Small molecule GTEx DepMap
ADH1C 133
1FOMEPIZOLE
 Small molecule GTEx DepMap
ALDH2 136
1DISULFIRAM
 Small molecule GTEx DepMap
MCL1 176
1AMG176
 Small molecule GTEx DepMap
BHMT2 177
1BETAINE
 Small molecule GTEx DepMap
CPS1 182
1CARGLUMIC ACID
 Small molecule GTEx DepMap
PAH 194
1SAPROPTERIN
 Small molecule GTEx DepMap
CFTR 198
4IVACAFTOR, CROFELEMER, LUMACAFTOR, LUMACAFTOR
 Small molecule GTEx DepMap
F10 213
3EDOXABAN, RIVAROXABAN, APIXABAN
 Small molecule GTEx DepMap
BHMT 234
1BETAINE
 Small molecule GTEx DepMap
FGFR3 243
2PAZOPANIB, NINTEDANIB
 Small molecule GTEx DepMap
C5 262
1ECULIZUMAB
 Antibody GTEx DepMap
FGFR2 306
2REGORAFENIB, NINTEDANIB
 Small molecule GTEx DepMap
CYP3A5 329
1COBICISTAT
 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
ATCGGATAGTGGTTGG-1_HTA4_1019_4075 Hepatocytes 0.41 5204.69
Raw ScoresHepatocytes: 0.62, Epithelial_cells: 0.31, Smooth_muscle_cells: 0.31, Tissue_stem_cells: 0.31, Osteoblasts: 0.3, Chondrocytes: 0.3, Fibroblasts: 0.3, Endothelial_cells: 0.28, iPS_cells: 0.27, Keratinocytes: 0.27
TAACGACTCGATACAC-1_HTA4_1019_4075 Hepatocytes 0.27 4218.18
Raw ScoresHepatocytes: 0.52, NK_cell: 0.29, Endothelial_cells: 0.29, Smooth_muscle_cells: 0.29, Osteoblasts: 0.29, Tissue_stem_cells: 0.29, Fibroblasts: 0.28, Macrophage: 0.28, Chondrocytes: 0.28, Platelets: 0.27
TGTAAGCCAGGCGATA-1_HTA4_1019_4075 Hepatocytes 0.28 4137.24
Raw ScoresHepatocytes: 0.53, Neurons: 0.31, Endothelial_cells: 0.31, iPS_cells: 0.3, Tissue_stem_cells: 0.3, Embryonic_stem_cells: 0.3, Astrocyte: 0.3, Fibroblasts: 0.3, Epithelial_cells: 0.3, Smooth_muscle_cells: 0.29
GTCTACCCACTTCAGA-1_HTA4_1019_4075 Hepatocytes 0.36 4001.00
Raw ScoresHepatocytes: 0.55, Endothelial_cells: 0.33, Smooth_muscle_cells: 0.33, Fibroblasts: 0.32, Osteoblasts: 0.32, Tissue_stem_cells: 0.32, Chondrocytes: 0.31, iPS_cells: 0.3, Epithelial_cells: 0.29, MSC: 0.28
GTTGCTCCAGTCCCGA-1_HTA4_1019_4075 Hepatocytes 0.37 3522.76
Raw ScoresHepatocytes: 0.54, Tissue_stem_cells: 0.26, Smooth_muscle_cells: 0.25, Epithelial_cells: 0.25, Chondrocytes: 0.25, Osteoblasts: 0.25, Fibroblasts: 0.25, Endothelial_cells: 0.24, iPS_cells: 0.24, Keratinocytes: 0.23
ATTGTTCCATGCCATA-1_HTA4_1019_4075 Hepatocytes 0.35 3499.20
Raw ScoresHepatocytes: 0.59, Epithelial_cells: 0.31, Endothelial_cells: 0.29, Embryonic_stem_cells: 0.29, Fibroblasts: 0.28, iPS_cells: 0.28, Smooth_muscle_cells: 0.28, Tissue_stem_cells: 0.28, Osteoblasts: 0.28, Neurons: 0.27
AATTCCTTCTGTGCTC-1_HTA4_1019_4074 Hepatocytes 0.34 3492.35
Raw ScoresHepatocytes: 0.53, Fibroblasts: 0.3, Astrocyte: 0.29, Smooth_muscle_cells: 0.29, Osteoblasts: 0.29, Embryonic_stem_cells: 0.29, Tissue_stem_cells: 0.28, iPS_cells: 0.28, Chondrocytes: 0.28, Epithelial_cells: 0.28
GGATGTTCAAGTTCCA-1_HTA4_1019_4075 Hepatocytes 0.37 3487.40
Raw ScoresHepatocytes: 0.56, Epithelial_cells: 0.32, Smooth_muscle_cells: 0.3, Tissue_stem_cells: 0.29, Fibroblasts: 0.29, Osteoblasts: 0.29, Embryonic_stem_cells: 0.29, iPS_cells: 0.28, Astrocyte: 0.28, Chondrocytes: 0.28
CTGCCATAGCGATCGA-1_HTA4_1019_4074 Hepatocytes 0.35 3274.78
Raw ScoresHepatocytes: 0.5, Epithelial_cells: 0.24, Tissue_stem_cells: 0.21, Smooth_muscle_cells: 0.2, Astrocyte: 0.2, Chondrocytes: 0.2, Fibroblasts: 0.2, Keratinocytes: 0.2, Osteoblasts: 0.2, iPS_cells: 0.19
AGTCAACGTCCTCCAT-1_HTA4_1019_4075 Hepatocytes 0.32 3133.13
Raw ScoresHepatocytes: 0.53, Macrophage: 0.29, DC: 0.28, Tissue_stem_cells: 0.27, Osteoblasts: 0.27, Smooth_muscle_cells: 0.26, Fibroblasts: 0.26, Endothelial_cells: 0.26, Epithelial_cells: 0.25, Monocyte: 0.25
CACTTCGCACTTCAGA-1_HTA4_1019_4075 Hepatocytes 0.38 3125.22
Raw ScoresHepatocytes: 0.57, Smooth_muscle_cells: 0.29, Tissue_stem_cells: 0.29, Osteoblasts: 0.28, Fibroblasts: 0.28, Epithelial_cells: 0.27, Chondrocytes: 0.27, Endothelial_cells: 0.27, iPS_cells: 0.26, MSC: 0.25
GATTCTTTCAAGCTGT-1_HTA4_1019_4075 Hepatocytes 0.37 3114.78
Raw ScoresHepatocytes: 0.54, Epithelial_cells: 0.25, Smooth_muscle_cells: 0.25, Osteoblasts: 0.24, Tissue_stem_cells: 0.24, Fibroblasts: 0.23, Chondrocytes: 0.22, Endothelial_cells: 0.22, iPS_cells: 0.22, Astrocyte: 0.21
ATTCACTGTGAGTTGG-1_HTA4_1019_4074 Hepatocytes 0.34 3059.45
Raw ScoresHepatocytes: 0.52, Epithelial_cells: 0.31, Osteoblasts: 0.31, Fibroblasts: 0.3, Smooth_muscle_cells: 0.3, Tissue_stem_cells: 0.29, Chondrocytes: 0.29, Astrocyte: 0.29, Embryonic_stem_cells: 0.28, Endothelial_cells: 0.28
TACGTCCTCAAACTGC-1_HTA4_1019_4074 Hepatocytes 0.37 2833.16
Raw ScoresHepatocytes: 0.55, Osteoblasts: 0.28, Tissue_stem_cells: 0.28, Chondrocytes: 0.27, Smooth_muscle_cells: 0.27, Fibroblasts: 0.27, Epithelial_cells: 0.27, Endothelial_cells: 0.25, iPS_cells: 0.25, Embryonic_stem_cells: 0.24
TGACTCCTCAGAGCGA-1_HTA4_1019_4075 Hepatocytes 0.35 2819.96
Raw ScoresHepatocytes: 0.54, Epithelial_cells: 0.28, Tissue_stem_cells: 0.27, Smooth_muscle_cells: 0.27, Fibroblasts: 0.27, Chondrocytes: 0.26, Osteoblasts: 0.26, Endothelial_cells: 0.25, Embryonic_stem_cells: 0.24, iPS_cells: 0.24
CTATAGGAGTCTCGTA-1_HTA4_1019_4075 Hepatocytes 0.37 2791.25
Raw ScoresHepatocytes: 0.53, Epithelial_cells: 0.23, Tissue_stem_cells: 0.23, Smooth_muscle_cells: 0.22, Osteoblasts: 0.22, Chondrocytes: 0.22, Fibroblasts: 0.21, Endothelial_cells: 0.2, Keratinocytes: 0.2, Astrocyte: 0.19
CAAGCTACACAACGCC-1_HTA4_1019_4074 Hepatocytes 0.37 2694.32
Raw ScoresHepatocytes: 0.53, Smooth_muscle_cells: 0.27, Fibroblasts: 0.27, Tissue_stem_cells: 0.27, Osteoblasts: 0.27, Chondrocytes: 0.26, iPS_cells: 0.25, Epithelial_cells: 0.25, Endothelial_cells: 0.25, Astrocyte: 0.24
GGGCGTTTCGGAGTGA-1_HTA4_1019_4075 Hepatocytes 0.37 2661.64
Raw ScoresHepatocytes: 0.52, Tissue_stem_cells: 0.25, Smooth_muscle_cells: 0.24, Osteoblasts: 0.24, Epithelial_cells: 0.24, Chondrocytes: 0.24, Fibroblasts: 0.24, Endothelial_cells: 0.22, iPS_cells: 0.22, Keratinocytes: 0.21
AACCAACGTTTGAACC-1_HTA4_1019_4075 Hepatocytes 0.35 2661.46
Raw ScoresHepatocytes: 0.54, Epithelial_cells: 0.27, Tissue_stem_cells: 0.27, Chondrocytes: 0.27, Smooth_muscle_cells: 0.26, Fibroblasts: 0.26, Osteoblasts: 0.26, Embryonic_stem_cells: 0.25, iPS_cells: 0.25, Endothelial_cells: 0.25
TACCGAACACGCTGTG-1_HTA4_1019_4075 Hepatocytes 0.34 2657.11
Raw ScoresHepatocytes: 0.52, Osteoblasts: 0.31, Fibroblasts: 0.31, Smooth_muscle_cells: 0.31, Endothelial_cells: 0.31, Tissue_stem_cells: 0.31, Chondrocytes: 0.3, iPS_cells: 0.29, MSC: 0.27, Epithelial_cells: 0.27
TCGATTTGTTTCGTTT-1_HTA4_1019_4074 Hepatocytes 0.34 2539.46
Raw ScoresHepatocytes: 0.54, Smooth_muscle_cells: 0.34, Fibroblasts: 0.34, Osteoblasts: 0.33, Tissue_stem_cells: 0.33, Endothelial_cells: 0.32, Chondrocytes: 0.32, iPS_cells: 0.32, Epithelial_cells: 0.31, MSC: 0.3
TGACGCGAGACAACTA-1_HTA4_1019_4075 Hepatocytes 0.36 2504.01
Raw ScoresHepatocytes: 0.56, Smooth_muscle_cells: 0.29, Osteoblasts: 0.28, Tissue_stem_cells: 0.28, Epithelial_cells: 0.28, Fibroblasts: 0.28, Chondrocytes: 0.27, Endothelial_cells: 0.27, iPS_cells: 0.26, Astrocyte: 0.24
TTACCATAGACTAGAT-1_HTA4_1019_4074 Hepatocytes 0.35 2421.56
Raw ScoresHepatocytes: 0.54, Epithelial_cells: 0.28, Smooth_muscle_cells: 0.27, Fibroblasts: 0.27, Osteoblasts: 0.27, Tissue_stem_cells: 0.26, Endothelial_cells: 0.25, Chondrocytes: 0.25, iPS_cells: 0.25, Keratinocytes: 0.25
CAAGCTACAGGCGATA-1_HTA4_1019_4075 Hepatocytes 0.39 2419.15
Raw ScoresHepatocytes: 0.58, Epithelial_cells: 0.29, Tissue_stem_cells: 0.28, Osteoblasts: 0.27, Smooth_muscle_cells: 0.27, Fibroblasts: 0.27, Chondrocytes: 0.26, Endothelial_cells: 0.25, Keratinocytes: 0.25, iPS_cells: 0.24
TCGTCCAGTTGAAGTA-1_HTA4_1019_4075 Hepatocytes 0.37 2302.95
Raw ScoresHepatocytes: 0.52, Epithelial_cells: 0.27, Smooth_muscle_cells: 0.26, Osteoblasts: 0.26, Fibroblasts: 0.25, Tissue_stem_cells: 0.25, Chondrocytes: 0.24, Endothelial_cells: 0.24, iPS_cells: 0.24, Astrocyte: 0.23
CCGTTCAAGGAAAGGT-1_HTA4_1019_4075 Hepatocytes 0.36 2280.51
Raw ScoresHepatocytes: 0.52, Tissue_stem_cells: 0.25, Smooth_muscle_cells: 0.25, Epithelial_cells: 0.24, Osteoblasts: 0.24, Fibroblasts: 0.23, Chondrocytes: 0.23, Endothelial_cells: 0.23, iPS_cells: 0.22, Keratinocytes: 0.21
CATGCGGCAAGCCATT-1_HTA4_1019_4074 Hepatocytes 0.37 2244.60
Raw ScoresHepatocytes: 0.55, Smooth_muscle_cells: 0.3, Fibroblasts: 0.29, Tissue_stem_cells: 0.29, Osteoblasts: 0.29, Endothelial_cells: 0.29, Chondrocytes: 0.28, Epithelial_cells: 0.28, iPS_cells: 0.27, Astrocyte: 0.26
CAGATCAAGAGAGCAA-1_HTA4_1019_4075 Hepatocytes 0.35 2202.26
Raw ScoresHepatocytes: 0.53, Tissue_stem_cells: 0.28, Osteoblasts: 0.27, Smooth_muscle_cells: 0.27, Epithelial_cells: 0.27, Fibroblasts: 0.27, Chondrocytes: 0.26, Endothelial_cells: 0.25, iPS_cells: 0.24, Astrocyte: 0.24
ATGCCTCGTTCGTACA-1_HTA4_1019_4075 Hepatocytes 0.35 2201.04
Raw ScoresHepatocytes: 0.54, Epithelial_cells: 0.26, Osteoblasts: 0.25, Tissue_stem_cells: 0.25, Smooth_muscle_cells: 0.24, Fibroblasts: 0.24, Chondrocytes: 0.24, Astrocyte: 0.24, Endothelial_cells: 0.23, iPS_cells: 0.23
TCGGTCTAGACTCATC-1_HTA4_1019_4075 Hepatocytes 0.35 2158.01
Raw ScoresHepatocytes: 0.49, Tissue_stem_cells: 0.22, Chondrocytes: 0.21, Smooth_muscle_cells: 0.21, Epithelial_cells: 0.2, Osteoblasts: 0.2, Fibroblasts: 0.2, Endothelial_cells: 0.19, Keratinocytes: 0.19, iPS_cells: 0.19
TGATTTCAGGCTCACC-1_HTA4_1019_4074 Hepatocytes 0.35 2148.56
Raw ScoresHepatocytes: 0.5, Epithelial_cells: 0.24, Smooth_muscle_cells: 0.22, Osteoblasts: 0.22, Tissue_stem_cells: 0.22, Embryonic_stem_cells: 0.21, iPS_cells: 0.21, Fibroblasts: 0.21, Chondrocytes: 0.21, Astrocyte: 0.21
TTGAACGTCAGCCCAG-1_HTA4_1019_4075 Hepatocytes 0.34 2127.19
Raw ScoresHepatocytes: 0.52, Smooth_muscle_cells: 0.27, Osteoblasts: 0.27, Fibroblasts: 0.26, Epithelial_cells: 0.26, Tissue_stem_cells: 0.26, Chondrocytes: 0.25, iPS_cells: 0.25, Endothelial_cells: 0.24, Astrocyte: 0.24
AAACCCAAGCGATGGT-1_HTA4_1019_4075 Hepatocytes 0.35 2060.55
Raw ScoresHepatocytes: 0.53, Smooth_muscle_cells: 0.26, Tissue_stem_cells: 0.26, Osteoblasts: 0.26, Fibroblasts: 0.26, Epithelial_cells: 0.26, Chondrocytes: 0.25, Endothelial_cells: 0.24, iPS_cells: 0.24, Keratinocytes: 0.23
TTCCTCTAGACTGTTC-1_HTA4_1019_4075 Hepatocytes 0.35 2051.03
Raw ScoresHepatocytes: 0.49, Fibroblasts: 0.27, Smooth_muscle_cells: 0.27, Tissue_stem_cells: 0.26, Osteoblasts: 0.26, Chondrocytes: 0.25, iPS_cells: 0.24, Endothelial_cells: 0.23, MSC: 0.23, Epithelial_cells: 0.22
GACATCACACCGTCTT-1_HTA4_1019_4075 Hepatocytes 0.37 2027.39
Raw ScoresHepatocytes: 0.54, Epithelial_cells: 0.26, Smooth_muscle_cells: 0.26, Tissue_stem_cells: 0.25, Osteoblasts: 0.25, Chondrocytes: 0.24, Fibroblasts: 0.24, Endothelial_cells: 0.24, iPS_cells: 0.23, Astrocyte: 0.22
GTACAACAGGTTTACC-1_HTA4_1019_4075 Hepatocytes 0.34 2009.49
Raw ScoresHepatocytes: 0.5, Smooth_muscle_cells: 0.25, Tissue_stem_cells: 0.25, Osteoblasts: 0.24, Fibroblasts: 0.24, Epithelial_cells: 0.24, Chondrocytes: 0.23, Endothelial_cells: 0.23, Keratinocytes: 0.22, iPS_cells: 0.21
CTGCCATCACTACTTT-1_HTA4_1019_4075 Hepatocytes 0.36 2002.49
Raw ScoresHepatocytes: 0.55, Epithelial_cells: 0.26, Smooth_muscle_cells: 0.25, Osteoblasts: 0.25, Tissue_stem_cells: 0.25, Endothelial_cells: 0.24, Fibroblasts: 0.24, Chondrocytes: 0.23, iPS_cells: 0.23, Astrocyte: 0.23
GGGACAATCAACTTTC-1_HTA4_1019_4075 Hepatocytes 0.36 1973.18
Raw ScoresHepatocytes: 0.53, Smooth_muscle_cells: 0.26, Epithelial_cells: 0.26, Fibroblasts: 0.25, Tissue_stem_cells: 0.25, Osteoblasts: 0.25, Endothelial_cells: 0.24, Chondrocytes: 0.24, Keratinocytes: 0.23, iPS_cells: 0.23
ATTTACCGTACACGCC-1_HTA4_1019_4075 Hepatocytes 0.35 1954.65
Raw ScoresHepatocytes: 0.54, Smooth_muscle_cells: 0.28, Tissue_stem_cells: 0.27, Osteoblasts: 0.27, Fibroblasts: 0.27, Chondrocytes: 0.26, Endothelial_cells: 0.26, Epithelial_cells: 0.26, iPS_cells: 0.26, Astrocyte: 0.24
ATTCCTACAATGCTCA-1_HTA4_1019_4075 Hepatocytes 0.36 1953.85
Raw ScoresHepatocytes: 0.51, Smooth_muscle_cells: 0.24, Tissue_stem_cells: 0.23, Chondrocytes: 0.23, Osteoblasts: 0.23, Epithelial_cells: 0.23, Fibroblasts: 0.23, Endothelial_cells: 0.21, iPS_cells: 0.21, Keratinocytes: 0.2
AAACGCTTCGTTCGCT-1_HTA4_1019_4075 Hepatocytes 0.33 1931.15
Raw ScoresHepatocytes: 0.49, Epithelial_cells: 0.25, Smooth_muscle_cells: 0.23, Osteoblasts: 0.23, Fibroblasts: 0.22, Keratinocytes: 0.22, Endothelial_cells: 0.22, Tissue_stem_cells: 0.22, Astrocyte: 0.21, iPS_cells: 0.21
ATGAGTCTCTTTGCGC-1_HTA4_1019_4075 Hepatocytes 0.36 1895.46
Raw ScoresHepatocytes: 0.52, Smooth_muscle_cells: 0.24, Tissue_stem_cells: 0.24, Epithelial_cells: 0.24, Osteoblasts: 0.24, Fibroblasts: 0.23, Chondrocytes: 0.23, Endothelial_cells: 0.23, iPS_cells: 0.21, Astrocyte: 0.21
ACGTTCCTCCACTGGG-1_HTA4_1019_4075 Hepatocytes 0.35 1878.15
Raw ScoresHepatocytes: 0.52, Tissue_stem_cells: 0.27, Smooth_muscle_cells: 0.26, Osteoblasts: 0.26, Fibroblasts: 0.26, Chondrocytes: 0.26, Epithelial_cells: 0.25, iPS_cells: 0.24, Endothelial_cells: 0.23, Keratinocytes: 0.22
CACATGAGTCTCGGGT-1_HTA4_1019_4074 Hepatocytes 0.34 1875.72
Raw ScoresHepatocytes: 0.5, Smooth_muscle_cells: 0.25, Tissue_stem_cells: 0.25, Chondrocytes: 0.25, Osteoblasts: 0.25, Fibroblasts: 0.24, Epithelial_cells: 0.24, Astrocyte: 0.23, Endothelial_cells: 0.23, iPS_cells: 0.23
ACACCAATCAGTAGGG-1_HTA4_1019_4075 Hepatocytes 0.39 1869.78
Raw ScoresHepatocytes: 0.57, Epithelial_cells: 0.29, Tissue_stem_cells: 0.27, Smooth_muscle_cells: 0.26, Osteoblasts: 0.26, Chondrocytes: 0.25, Fibroblasts: 0.25, Endothelial_cells: 0.25, Keratinocytes: 0.25, iPS_cells: 0.23
TCTGGCTTCAATGCAC-1_HTA4_1019_4075 Hepatocytes 0.36 1859.83
Raw ScoresHepatocytes: 0.53, Smooth_muscle_cells: 0.25, Tissue_stem_cells: 0.25, Osteoblasts: 0.25, Fibroblasts: 0.25, Chondrocytes: 0.24, Epithelial_cells: 0.24, Endothelial_cells: 0.23, iPS_cells: 0.23, MSC: 0.21
TTCCTTCGTTGGGTAG-1_HTA4_1019_4074 Hepatocytes 0.36 1859.26
Raw ScoresHepatocytes: 0.55, Tissue_stem_cells: 0.29, Epithelial_cells: 0.28, Smooth_muscle_cells: 0.28, Chondrocytes: 0.28, Fibroblasts: 0.27, Osteoblasts: 0.27, Endothelial_cells: 0.26, iPS_cells: 0.25, Keratinocytes: 0.25
CCCTGATTCTCGGTAA-1_HTA4_1019_4075 Hepatocytes 0.35 1847.41
Raw ScoresHepatocytes: 0.51, Smooth_muscle_cells: 0.25, Tissue_stem_cells: 0.25, Osteoblasts: 0.25, Epithelial_cells: 0.24, Fibroblasts: 0.24, Chondrocytes: 0.24, Endothelial_cells: 0.23, iPS_cells: 0.22, Neurons: 0.21
CAGGCCATCCTATTTG-1_HTA4_1019_4074 Hepatocytes 0.34 1845.89
Raw ScoresHepatocytes: 0.51, Epithelial_cells: 0.3, Embryonic_stem_cells: 0.28, Smooth_muscle_cells: 0.28, Fibroblasts: 0.27, Neurons: 0.27, Osteoblasts: 0.27, Astrocyte: 0.27, iPS_cells: 0.27, Tissue_stem_cells: 0.26
CATCCACCAAGACGGT-1_HTA4_1019_4075 Hepatocytes 0.34 1839.86
Raw ScoresHepatocytes: 0.5, Smooth_muscle_cells: 0.24, Tissue_stem_cells: 0.24, Fibroblasts: 0.24, Osteoblasts: 0.24, Epithelial_cells: 0.23, Chondrocytes: 0.23, Endothelial_cells: 0.22, iPS_cells: 0.22, Keratinocytes: 0.21


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.


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: 2.07e-10
Mean rank of genes in gene set: 4427.48
Rank on gene expression program of genes in gene set:
Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
ADH1B 0.0085518 30 GTEx DepMap Descartes 3.42 376.23
SERPING1 0.0060752 57 GTEx DepMap Descartes 2.43 624.06
C1R 0.0048012 80 GTEx DepMap Descartes 1.16 219.78
C1S 0.0041561 96 GTEx DepMap Descartes 1.85 387.95
CFB 0.0040676 100 GTEx DepMap Descartes 0.16 42.55
C3 0.0039518 105 GTEx DepMap Descartes 14.11 1355.48
SAA1 0.0038199 115 GTEx DepMap Descartes 0.23 210.39
GPX3 0.0015878 341 GTEx DepMap Descartes 0.44 175.81
CXCL2 0.0014073 386 GTEx DepMap Descartes 1.46 624.97
HGF 0.0013806 398 GTEx DepMap Descartes 0.52 71.70
CXCL12 0.0012984 421 GTEx DepMap Descartes 0.29 69.67
CXCL1 0.0009523 639 GTEx DepMap Descartes 0.05 33.56
CCL2 0.0009282 657 GTEx DepMap Descartes 0.34 291.69
IL1R1 0.0007256 893 GTEx DepMap Descartes 2.04 213.96
CXCL10 0.0005820 1101 GTEx DepMap Descartes 0.03 16.14
LIF 0.0005548 1158 GTEx DepMap Descartes 0.05 8.24
PDGFD 0.0005398 1205 GTEx DepMap Descartes 0.77 94.40
C7 0.0005174 1254 GTEx DepMap Descartes 0.92 131.80
C1QA 0.0004542 1421 GTEx DepMap Descartes 0.13 84.40
C1QC 0.0003425 1851 GTEx DepMap Descartes 0.05 22.85
C4B 0.0002500 2341 GTEx DepMap Descartes 0.02 1.67
PDGFRA 0.0001929 2788 GTEx DepMap Descartes 0.06 7.92
CFD 0.0001915 2799 GTEx DepMap Descartes 0.02 9.85
PDPN 0.0001910 2805 GTEx DepMap Descartes 0.03 7.72
SOD2 0.0001764 2949 GTEx DepMap Descartes 0.14 4.26
CCL8 0.0000741 4452 GTEx DepMap Descartes 0.01 3.79
IL33 0.0000712 4513 GTEx DepMap Descartes 0.11 24.76
CCL21 0.0000701 4537 GTEx DepMap Descartes 0.22 184.42
IL10 0.0000497 5075 GTEx DepMap Descartes 0.00 1.06
PDGFRB 0.0000338 5576 GTEx DepMap Descartes 0.21 30.04
CXCL14 -0.0000026 8321 GTEx DepMap Descartes 0.04 14.44
CCL7 -0.0000039 8480 GTEx DepMap Descartes 0.00 0.15
IL6 -0.0000235 10665 GTEx DepMap Descartes 0.02 10.55
CXCL9 -0.0000347 11606 GTEx DepMap Descartes 0.02 4.12
IGF1 -0.0000437 12214 GTEx DepMap Descartes 0.14 9.57
SCARA5 -0.0000829 14207 GTEx DepMap Descartes 0.01 1.03
CXCL13 -0.0000877 14417 GTEx DepMap Descartes 0.01 6.10
IGFBP6 -0.0000902 14521 GTEx DepMap Descartes 0.01 9.52
SCARA3 -0.0001115 15355 GTEx DepMap Descartes 0.02 3.13
RGMA -0.0001724 17170 GTEx DepMap Descartes 0.01 0.60


PMN-MDSC
These marker genes were curated for MDSC subtypes as reviewed in Veglia et. al. (PMID 33526920):
Wilcoxon ranksum test P-value for gene set overrepresentation: 8.79e-09
Mean rank of genes in gene set: 3158.77
Rank on gene expression program of genes in gene set:

Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
ARG1 0.0029616 152 GTEx DepMap Descartes 0.81 283.15
SLC27A2 0.0015283 355 GTEx DepMap Descartes 0.36 85.55
CD36 0.0006274 1023 GTEx DepMap Descartes 0.56 55.67
STAT1 0.0005843 1097 GTEx DepMap Descartes 2.59 304.20
IRF1 0.0005367 1211 GTEx DepMap Descartes 0.44 43.94
IL4R 0.0005068 1275 GTEx DepMap Descartes 3.11 400.55
PTGS2 0.0004634 1385 GTEx DepMap Descartes 0.07 12.23
HIF1A 0.0004303 1495 GTEx DepMap Descartes 2.18 278.37
STAT6 0.0004127 1558 GTEx DepMap Descartes 0.90 105.61
TNFRSF10B 0.0003937 1638 GTEx DepMap Descartes 1.45 175.82
ANXA1 0.0003533 1807 GTEx DepMap Descartes 0.36 115.29
TGFB1 0.0002760 2175 GTEx DepMap Descartes 0.35 84.44
STAT3 0.0002300 2482 GTEx DepMap Descartes 7.60 717.60
IL1B 0.0002034 2692 GTEx DepMap Descartes 0.02 10.59
S100A8 0.0001856 2864 GTEx DepMap Descartes 0.01 11.65
CSF1 0.0001360 3404 GTEx DepMap Descartes 0.21 28.01
CD84 0.0001271 3529 GTEx DepMap Descartes 0.06 4.24
ITGAM 0.0001255 3551 GTEx DepMap Descartes 0.06 8.75
CD244 0.0000788 4339 GTEx DepMap Descartes 0.01 2.11
S100A9 0.0000636 4706 GTEx DepMap Descartes 0.01 21.32
IL6 -0.0000235 10665 GTEx DepMap Descartes 0.02 10.55
ARG2 -0.0001332 16090 GTEx DepMap Descartes 0.07 18.85


M1 Macrophage
These genes were collated from multiple sources:
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.77e-06
Mean rank of genes in gene set: 3974.79
Rank on gene expression program of genes in gene set:

Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
CD14 0.0020225 244 GTEx DepMap Descartes 0.29 112.66
CCL2 0.0009282 657 GTEx DepMap Descartes 0.34 291.69
CXCL8 0.0008748 707 GTEx DepMap Descartes 0.18 NA
CXCL10 0.0005820 1101 GTEx DepMap Descartes 0.03 16.14
CXCL16 0.0005732 1122 GTEx DepMap Descartes 0.10 23.78
CCL4 0.0003199 1948 GTEx DepMap Descartes 0.03 14.81
ITGAX 0.0002774 2169 GTEx DepMap Descartes 0.24 36.13
CCL3 0.0002660 2231 GTEx DepMap Descartes 0.03 14.75
CD80 0.0002120 2623 GTEx DepMap Descartes 0.03 8.09
IL1B 0.0002034 2692 GTEx DepMap Descartes 0.02 10.59
CD86 0.0001950 2774 GTEx DepMap Descartes 0.16 40.09
CXCL11 0.0001556 3161 GTEx DepMap Descartes 0.00 1.63
IL18 0.0001346 3424 GTEx DepMap Descartes 0.16 57.87
CCL5 0.0001114 3755 GTEx DepMap Descartes 0.04 31.18
IL33 0.0000712 4513 GTEx DepMap Descartes 0.11 24.76
TLR4 0.0000034 7078 GTEx DepMap Descartes 0.00 0.01
IL6 -0.0000235 10665 GTEx DepMap Descartes 0.02 10.55
CXCL9 -0.0000347 11606 GTEx DepMap Descartes 0.02 4.12
TNF -0.0000579 13051 GTEx DepMap Descartes 0.00 1.63




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: 17563.92
Median rank of genes in gene set: 19333
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
DNAJB1 0.0008110 774 GTEx DepMap Descartes 0.31 84.21
EML4 0.0007915 803 GTEx DepMap Descartes 8.42 725.09
GRB10 0.0007748 827 GTEx DepMap Descartes 2.38 243.85
FAM107B 0.0006444 998 GTEx DepMap Descartes 4.10 504.85
NFIL3 0.0005665 1138 GTEx DepMap Descartes 1.54 337.35
DAPK1 0.0005243 1237 GTEx DepMap Descartes 3.49 296.00
MYRIP 0.0004865 1325 GTEx DepMap Descartes 2.06 201.94
LYN 0.0003757 1707 GTEx DepMap Descartes 1.16 107.39
GGH 0.0003428 1849 GTEx DepMap Descartes 0.12 60.09
IRS2 0.0003342 1882 GTEx DepMap Descartes 1.29 75.59
ABCB1 0.0002542 2304 GTEx DepMap Descartes 3.13 254.35
GLRX 0.0002215 2557 GTEx DepMap Descartes 0.32 39.22
GNB1 0.0001702 3017 GTEx DepMap Descartes 3.52 598.76
RBBP8 0.0001677 3036 GTEx DepMap Descartes 0.74 110.11
MTCL1 0.0001583 3134 GTEx DepMap Descartes 0.33 NA
KLF13 0.0001567 3147 GTEx DepMap Descartes 0.47 41.61
CXADR 0.0001495 3243 GTEx DepMap Descartes 1.48 122.94
TUBB4B 0.0001251 3554 GTEx DepMap Descartes 0.23 69.87
NET1 0.0001024 3896 GTEx DepMap Descartes 0.19 26.83
PTS 0.0000974 3979 GTEx DepMap Descartes 0.94 391.94
SETD7 0.0000884 4137 GTEx DepMap Descartes 0.49 35.23
DIABLO 0.0000870 4169 GTEx DepMap Descartes 0.00 0.03
TMEM97 0.0000597 4799 GTEx DepMap Descartes 0.11 26.85
ZNF22 0.0000212 6080 GTEx DepMap Descartes 0.07 18.00
INO80C 0.0000102 6608 GTEx DepMap Descartes 0.00 0.25
HEY1 0.0000075 6771 GTEx DepMap Descartes 0.01 1.76
AKAP12 0.0000054 6919 GTEx DepMap Descartes 3.74 239.10
SATB1 0.0000043 7011 GTEx DepMap Descartes 0.01 0.47
HK2 0.0000002 7369 GTEx DepMap Descartes 0.03 2.82
PEG3 -0.0000128 9576 GTEx DepMap Descartes 0.00 NA


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: 4.30e-66
Mean rank of genes in gene set: 5651.27
Median rank of genes in gene set: 2826
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
APOE 0.0065697 51 GTEx DepMap Descartes 4.76 2600.75
IFITM3 0.0045063 89 GTEx DepMap Descartes 0.86 800.21
GDF15 0.0038085 117 GTEx DepMap Descartes 0.57 265.12
HLA-B 0.0032528 137 GTEx DepMap Descartes 1.02 420.05
KLF6 0.0031648 142 GTEx DepMap Descartes 6.18 696.28
SDC4 0.0031610 143 GTEx DepMap Descartes 3.90 735.85
A2M 0.0030456 148 GTEx DepMap Descartes 24.13 2407.43
MGST1 0.0029358 155 GTEx DepMap Descartes 3.66 796.19
INSIG1 0.0028081 163 GTEx DepMap Descartes 2.57 476.80
CFH 0.0027788 164 GTEx DepMap Descartes 9.18 626.15
CPS1 0.0025372 182 GTEx DepMap Descartes 7.52 595.78
B2M 0.0023570 200 GTEx DepMap Descartes 5.20 1435.98
IL6ST 0.0022493 206 GTEx DepMap Descartes 4.80 268.90
EGR1 0.0021784 216 GTEx DepMap Descartes 2.32 462.30
HLA-A 0.0020565 237 GTEx DepMap Descartes 1.03 122.80
TNFRSF12A 0.0019986 249 GTEx DepMap Descartes 0.54 171.63
KLF4 0.0019575 251 GTEx DepMap Descartes 0.35 75.78
ZFP36L1 0.0019515 254 GTEx DepMap Descartes 1.74 332.40
THBS1 0.0018990 265 GTEx DepMap Descartes 3.24 280.64
HLA-C 0.0017776 283 GTEx DepMap Descartes 0.49 165.46
ID1 0.0017704 285 GTEx DepMap Descartes 0.68 299.77
SLC38A2 0.0017017 305 GTEx DepMap Descartes 11.24 1091.76
PTPRK 0.0017000 307 GTEx DepMap Descartes 10.31 NA
SLC30A1 0.0016739 317 GTEx DepMap Descartes 0.30 27.87
VCL 0.0016693 321 GTEx DepMap Descartes 4.11 269.96
YAP1 0.0016535 326 GTEx DepMap Descartes 3.29 305.16
TM4SF1 0.0016386 331 GTEx DepMap Descartes 0.61 108.96
PDLIM1 0.0015161 361 GTEx DepMap Descartes 1.82 649.88
DUSP6 0.0015092 363 GTEx DepMap Descartes 1.22 171.84
RRBP1 0.0015056 364 GTEx DepMap Descartes 3.83 366.06


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: 1.32e-04
Mean rank of genes in gene set: 7064.33
Median rank of genes in gene set: 4391
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
APOC1 0.0155098 6 GTEx DepMap Descartes 6.17 6328.76
SULT2A1 0.0032136 140 GTEx DepMap Descartes 3.37 853.56
DHCR24 0.0017609 289 GTEx DepMap Descartes 2.56 226.34
LDLR 0.0010249 574 GTEx DepMap Descartes 6.46 567.65
MSMO1 0.0010235 576 GTEx DepMap Descartes 1.27 303.29
BAIAP2L1 0.0008413 740 GTEx DepMap Descartes 2.97 360.81
DHCR7 0.0007041 916 GTEx DepMap Descartes 0.18 37.07
TM7SF2 0.0005223 1241 GTEx DepMap Descartes 0.19 47.66
POR 0.0004615 1397 GTEx DepMap Descartes 7.79 1349.43
CLU 0.0004591 1404 GTEx DepMap Descartes 1.90 438.54
CYP17A1 0.0004310 1491 GTEx DepMap Descartes 0.45 45.44
PAPSS2 0.0003475 1826 GTEx DepMap Descartes 2.47 269.00
HMGCS1 0.0003414 1858 GTEx DepMap Descartes 2.51 222.49
CYP21A2 0.0003064 2005 GTEx DepMap Descartes 0.58 60.31
STAR 0.0002561 2288 GTEx DepMap Descartes 0.61 36.90
HSPD1 0.0002389 2419 GTEx DepMap Descartes 3.35 667.81
HMGCR 0.0001896 2823 GTEx DepMap Descartes 0.82 85.35
FDX1 0.0001855 2865 GTEx DepMap Descartes 1.88 169.86
FREM2 0.0001853 2869 GTEx DepMap Descartes 0.09 3.16
ERN1 0.0001826 2893 GTEx DepMap Descartes 2.84 155.48
NPC1 0.0001003 3932 GTEx DepMap Descartes 1.36 127.33
CYP11B1 0.0000921 4072 GTEx DepMap Descartes 0.81 45.62
CYB5B 0.0000760 4391 GTEx DepMap Descartes 0.48 46.78
HSPE1 0.0000745 4444 GTEx DepMap Descartes 0.32 171.49
FDXR 0.0000710 4522 GTEx DepMap Descartes 0.10 11.82
SH3BP5 0.0000709 4523 GTEx DepMap Descartes 1.13 139.10
MC2R 0.0000606 4774 GTEx DepMap Descartes 0.10 5.48
INHA 0.0000400 5376 GTEx DepMap Descartes 0.02 3.30
CYP11A1 0.0000158 6322 GTEx DepMap Descartes 0.39 40.65
SCARB1 0.0000100 6619 GTEx DepMap Descartes 3.24 173.56


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: 19313.09
Median rank of genes in gene set: 20049
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
GREM1 0.0002130 2615 GTEx DepMap Descartes 0.08 4.66
NPY -0.0000660 13458 GTEx DepMap Descartes 0.10 66.13
PLXNA4 -0.0001246 15805 GTEx DepMap Descartes 0.26 10.75
RPH3A -0.0001387 16273 GTEx DepMap Descartes 0.03 3.52
ANKFN1 -0.0002906 19067 GTEx DepMap Descartes 0.07 7.99
EYA4 -0.0003036 19190 GTEx DepMap Descartes 0.05 4.48
GAL -0.0003195 19333 GTEx DepMap Descartes 0.02 6.00
NTRK1 -0.0003243 19370 GTEx DepMap Descartes 0.02 2.86
CNTFR -0.0003363 19454 GTEx DepMap Descartes 0.03 9.78
SLC6A2 -0.0003587 19603 GTEx DepMap Descartes 0.03 3.92
PTCHD1 -0.0003643 19640 GTEx DepMap Descartes 0.02 0.72
EPHA6 -0.0003685 19664 GTEx DepMap Descartes 0.22 31.66
TMEFF2 -0.0003910 19787 GTEx DepMap Descartes 0.08 12.45
TUBB2A -0.0004054 19845 GTEx DepMap Descartes 0.08 28.14
FAT3 -0.0004144 19889 GTEx DepMap Descartes 0.12 4.41
MAB21L1 -0.0004159 19899 GTEx DepMap Descartes 0.01 2.25
MAB21L2 -0.0004240 19926 GTEx DepMap Descartes 0.01 2.19
SLC44A5 -0.0004277 19936 GTEx DepMap Descartes 0.19 24.49
REEP1 -0.0004340 19962 GTEx DepMap Descartes 0.06 9.32
SYNPO2 -0.0004386 19980 GTEx DepMap Descartes 0.46 22.67
RGMB -0.0004400 19985 GTEx DepMap Descartes 0.08 8.75
PRPH -0.0004665 20049 GTEx DepMap Descartes 0.04 4.10
RYR2 -0.0004819 20091 GTEx DepMap Descartes 0.73 31.03
HMX1 -0.0004900 20114 GTEx DepMap Descartes 0.01 3.02
CCND1 -0.0004988 20140 GTEx DepMap Descartes 0.81 106.72
IL7 -0.0005019 20147 GTEx DepMap Descartes 0.32 92.92
HS3ST5 -0.0005038 20153 GTEx DepMap Descartes 0.05 6.46
TMEM132C -0.0006005 20322 GTEx DepMap Descartes 0.17 12.83
RBFOX1 -0.0006032 20327 GTEx DepMap Descartes 3.00 434.92
CNKSR2 -0.0006095 20330 GTEx DepMap Descartes 0.37 20.65


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: 1.46e-07
Mean rank of genes in gene set: 5703.93
Median rank of genes in gene set: 2931.5
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
ID1 0.0017704 285 GTEx DepMap Descartes 0.68 299.77
NR5A2 0.0014470 376 GTEx DepMap Descartes 6.97 630.13
CRHBP 0.0010280 570 GTEx DepMap Descartes 0.12 47.25
CALCRL 0.0008943 689 GTEx DepMap Descartes 0.73 78.23
CDH5 0.0007001 922 GTEx DepMap Descartes 0.17 27.64
SHANK3 0.0005919 1089 GTEx DepMap Descartes 0.55 39.70
PTPRB 0.0005795 1108 GTEx DepMap Descartes 0.66 33.40
DNASE1L3 0.0005507 1172 GTEx DepMap Descartes 0.21 67.59
RASIP1 0.0005337 1217 GTEx DepMap Descartes 0.12 23.42
MYRIP 0.0004865 1325 GTEx DepMap Descartes 2.06 201.94
CLDN5 0.0003635 1762 GTEx DepMap Descartes 0.11 24.56
SOX18 0.0003582 1786 GTEx DepMap Descartes 0.07 25.23
CEACAM1 0.0003545 1800 GTEx DepMap Descartes 0.62 81.99
KDR 0.0003079 1997 GTEx DepMap Descartes 0.14 16.12
APLNR 0.0002915 2088 GTEx DepMap Descartes 0.04 9.15
NPR1 0.0002347 2450 GTEx DepMap Descartes 0.04 5.06
SHE 0.0002259 2511 GTEx DepMap Descartes 0.09 7.91
TMEM88 0.0002100 2641 GTEx DepMap Descartes 0.11 67.70
FLT4 0.0002063 2671 GTEx DepMap Descartes 0.08 10.06
BTNL9 0.0002040 2689 GTEx DepMap Descartes 0.07 14.87
TIE1 0.0001926 2792 GTEx DepMap Descartes 0.08 13.60
TM4SF18 0.0001816 2902 GTEx DepMap Descartes 0.04 6.54
TEK 0.0001753 2961 GTEx DepMap Descartes 0.17 21.94
NOTCH4 0.0001662 3054 GTEx DepMap Descartes 0.09 7.73
PODXL 0.0001494 3247 GTEx DepMap Descartes 0.18 18.10
MMRN2 0.0001481 3269 GTEx DepMap Descartes 0.06 8.64
KANK3 0.0001231 3580 GTEx DepMap Descartes 0.08 18.06
ARHGAP29 0.0001166 3687 GTEx DepMap Descartes 1.11 66.19
F8 0.0001113 3758 GTEx DepMap Descartes 0.20 11.56
FCGR2B 0.0000265 5858 GTEx DepMap Descartes 0.02 2.49


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: 5.87e-01
Mean rank of genes in gene set: 10480.39
Median rank of genes in gene set: 12382
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
BICC1 0.0023947 195 GTEx DepMap Descartes 6.02 597.61
IGFBP3 0.0017698 286 GTEx DepMap Descartes 0.59 161.72
ADAMTS2 0.0009163 668 GTEx DepMap Descartes 0.65 78.23
C7 0.0005174 1254 GTEx DepMap Descartes 0.92 131.80
DCN 0.0005082 1271 GTEx DepMap Descartes 0.40 40.45
HHIP 0.0004281 1500 GTEx DepMap Descartes 0.21 15.66
LAMC3 0.0003968 1623 GTEx DepMap Descartes 0.07 6.67
RSPO3 0.0003772 1698 GTEx DepMap Descartes 0.07 NA
ABCA6 0.0003661 1747 GTEx DepMap Descartes 0.88 54.03
PAMR1 0.0002998 2035 GTEx DepMap Descartes 0.11 30.17
ADAMTSL3 0.0002705 2199 GTEx DepMap Descartes 3.14 192.23
GAS2 0.0002120 2624 GTEx DepMap Descartes 5.97 1131.49
COL27A1 0.0001995 2734 GTEx DepMap Descartes 1.17 72.67
PDGFRA 0.0001929 2788 GTEx DepMap Descartes 0.06 7.92
ABCC9 0.0001744 2977 GTEx DepMap Descartes 0.31 20.28
GLI2 0.0000929 4052 GTEx DepMap Descartes 0.15 17.67
EDNRA 0.0000460 5185 GTEx DepMap Descartes 0.10 17.62
COL12A1 0.0000433 5282 GTEx DepMap Descartes 0.32 20.10
ACTA2 0.0000367 5470 GTEx DepMap Descartes 0.24 109.30
ISLR 0.0000192 6160 GTEx DepMap Descartes 0.02 7.53
COL6A3 0.0000142 6401 GTEx DepMap Descartes 0.45 33.97
LRRC17 -0.0000074 8945 GTEx DepMap Descartes 0.04 13.61
CLDN11 -0.0000157 9911 GTEx DepMap Descartes 0.00 0.05
MXRA5 -0.0000417 12079 GTEx DepMap Descartes 0.04 1.69
SULT1E1 -0.0000465 12382 GTEx DepMap Descartes 0.03 8.37
PCDH18 -0.0000470 12418 GTEx DepMap Descartes 0.02 1.89
CCDC80 -0.0000808 14118 GTEx DepMap Descartes 0.13 7.18
SCARA5 -0.0000829 14207 GTEx DepMap Descartes 0.01 1.03
CCDC102B -0.0000971 14815 GTEx DepMap Descartes 0.78 218.54
ELN -0.0001071 15198 GTEx DepMap Descartes 0.12 21.47


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: 17807.44
Median rank of genes in gene set: 19649
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
ST18 0.0001261 3540 GTEx DepMap Descartes 0.20 19.49
LAMA3 0.0001134 3725 GTEx DepMap Descartes 0.25 14.16
SLC35F3 0.0000727 4477 GTEx DepMap Descartes 0.43 70.66
CNTN3 -0.0000066 8838 GTEx DepMap Descartes 0.13 13.39
PNMT -0.0000573 13009 GTEx DepMap Descartes 0.00 0.54
MGAT4C -0.0000673 13523 GTEx DepMap Descartes 0.68 21.10
DGKK -0.0001461 16502 GTEx DepMap Descartes 0.01 0.64
PENK -0.0001694 17103 GTEx DepMap Descartes 0.00 0.30
SCG2 -0.0001930 17612 GTEx DepMap Descartes 0.27 34.52
SLC24A2 -0.0002015 17776 GTEx DepMap Descartes 0.04 1.45
ARC -0.0002036 17818 GTEx DepMap Descartes 0.00 0.35
GCH1 -0.0002064 17860 GTEx DepMap Descartes 1.09 179.35
HTATSF1 -0.0002206 18109 GTEx DepMap Descartes 0.10 21.55
C1QL1 -0.0002489 18570 GTEx DepMap Descartes 0.00 1.26
SLC18A1 -0.0002737 18870 GTEx DepMap Descartes 0.01 1.82
SORCS3 -0.0002809 18964 GTEx DepMap Descartes 0.03 3.22
GRID2 -0.0002930 19092 GTEx DepMap Descartes 0.15 11.63
PACRG -0.0002958 19121 GTEx DepMap Descartes 0.77 208.88
PCSK2 -0.0002964 19123 GTEx DepMap Descartes 0.04 4.03
CNTNAP5 -0.0003017 19177 GTEx DepMap Descartes 0.06 4.87
INSM1 -0.0003214 19344 GTEx DepMap Descartes 0.00 0.35
KSR2 -0.0003656 19649 GTEx DepMap Descartes 0.08 2.60
EML6 -0.0003729 19695 GTEx DepMap Descartes 0.24 8.47
TMEM130 -0.0003849 19755 GTEx DepMap Descartes 0.03 3.25
GRM7 -0.0003932 19794 GTEx DepMap Descartes 0.09 16.02
TBX20 -0.0004033 19833 GTEx DepMap Descartes 0.04 11.45
SPOCK3 -0.0004041 19838 GTEx DepMap Descartes 0.03 6.19
CDH18 -0.0004086 19861 GTEx DepMap Descartes 0.07 5.60
CDH12 -0.0004275 19935 GTEx DepMap Descartes 0.37 34.27
GALNTL6 -0.0004623 20042 GTEx DepMap Descartes 0.09 10.51


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: 4.82e-03
Mean rank of genes in gene set: 8029.72
Median rank of genes in gene set: 6435.5
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
SELENBP1 0.0015235 358 GTEx DepMap Descartes 0.13 24.51
TFR2 0.0012437 445 GTEx DepMap Descartes 0.82 130.70
CAT 0.0012124 458 GTEx DepMap Descartes 0.93 210.25
SOX6 0.0007866 808 GTEx DepMap Descartes 2.10 138.56
DENND4A 0.0005951 1083 GTEx DepMap Descartes 8.71 469.09
BLVRB 0.0004174 1534 GTEx DepMap Descartes 0.27 107.03
SLC25A21 0.0003909 1646 GTEx DepMap Descartes 0.21 26.21
GYPC 0.0002608 2252 GTEx DepMap Descartes 0.09 34.89
RAPGEF2 0.0002258 2513 GTEx DepMap Descartes 2.56 169.03
GCLC 0.0002113 2632 GTEx DepMap Descartes 5.63 656.77
SLC4A1 0.0001772 2942 GTEx DepMap Descartes 0.02 3.07
SPTA1 0.0001492 3252 GTEx DepMap Descartes 0.02 1.75
HBA2 0.0001290 3500 GTEx DepMap Descartes 0.10 151.24
GYPA 0.0001167 3684 GTEx DepMap Descartes 0.00 1.59
AHSP 0.0001148 3707 GTEx DepMap Descartes 0.01 13.18
RGS6 0.0001011 3918 GTEx DepMap Descartes 0.29 29.18
SLC25A37 0.0001007 3925 GTEx DepMap Descartes 0.71 71.55
HBM 0.0000556 4908 GTEx DepMap Descartes 0.01 11.03
HEMGN 0.0000523 4983 GTEx DepMap Descartes 0.01 1.77
HBA1 0.0000490 5100 GTEx DepMap Descartes 0.03 45.27
ALAS2 0.0000298 5718 GTEx DepMap Descartes 0.01 2.05
MICAL2 0.0000297 5719 GTEx DepMap Descartes 0.82 67.74
RHCE 0.0000143 6388 GTEx DepMap Descartes 0.02 6.60
RHD 0.0000127 6483 GTEx DepMap Descartes 0.06 10.34
HBZ 0.0000102 6609 GTEx DepMap Descartes 0.00 3.05
EPB42 0.0000045 6991 GTEx DepMap Descartes 0.00 0.77
HBG1 0.0000040 7021 GTEx DepMap Descartes 0.00 0.00
HBG2 0.0000000 7751 GTEx DepMap Descartes 0.00 0.00
ABCB10 -0.0000023 8287 GTEx DepMap Descartes 0.32 43.44
RHAG -0.0000064 8809 GTEx DepMap Descartes 0.01 2.52


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: 5.95e-07
Mean rank of genes in gene set: 6174.82
Median rank of genes in gene set: 3222
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
CD14 0.0020225 244 GTEx DepMap Descartes 0.29 112.66
CTSB 0.0009678 628 GTEx DepMap Descartes 2.07 289.27
CST3 0.0004838 1332 GTEx DepMap Descartes 0.46 89.95
LGMN 0.0004639 1383 GTEx DepMap Descartes 0.42 123.42
C1QA 0.0004542 1421 GTEx DepMap Descartes 0.13 84.40
WWP1 0.0004281 1501 GTEx DepMap Descartes 2.39 238.41
ABCA1 0.0004148 1548 GTEx DepMap Descartes 2.73 121.79
HLA-DRB1 0.0004078 1580 GTEx DepMap Descartes 0.10 54.01
CD74 0.0004018 1604 GTEx DepMap Descartes 0.61 140.16
HLA-DRA 0.0003956 1628 GTEx DepMap Descartes 0.34 198.73
CTSS 0.0003807 1680 GTEx DepMap Descartes 0.27 44.11
SLC9A9 0.0003661 1746 GTEx DepMap Descartes 1.10 207.66
TGFBI 0.0003487 1819 GTEx DepMap Descartes 0.96 98.74
C1QC 0.0003425 1851 GTEx DepMap Descartes 0.05 22.85
HLA-DPA1 0.0003060 2007 GTEx DepMap Descartes 0.15 21.80
IFNGR1 0.0003004 2031 GTEx DepMap Descartes 0.76 142.02
AXL 0.0002945 2071 GTEx DepMap Descartes 0.33 46.14
ITPR2 0.0002820 2141 GTEx DepMap Descartes 8.30 299.59
C1QB 0.0002776 2167 GTEx DepMap Descartes 0.08 38.29
FGL2 0.0002201 2566 GTEx DepMap Descartes 0.07 11.61
SLCO2B1 0.0002020 2708 GTEx DepMap Descartes 1.40 111.25
SPP1 0.0001752 2962 GTEx DepMap Descartes 0.56 188.27
SLC1A3 0.0001725 2997 GTEx DepMap Descartes 0.12 12.45
MSR1 0.0001595 3122 GTEx DepMap Descartes 0.27 49.65
MPEG1 0.0001508 3222 GTEx DepMap Descartes 0.04 6.57
RNASE1 0.0001378 3385 GTEx DepMap Descartes 0.05 29.51
MS4A7 0.0000972 3983 GTEx DepMap Descartes 0.01 1.60
VSIG4 0.0000722 4489 GTEx DepMap Descartes 0.01 4.12
RGL1 0.0000355 5509 GTEx DepMap Descartes 0.56 63.42
CYBB 0.0000309 5674 GTEx DepMap Descartes 0.01 0.82


Descartes Schwann markers
Top 50 marker genes of Schwann cells in the Decartes fetal adrenal single cell map (https://atlas.brotmanbaty.org/bbi/human-gene-expression-during-development/cell/schwann/in/adrenal)
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.00e+00
Mean rank of genes in gene set: 13681.88
Median rank of genes in gene set: 16827
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
COL25A1 0.0007532 853 GTEx DepMap Descartes 0.60 57.93
COL18A1 0.0006529 986 GTEx DepMap Descartes 2.07 166.87
LAMC1 0.0005416 1199 GTEx DepMap Descartes 1.73 112.94
EDNRB 0.0003888 1658 GTEx DepMap Descartes 0.12 20.56
STARD13 0.0003718 1725 GTEx DepMap Descartes 2.80 242.49
VIM 0.0003715 1726 GTEx DepMap Descartes 0.92 229.48
KCTD12 0.0002259 2512 GTEx DepMap Descartes 0.13 12.34
ERBB3 0.0001968 2760 GTEx DepMap Descartes 0.18 16.43
ADAMTS5 0.0001626 3085 GTEx DepMap Descartes 0.06 4.16
COL5A2 0.0001522 3205 GTEx DepMap Descartes 0.62 60.27
ABCA8 0.0000974 3977 GTEx DepMap Descartes 1.17 85.52
GAS7 0.0000865 4180 GTEx DepMap Descartes 0.51 47.36
HMGA2 0.0000660 4627 GTEx DepMap Descartes 0.04 3.10
PAG1 -0.0000485 12493 GTEx DepMap Descartes 0.81 44.82
PTN -0.0000628 13300 GTEx DepMap Descartes 0.06 25.49
MDGA2 -0.0000760 13919 GTEx DepMap Descartes 0.16 18.98
TRPM3 -0.0000804 14106 GTEx DepMap Descartes 0.57 22.20
IL1RAPL1 -0.0000967 14802 GTEx DepMap Descartes 0.34 71.19
CDH19 -0.0000986 14888 GTEx DepMap Descartes 0.20 25.70
MPZ -0.0001043 15093 GTEx DepMap Descartes 0.01 3.18
LAMA4 -0.0001064 15171 GTEx DepMap Descartes 0.73 54.95
OLFML2A -0.0001174 15569 GTEx DepMap Descartes 0.02 2.44
PTPRZ1 -0.0001319 16052 GTEx DepMap Descartes 0.02 1.56
SOX10 -0.0001515 16647 GTEx DepMap Descartes 0.01 2.57
PLP1 -0.0001585 16827 GTEx DepMap Descartes 0.01 1.15
PLCE1 -0.0001666 17036 GTEx DepMap Descartes 0.16 8.01
SCN7A -0.0001864 17474 GTEx DepMap Descartes 0.08 8.34
SOX5 -0.0001888 17529 GTEx DepMap Descartes 12.68 826.64
PMP22 -0.0001899 17548 GTEx DepMap Descartes 0.16 60.62
FIGN -0.0001982 17724 GTEx DepMap Descartes 0.50 32.31


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: 8.83e-06
Mean rank of genes in gene set: 6653.67
Median rank of genes in gene set: 3679
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
STOM 0.0021039 225 GTEx DepMap Descartes 1.66 269.61
THBS1 0.0018990 265 GTEx DepMap Descartes 3.24 280.64
VCL 0.0016693 321 GTEx DepMap Descartes 4.11 269.96
MYH9 0.0013766 400 GTEx DepMap Descartes 5.20 350.70
ACTN1 0.0006212 1036 GTEx DepMap Descartes 2.06 231.85
TPM4 0.0005994 1074 GTEx DepMap Descartes 1.12 155.22
FLNA 0.0005983 1075 GTEx DepMap Descartes 0.39 32.57
MYLK 0.0005820 1102 GTEx DepMap Descartes 0.44 26.48
ARHGAP6 0.0005038 1279 GTEx DepMap Descartes 0.43 50.47
RAP1B 0.0004976 1293 GTEx DepMap Descartes 2.37 91.95
UBASH3B 0.0004836 1333 GTEx DepMap Descartes 0.61 56.46
LTBP1 0.0004446 1444 GTEx DepMap Descartes 2.43 176.91
TLN1 0.0004407 1457 GTEx DepMap Descartes 0.81 47.13
ACTB 0.0004045 1592 GTEx DepMap Descartes 2.42 715.08
LIMS1 0.0003534 1804 GTEx DepMap Descartes 1.94 229.72
TGFB1 0.0002760 2175 GTEx DepMap Descartes 0.35 84.44
SLC24A3 0.0002619 2244 GTEx DepMap Descartes 0.29 54.18
PSTPIP2 0.0002098 2642 GTEx DepMap Descartes 0.26 45.56
PDE3A 0.0001616 3094 GTEx DepMap Descartes 1.23 123.87
PF4 0.0001497 3241 GTEx DepMap Descartes 0.00 0.83
MMRN1 0.0001453 3296 GTEx DepMap Descartes 0.10 13.91
INPP4B 0.0001416 3336 GTEx DepMap Descartes 0.70 56.57
ZYX 0.0001382 3380 GTEx DepMap Descartes 0.45 100.60
CD84 0.0001271 3529 GTEx DepMap Descartes 0.06 4.24
ANGPT1 0.0001170 3679 GTEx DepMap Descartes 0.09 12.26
HIPK2 0.0001081 3802 GTEx DepMap Descartes 2.15 70.44
FERMT3 0.0001073 3814 GTEx DepMap Descartes 0.10 23.26
FLI1 0.0000755 4407 GTEx DepMap Descartes 0.48 62.01
PPBP 0.0000712 4512 GTEx DepMap Descartes 0.00 1.22
GP9 0.0000172 6244 GTEx DepMap Descartes 0.00 0.35


Descartes Lyphoid markers
Top 50 marker genes of Lyphoid cells in the Decartes fetal adrenal single cell map (https://atlas.brotmanbaty.org/bbi/human-gene-expression-during-development/cell/lymphoid/in/adrenal)
Wilcoxon ranksum test P-value for gene set overrepresentation: 8.17e-01
Mean rank of genes in gene set: 11077.4
Median rank of genes in gene set: 12996
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
HLA-B 0.0032528 137 GTEx DepMap Descartes 1.02 420.05
B2M 0.0023570 200 GTEx DepMap Descartes 5.20 1435.98
HLA-A 0.0020565 237 GTEx DepMap Descartes 1.03 122.80
HLA-C 0.0017776 283 GTEx DepMap Descartes 0.49 165.46
MSN 0.0007594 847 GTEx DepMap Descartes 1.00 146.29
MBNL1 0.0007174 903 GTEx DepMap Descartes 9.28 752.44
ARID5B 0.0006764 951 GTEx DepMap Descartes 3.12 210.16
SP100 0.0006526 987 GTEx DepMap Descartes 2.06 192.27
NCALD 0.0004225 1520 GTEx DepMap Descartes 1.06 175.56
ETS1 0.0002964 2058 GTEx DepMap Descartes 0.66 92.50
FOXP1 0.0002704 2200 GTEx DepMap Descartes 0.38 22.14
PRKCH 0.0002164 2589 GTEx DepMap Descartes 0.87 153.37
IFI16 0.0001912 2802 GTEx DepMap Descartes 0.37 63.46
CCL5 0.0001114 3755 GTEx DepMap Descartes 0.04 31.18
PLEKHA2 0.0000863 4188 GTEx DepMap Descartes 0.38 39.47
NKG7 0.0000592 4808 GTEx DepMap Descartes 0.01 12.62
LCP1 0.0000590 4815 GTEx DepMap Descartes 0.12 22.78
ITPKB 0.0000528 4971 GTEx DepMap Descartes 0.25 27.96
PTPRC 0.0000491 5094 GTEx DepMap Descartes 0.52 76.09
CCND3 0.0000418 5314 GTEx DepMap Descartes 1.78 386.17
ARHGDIB 0.0000072 6793 GTEx DepMap Descartes 0.07 43.07
PDE3B -0.0000297 11206 GTEx DepMap Descartes 4.29 316.41
SORL1 -0.0000537 12819 GTEx DepMap Descartes 1.06 47.08
MCTP2 -0.0000570 12996 GTEx DepMap Descartes 0.17 12.07
SAMD3 -0.0000999 14936 GTEx DepMap Descartes 0.13 23.53
ARHGAP15 -0.0001011 14973 GTEx DepMap Descartes 0.81 201.01
SKAP1 -0.0001136 15436 GTEx DepMap Descartes 0.49 172.30
ANKRD44 -0.0001297 15989 GTEx DepMap Descartes 2.72 189.21
WIPF1 -0.0001726 17172 GTEx DepMap Descartes 0.37 55.62
IKZF1 -0.0001739 17211 GTEx DepMap Descartes 0.19 23.85


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: 1.52e-02
Mean rank of genes in gene set: 6870.07
Median rank of genes in gene set: 4649
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
APOE 0.0065697 51 GTEx DepMap Descartes 4.76 2600.75
ALDH6A1 0.0028105 162 GTEx DepMap Descartes 0.43 54.76
CTSL 0.0008864 694 GTEx DepMap Descartes 0.48 NA
HEXB 0.0004916 1303 GTEx DepMap Descartes 0.60 147.24
HEXA 0.0001896 2822 GTEx DepMap Descartes 0.02 1.84
SPRY1 0.0000815 4280 GTEx DepMap Descartes 0.15 41.28
YPEL2 0.0000746 4440 GTEx DepMap Descartes 0.82 73.29
ACSS1 0.0000575 4858 GTEx DepMap Descartes 0.07 10.86
DPP7 0.0000208 6096 GTEx DepMap Descartes 0.15 51.91
LY6G6E 0.0000000 7844 GTEx DepMap Descartes 0.00 0.00
RENBP -0.0000605 13187 GTEx DepMap Descartes 0.02 12.44
PDCD4 -0.0000858 14350 GTEx DepMap Descartes 0.86 113.93
CCNG2 -0.0001905 17559 GTEx DepMap Descartes 0.09 11.20
AUH -0.0002465 18535 GTEx DepMap Descartes 1.64 491.23


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: 6.63e-01
Mean rank of genes in gene set: 10536.4
Median rank of genes in gene set: 11460
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
PEBP1 0.0016787 314 GTEx DepMap Descartes 2.12 841.21
UQCRQ 0.0007952 798 GTEx DepMap Descartes 0.37 144.93
P4HB 0.0007473 863 GTEx DepMap Descartes 1.30 273.49
ATOX1 0.0006597 982 GTEx DepMap Descartes 0.34 52.03
MGMT 0.0003800 1686 GTEx DepMap Descartes 1.61 168.44
SLC25A5 0.0003711 1727 GTEx DepMap Descartes 0.15 67.71
NDUFC1 0.0003096 1992 GTEx DepMap Descartes 0.21 90.65
HDLBP 0.0003058 2008 GTEx DepMap Descartes 1.54 122.41
ID3 0.0002945 2070 GTEx DepMap Descartes 0.15 93.90
ARPC1B 0.0002634 2240 GTEx DepMap Descartes 0.09 27.95
RPS27L 0.0002599 2255 GTEx DepMap Descartes 0.41 36.60
CDC34 0.0002147 2600 GTEx DepMap Descartes 0.15 54.30
TMEM109 0.0001621 3090 GTEx DepMap Descartes 0.05 12.91
POLR2L 0.0001468 3284 GTEx DepMap Descartes 0.13 82.50
PRADC1 0.0001386 3377 GTEx DepMap Descartes 0.03 14.91
DUSP14 0.0001377 3387 GTEx DepMap Descartes 0.32 69.23
NUDC 0.0001235 3575 GTEx DepMap Descartes 0.58 158.65
DPH3 0.0001234 3576 GTEx DepMap Descartes 0.07 9.91
SEC13 0.0001201 3624 GTEx DepMap Descartes 0.37 76.33
LDHA 0.0000970 3987 GTEx DepMap Descartes 0.89 190.82
UQCR10 0.0000895 4121 GTEx DepMap Descartes 0.20 125.03
MRPS18A 0.0000822 4265 GTEx DepMap Descartes 0.06 33.72
CYB5B 0.0000760 4391 GTEx DepMap Descartes 0.48 46.78
HSPE1 0.0000745 4444 GTEx DepMap Descartes 0.32 171.49
TMEM97 0.0000597 4799 GTEx DepMap Descartes 0.11 26.85
ANKRD37 0.0000530 4968 GTEx DepMap Descartes 0.03 13.61
LRRC42 0.0000498 5071 GTEx DepMap Descartes 0.11 33.27
CAPG 0.0000443 5246 GTEx DepMap Descartes 0.03 9.64
PLAC8 0.0000420 5310 GTEx DepMap Descartes 0.05 17.00
DGCR6 0.0000341 5569 GTEx DepMap Descartes 0.00 0.02


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.


Macrophages: Macrophages (model markers)
specialised mononuclear phagocytic cells which recognise:
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.64e-05
Mean rank of genes in gene set: 2490.7
Rank on gene expression program of genes in gene set:
Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
APOC1 0.0155098 6 GTEx DepMap Descartes 6.17 6328.76
APOE 0.0065697 51 GTEx DepMap Descartes 4.76 2600.75
SELENOP 0.0057501 63 GTEx DepMap Descartes 1.99 NA
FTL 0.0020885 228 GTEx DepMap Descartes 4.17 2884.21
C1QA 0.0004542 1421 GTEx DepMap Descartes 0.13 84.40
CD5L 0.0004406 1458 GTEx DepMap Descartes 0.03 8.93
C1QB 0.0002776 2167 GTEx DepMap Descartes 0.08 38.29
FTH1 0.0002001 2732 GTEx DepMap Descartes 1.66 797.97
RNASE1 0.0001378 3385 GTEx DepMap Descartes 0.05 29.51
GNLY -0.0000648 13396 GTEx DepMap Descartes 0.01 4.84


Myelocytes: Myelocytes (model markers)
early granulocyte precursors that are derive from promyelocytes and later mature into metamyelocytes:
Wilcoxon ranksum test P-value for gene set overrepresentation: 4.36e-04
Mean rank of genes in gene set: 3701.11
Rank on gene expression program of genes in gene set:

Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
FTL 0.0020885 228 GTEx DepMap Descartes 4.17 2884.21
LYZ 0.0009867 613 GTEx DepMap Descartes 0.38 164.48
MT-ND3 0.0004913 1307 GTEx DepMap Descartes 4.59 6408.57
ACTB 0.0004045 1592 GTEx DepMap Descartes 2.42 715.08
SRGN 0.0003346 1879 GTEx DepMap Descartes 0.43 256.77
TYROBP 0.0002031 2696 GTEx DepMap Descartes 0.05 47.05
FTH1 0.0002001 2732 GTEx DepMap Descartes 1.66 797.97
GPIHBP1 0.0000644 4677 GTEx DepMap Descartes 0.01 1.75
S100A6 -0.0001918 17586 GTEx DepMap Descartes 0.28 251.56


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: 2.43e-03
Mean rank of genes in gene set: 632
Rank on gene expression program of genes in gene set:

Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
HES1 0.0010086 594 GTEx DepMap Descartes 0.30 103.63
FXYD2 0.0009447 646 GTEx DepMap Descartes 0.02 5.03
CD99 0.0009296 656 GTEx DepMap Descartes 0.76 360.78