Program: 48. Inflammatory Cancer-Associated Fibroblasts.

Program: 48. Inflammatory Cancer-Associated Fibroblasts.


Program description and justification of annotation generated by GPT5: Inflammatory cancer-associated fibroblasts (iCAF) with EMT/stress and hyaluronan-ECM remodeling.

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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 CRISPLD2 0.0097166 cysteine rich secretory protein LCCL domain containing 2 GTEx DepMap Descartes 5.12 1133.49
2 LMNA 0.0084675 lamin A/C GTEx DepMap Descartes 6.62 1852.26
3 GFPT2 0.0082721 glutamine-fructose-6-phosphate transaminase 2 GTEx DepMap Descartes 1.32 427.38
4 FOSB 0.0077804 FosB proto-oncogene, AP-1 transcription factor subunit GTEx DepMap Descartes 4.00 938.15
5 HAS2 0.0075740 hyaluronan synthase 2 GTEx DepMap Descartes 0.83 195.73
6 EMP1 0.0073940 epithelial membrane protein 1 GTEx DepMap Descartes 6.85 1059.63
7 TWIST2 0.0071006 twist family bHLH transcription factor 2 GTEx DepMap Descartes 0.64 532.98
8 ESYT2 0.0070422 extended synaptotagmin 2 GTEx DepMap Descartes 5.64 743.97
9 RFX2 0.0067545 regulatory factor X2 GTEx DepMap Descartes 3.17 676.17
10 FGFR1 0.0063647 fibroblast growth factor receptor 1 GTEx DepMap Descartes 2.30 322.99
11 HAS1 0.0062255 hyaluronan synthase 1 GTEx DepMap Descartes 0.24 115.14
12 NFATC2 0.0060898 nuclear factor of activated T cells 2 GTEx DepMap Descartes 7.74 1036.89
13 PRICKLE2 0.0059370 prickle planar cell polarity protein 2 GTEx DepMap Descartes 2.98 244.38
14 MMP19 0.0058856 matrix metallopeptidase 19 GTEx DepMap Descartes 1.34 304.91
15 NR4A1 0.0058689 nuclear receptor subfamily 4 group A member 1 GTEx DepMap Descartes 4.85 783.39
16 B4GALT1 0.0057794 beta-1,4-galactosyltransferase 1 GTEx DepMap Descartes 2.22 381.22
17 GPRC5A 0.0057568 G protein-coupled receptor class C group 5 member A GTEx DepMap Descartes 0.53 71.96
18 FGF7 0.0057284 fibroblast growth factor 7 GTEx DepMap Descartes 1.55 249.73
19 NFATC1 0.0057003 nuclear factor of activated T cells 1 GTEx DepMap Descartes 2.08 396.04
20 TACC1 0.0056579 transforming acidic coiled-coil containing protein 1 GTEx DepMap Descartes 4.75 521.57
21 UAP1 0.0054367 UDP-N-acetylglucosamine pyrophosphorylase 1 GTEx DepMap Descartes 1.06 310.86
22 ERCC1 0.0054204 ERCC excision repair 1, endonuclease non-catalytic subunit GTEx DepMap Descartes 1.77 441.83
23 IL1R1 0.0053024 interleukin 1 receptor type 1 GTEx DepMap Descartes 2.47 378.89
24 SEMA4A 0.0052649 semaphorin 4A GTEx DepMap Descartes 1.02 331.82
25 SLC19A2 0.0051996 solute carrier family 19 member 2 GTEx DepMap Descartes 1.04 224.63
26 SVEP1 0.0051828 sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1 GTEx DepMap Descartes 1.54 107.30
27 SAMD4A 0.0051354 sterile alpha motif domain containing 4A GTEx DepMap Descartes 8.71 881.69
28 STAT3 0.0051113 signal transducer and activator of transcription 3 GTEx DepMap Descartes 6.62 822.99
29 ABI3BP 0.0050239 ABI family member 3 binding protein GTEx DepMap Descartes 1.68 209.78
30 ADAMTS1 0.0049896 ADAM metallopeptidase with thrombospondin type 1 motif 1 GTEx DepMap Descartes 1.54 254.37
31 MEDAG 0.0049298 mesenteric estrogen dependent adipogenesis GTEx DepMap Descartes 0.47 NA
32 SIK3 0.0048808 SIK family kinase 3 GTEx DepMap Descartes 9.60 1016.20
33 EGFR 0.0048645 epidermal growth factor receptor GTEx DepMap Descartes 3.98 301.96
34 OSMR 0.0048028 oncostatin M receptor GTEx DepMap Descartes 2.32 282.80
35 FOS 0.0046891 Fos proto-oncogene, AP-1 transcription factor subunit GTEx DepMap Descartes 5.69 1942.14
36 SPON1 0.0045938 spondin 1 GTEx DepMap Descartes 0.87 136.07
37 PRRX1 0.0044597 paired related homeobox 1 GTEx DepMap Descartes 1.66 335.61
38 AXL 0.0044290 AXL receptor tyrosine kinase GTEx DepMap Descartes 1.29 243.26
39 DPYSL3 0.0043736 dihydropyrimidinase like 3 GTEx DepMap Descartes 2.80 357.64
40 COL4A4 0.0043707 collagen type IV alpha 4 chain GTEx DepMap Descartes 0.69 58.14
41 MYOF 0.0043649 myoferlin GTEx DepMap Descartes 1.89 225.81
42 RAD51B 0.0043640 RAD51 paralog B GTEx DepMap Descartes 4.01 1208.83
43 SPSB1 0.0042782 splA/ryanodine receptor domain and SOCS box containing 1 GTEx DepMap Descartes 3.81 741.43
44 CCN1 0.0042375 cellular communication network factor 1 GTEx DepMap Descartes 2.75 NA
45 SIK2 0.0042251 salt inducible kinase 2 GTEx DepMap Descartes 4.26 289.01
46 ADAMTS15 0.0041647 ADAM metallopeptidase with thrombospondin type 1 motif 15 GTEx DepMap Descartes 0.17 33.81
47 SLC2A3 0.0040398 solute carrier family 2 member 3 GTEx DepMap Descartes 3.01 544.69
48 ADGRD1 0.0040086 adhesion G protein-coupled receptor D1 GTEx DepMap Descartes 0.50 NA
49 THBS1 0.0040045 thrombospondin 1 GTEx DepMap Descartes 5.13 501.17
50 ERRFI1 0.0039704 ERBB receptor feedback inhibitor 1 GTEx DepMap Descartes 2.93 551.92


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UMAP plots showing activity of gene expression program identified in GEP 48. Inflammatory Cancer-Associated Fibroblasts:

Interactive UMAP Plot

Boxlot showing activity of gene expression program identified in GEP 48. Inflammatory Cancer-Associated Fibroblasts:
Interactive Boxplot

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


mSigDB Cell Types Gene Set:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
TRAVAGLINI_LUNG_ADVENTITIAL_FIBROBLAST_CELL 1.47e-31 69.68 37.79 9.89e-29 9.89e-29
24LMNA, GFPT2, FOSB, HAS2, EMP1, ESYT2, FGFR1, HAS1, NR4A1, B4GALT1, GPRC5A, FGF7, UAP1, IL1R1, SLC19A2, SVEP1, ABI3BP, MEDAG, FOS, PRRX1, DPYSL3, SPSB1, CCN1, ERRFI1
 296
TRAVAGLINI_LUNG_LIPOFIBROBLAST_CELL 2.95e-19 60.41 29.39 9.88e-17 1.98e-16
14GFPT2, HAS2, ESYT2, HAS1, MMP19, B4GALT1, GPRC5A, FGF7, UAP1, IL1R1, SLC19A2, STAT3, MEDAG, ERRFI1
 146
CUI_DEVELOPING_HEART_C5_VALVAR_CELL 6.34e-14 33.07 15.49 7.10e-12 4.26e-11
12LMNA, MMP19, NR4A1, B4GALT1, NFATC1, UAP1, ADAMTS1, FOS, PRRX1, DPYSL3, THBS1, ERRFI1
 208
AIZARANI_LIVER_C29_MVECS_2 4.30e-16 29.53 14.81 7.21e-14 2.88e-13
15LMNA, FOSB, EMP1, RFX2, NFATC2, B4GALT1, GPRC5A, NFATC1, TACC1, IL1R1, ABI3BP, ADAMTS1, DPYSL3, MYOF, CCN1
 313
HAY_BONE_MARROW_STROMAL 8.41e-18 20.00 10.79 1.88e-15 5.65e-15
21LMNA, FOSB, HAS2, EMP1, TWIST2, FGFR1, PRICKLE2, MMP19, GPRC5A, FGF7, IL1R1, SVEP1, ABI3BP, ADAMTS1, MEDAG, EGFR, OSMR, PRRX1, DPYSL3, CCN1, ERRFI1
 765
AIZARANI_LIVER_C21_STELLATE_CELLS_1 8.05e-10 24.35 10.26 6.01e-08 5.40e-07
9CRISPLD2, LMNA, FOSB, EMP1, MMP19, ADAMTS1, FOS, CCN1, THBS1
 194
LAKE_ADULT_KIDNEY_C17_COLLECTING_SYSTEM_PCS_STRESSED_DISSOC_SUBSET 2.35e-10 22.33 9.83 1.97e-08 1.58e-07
10LMNA, FOSB, ESYT2, NR4A1, SLC19A2, STAT3, SIK3, FOS, RAD51B, SIK2
 240
DESCARTES_FETAL_PANCREAS_MESOTHELIAL_CELLS 1.33e-06 30.81 9.28 4.46e-05 8.92e-04
5GFPT2, HAS1, NFATC2, GPRC5A, ADGRD1
 79
MURARO_PANCREAS_MESENCHYMAL_STROMAL_CELL 6.79e-15 17.46 9.17 9.11e-13 4.56e-12
18CRISPLD2, LMNA, GFPT2, HAS2, EMP1, B4GALT1, FGF7, IL1R1, MEDAG, OSMR, SPON1, PRRX1, AXL, MYOF, SPSB1, CCN1, SLC2A3, THBS1
 680
RUBENSTEIN_SKELETAL_MUSCLE_FBN1_FAP_CELLS 1.40e-09 18.40 8.12 9.36e-08 9.36e-07
10LMNA, GFPT2, FGFR1, UAP1, ABI3BP, MEDAG, PRRX1, AXL, MYOF, CCN1
 289
DESCARTES_MAIN_FETAL_MESOTHELIAL_CELLS 7.61e-05 42.17 7.99 1.50e-03 5.11e-02
3GFPT2, HAS1, NFATC2
 34
BUSSLINGER_ESOPHAGEAL_DENDRITIC_CELLS 4.08e-08 18.98 7.60 1.96e-06 2.74e-05
8LMNA, FOSB, NFATC2, NR4A1, TACC1, FOS, AXL, SLC2A3
 214
AIZARANI_LIVER_C20_LSECS_3 2.99e-08 15.76 6.67 1.55e-06 2.01e-05
9LMNA, EMP1, FGFR1, PRICKLE2, GPRC5A, IL1R1, ADAMTS1, OSMR, SLC2A3
 295
LAKE_ADULT_KIDNEY_C27_VASCULAR_SMOOTH_MUSCLE_CELLS_AND_PERICYTES 1.91e-06 18.79 6.44 6.12e-05 1.28e-03
6FOSB, ESYT2, NR4A1, TACC1, SIK3, FOS
 155
MANNO_MIDBRAIN_NEUROTYPES_HPERIC 1.73e-11 12.41 6.37 1.66e-09 1.16e-08
16CRISPLD2, LMNA, FOSB, NR4A1, TACC1, IL1R1, SVEP1, STAT3, ADAMTS1, OSMR, FOS, AXL, MYOF, CCN1, SLC2A3, ADGRD1
 795
FAN_OVARY_CL1_GPRC5A_TNFRS12A_HIGH_SELECTABLE_FOLLICLE_STROMAL_CELL 1.83e-08 13.88 6.14 1.02e-06 1.23e-05
10LMNA, EMP1, FGFR1, GPRC5A, FGF7, UAP1, STAT3, AXL, SPSB1, ERRFI1
 380
TRAVAGLINI_LUNG_BRONCHIAL_VESSEL_2_CELL 2.52e-07 14.82 5.95 1.06e-05 1.69e-04
8LMNA, FOSB, EMP1, NR4A1, UAP1, ADAMTS1, CCN1, SLC2A3
 272
FAN_OVARY_CL17_PUTATIVE_APOPTOTIC_SMOOTH_MUSCLE_CELL 1.26e-06 14.92 5.60 4.45e-05 8.45e-04
7CRISPLD2, LMNA, FGFR1, NR4A1, STAT3, ADAMTS1, AXL
 231
DESCARTES_MAIN_FETAL_IGFBP1_DKK1_POSITIVE_CELLS 4.24e-06 16.28 5.59 1.29e-04 2.84e-03
6CRISPLD2, MMP19, ABI3BP, ADAMTS1, SPSB1, ADAMTS15
 178
LAKE_ADULT_KIDNEY_C28_INTERSTITIUM 5.56e-05 21.76 5.56 1.24e-03 3.73e-02
4TACC1, COL4A4, CCN1, THBS1
 86

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mSigDB Hallmark Gene Sets:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
HALLMARK_TNFA_SIGNALING_VIA_NFKB 2.42e-08 20.36 8.15 1.21e-06 1.21e-06
8GFPT2, FOSB, NR4A1, B4GALT1, FOS, SPSB1, CCN1, SLC2A3
 200
HALLMARK_HYPOXIA 8.22e-06 14.43 4.97 2.06e-04 4.11e-04
6HAS1, EGFR, FOS, CCN1, SLC2A3, ERRFI1
 200
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION 1.17e-04 11.70 3.59 1.95e-03 5.85e-03
5ABI3BP, PRRX1, DPYSL3, CCN1, THBS1
 200
HALLMARK_IL6_JAK_STAT3_SIGNALING 1.22e-03 15.60 3.05 9.68e-03 6.12e-02
3IL1R1, STAT3, OSMR
 87
HALLMARK_ANDROGEN_RESPONSE 1.82e-03 13.51 2.64 1.14e-02 9.11e-02
3B4GALT1, UAP1, ADAMTS1
 100
HALLMARK_ESTROGEN_RESPONSE_EARLY 1.36e-03 9.11 2.36 9.68e-03 6.78e-02
4B4GALT1, SLC19A2, FOS, MYOF
 200
HALLMARK_INFLAMMATORY_RESPONSE 1.36e-03 9.11 2.36 9.68e-03 6.78e-02
4HAS2, IL1R1, OSMR, AXL
 200
HALLMARK_KRAS_SIGNALING_UP 1.36e-03 9.11 2.36 9.68e-03 6.78e-02
4GFPT2, EMP1, SPON1, PRRX1
 200
HALLMARK_UV_RESPONSE_UP 6.54e-03 8.46 1.67 3.63e-02 3.27e-01
3FOSB, NR4A1, FOS
 158
HALLMARK_UV_RESPONSE_DN 4.73e-02 6.02 0.70 2.36e-01 1.00e+00
2HAS2, CCN1
 144
HALLMARK_APOPTOSIS 5.75e-02 5.38 0.63 2.46e-01 1.00e+00
2LMNA, EMP1
 161
HALLMARK_IL2_STAT5_SIGNALING 8.29e-02 4.34 0.51 2.46e-01 1.00e+00
2EMP1, SLC2A3
 199
HALLMARK_ESTROGEN_RESPONSE_LATE 8.36e-02 4.32 0.51 2.46e-01 1.00e+00
2FOS, MYOF
 200
HALLMARK_APICAL_JUNCTION 8.36e-02 4.32 0.51 2.46e-01 1.00e+00
2B4GALT1, EGFR
 200
HALLMARK_GLYCOLYSIS 8.36e-02 4.32 0.51 2.46e-01 1.00e+00
2B4GALT1, EGFR
 200
HALLMARK_P53_PATHWAY 8.36e-02 4.32 0.51 2.46e-01 1.00e+00
2SLC19A2, FOS
 200
HALLMARK_ANGIOGENESIS 8.37e-02 11.97 0.29 2.46e-01 1.00e+00
1FGFR1
 36
HALLMARK_APICAL_SURFACE 1.01e-01 9.74 0.24 2.82e-01 1.00e+00
1B4GALT1
 44
HALLMARK_TGF_BETA_SIGNALING 1.23e-01 7.91 0.19 3.23e-01 1.00e+00
1THBS1
 54
HALLMARK_CHOLESTEROL_HOMEOSTASIS 1.64e-01 5.74 0.14 4.11e-01 1.00e+00
1ERRFI1
 74

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KEGG Pathways:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
KEGG_MAPK_SIGNALING_PATHWAY 3.26e-06 12.86 4.83 6.05e-04 6.05e-04
7FGFR1, NFATC2, NR4A1, FGF7, IL1R1, EGFR, FOS
 267
KEGG_MELANOMA 6.79e-04 19.27 3.75 3.70e-02 1.26e-01
3FGFR1, FGF7, EGFR
 71
KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY 7.97e-04 18.19 3.54 3.70e-02 1.48e-01
3NFATC2, NFATC1, FOS
 75
KEGG_PATHWAYS_IN_CANCER 1.20e-04 8.78 3.03 1.12e-02 2.24e-02
6FGFR1, FGF7, STAT3, EGFR, FOS, COL4A4
 325
KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY 2.27e-03 12.48 2.45 8.43e-02 4.22e-01
3NFATC2, NFATC1, FOS
 108
KEGG_BLADDER_CANCER 4.66e-03 21.38 2.43 1.19e-01 8.67e-01
2EGFR, THBS1
 42
KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM 5.10e-03 20.35 2.32 1.19e-01 9.49e-01
2GFPT2, UAP1
 44
KEGG_AXON_GUIDANCE 3.74e-03 10.40 2.04 1.16e-01 6.95e-01
3NFATC2, NFATC1, SEMA4A
 129
KEGG_WNT_SIGNALING_PATHWAY 5.78e-03 8.86 1.74 1.19e-01 1.00e+00
3NFATC2, PRICKLE2, NFATC1
 151
KEGG_PANCREATIC_CANCER 1.25e-02 12.58 1.45 1.94e-01 1.00e+00
2STAT3, EGFR
 70
KEGG_ADHERENS_JUNCTION 1.35e-02 12.05 1.39 1.94e-01 1.00e+00
2FGFR1, EGFR
 73
KEGG_VEGF_SIGNALING_PATHWAY 1.46e-02 11.56 1.34 1.94e-01 1.00e+00
2NFATC2, NFATC1
 76
KEGG_FOCAL_ADHESION 1.22e-02 6.69 1.32 1.94e-01 1.00e+00
3EGFR, COL4A4, THBS1
 199
KEGG_REGULATION_OF_ACTIN_CYTOSKELETON 1.46e-02 6.24 1.23 1.94e-01 1.00e+00
3FGFR1, FGF7, EGFR
 213
KEGG_ECM_RECEPTOR_INTERACTION 1.76e-02 10.43 1.21 2.18e-01 1.00e+00
2COL4A4, THBS1
 84
KEGG_PROSTATE_CANCER 1.96e-02 9.83 1.14 2.28e-01 1.00e+00
2FGFR1, EGFR
 89
KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION 2.57e-02 5.00 0.99 2.81e-01 1.00e+00
3IL1R1, EGFR, OSMR
 265
KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY 4.32e-02 6.34 0.74 4.23e-01 1.00e+00
2NFATC2, NFATC1
 137
KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_KERATAN_SULFATE 3.58e-02 29.90 0.69 3.70e-01 1.00e+00
1B4GALT1
 15
KEGG_JAK_STAT_SIGNALING_PATHWAY 5.38e-02 5.59 0.65 4.95e-01 1.00e+00
2STAT3, OSMR
 155

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CHR Positional Gene Sets:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
chr1q22 1.25e-02 12.58 1.45 1.00e+00 1.00e+00
2LMNA, SEMA4A
 70
chr8p11 2.22e-02 9.20 1.07 1.00e+00 1.00e+00
2FGFR1, TACC1
 95
chr1q24 3.56e-02 7.07 0.82 1.00e+00 1.00e+00
2SLC19A2, PRRX1
 123
chr12p13 4.52e-02 3.97 0.79 1.00e+00 1.00e+00
3EMP1, GPRC5A, SLC2A3
 333
chr14q24 7.73e-02 4.53 0.53 1.00e+00 1.00e+00
2FOS, RAD51B
 191
chr11q23 8.71e-02 4.21 0.49 1.00e+00 1.00e+00
2SIK3, SIK2
 205
chr19q13 3.43e-01 1.54 0.40 1.00e+00 1.00e+00
4FOSB, HAS1, ERCC1, AXL
 1165
chr18q23 9.04e-02 11.03 0.27 1.00e+00 1.00e+00
1NFATC1
 39
chr12q13 2.53e-01 2.11 0.25 1.00e+00 1.00e+00
2MMP19, NR4A1
 407
chr3q12 1.06e-01 9.31 0.23 1.00e+00 1.00e+00
1ABI3BP
 46
chr15q14 1.27e-01 7.62 0.19 1.00e+00 1.00e+00
1THBS1
 56
chr1p36 6.68e-01 1.31 0.15 1.00e+00 1.00e+00
2SPSB1, ERRFI1
 656
chr2q36 1.80e-01 5.17 0.13 1.00e+00 1.00e+00
1COL4A4
 82
chr7p11 1.80e-01 5.17 0.13 1.00e+00 1.00e+00
1EGFR
 82
chr14q22 1.96e-01 4.71 0.12 1.00e+00 1.00e+00
1SAMD4A
 90
chr21q21 2.51e-01 3.55 0.09 1.00e+00 1.00e+00
1ADAMTS1
 119
chr3p14 2.56e-01 3.46 0.09 1.00e+00 1.00e+00
1PRICKLE2
 122
chr5p13 2.67e-01 3.30 0.08 1.00e+00 1.00e+00
1OSMR
 128
chr9q31 2.67e-01 3.30 0.08 1.00e+00 1.00e+00
1SVEP1
 128
chr1p22 2.69e-01 3.27 0.08 1.00e+00 1.00e+00
1CCN1
 129

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Transcription Factor Targets:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
SRF_01 2.57e-04 27.29 5.25 2.36e-02 2.91e-01
3FOSB, FOS, THBS1
 51
SRF_C 1.24e-05 13.39 4.61 7.00e-03 1.40e-02
6GFPT2, FOSB, NR4A1, FOS, CCN1, THBS1
 215
PSMB5_TARGET_GENES 8.03e-06 11.14 4.20 7.00e-03 9.10e-03
7LMNA, EMP1, UAP1, ADAMTS1, CCN1, SLC2A3, THBS1
 307
HTF_01 6.79e-04 19.27 3.75 3.50e-02 7.70e-01
3STAT3, PRRX1, SIK2
 71
ZNF26_TARGET_GENES 2.24e-03 31.65 3.55 8.15e-02 1.00e+00
2UAP1, OSMR
 29
FOXD3_01 1.22e-04 11.58 3.55 2.36e-02 1.39e-01
5HAS2, PRICKLE2, NR4A1, CCN1, ERRFI1
 202
HMEF2_Q6 3.71e-04 13.03 3.36 2.63e-02 4.20e-01
4HAS2, PRICKLE2, NR4A1, FOS
 141
NR0B1_TARGET_GENES 2.36e-04 10.01 3.07 2.36e-02 2.68e-01
5NR4A1, GPRC5A, NFATC1, OSMR, SIK2
 233
RTTTNNNYTGGM_UNKNOWN 5.29e-04 11.82 3.05 3.00e-02 5.99e-01
4HAS2, NFATC2, NFATC1, EGFR
 155
CCAWWNAAGG_SRF_Q4 1.26e-03 15.41 3.01 5.97e-02 1.00e+00
3FOSB, NR4A1, THBS1
 88
ZNF239_TARGET_GENES 3.83e-03 23.75 2.70 8.15e-02 1.00e+00
2ERCC1, CCN1
 38
CTAWWWATA_RSRFC4_Q2 2.27e-04 7.78 2.69 2.36e-02 2.57e-01
6NR4A1, NFATC1, SIK3, PRRX1, DPYSL3, ADGRD1
 366
ATF_01 4.39e-04 8.71 2.68 2.71e-02 4.97e-01
5FOSB, NFATC1, FOS, CCN1, SIK2
 267
NKX25_02 4.39e-04 8.71 2.68 2.71e-02 4.97e-01
5HAS2, FGF7, STAT3, SIK3, PRRX1
 267
TAZ_TARGET_GENES 1.31e-04 7.07 2.67 2.36e-02 1.48e-01
7LMNA, RFX2, MMP19, NR4A1, SAMD4A, AXL, THBS1
 480
CREB_Q2 4.54e-04 8.64 2.66 2.71e-02 5.14e-01
5FOSB, NFATC1, STAT3, FOS, SIK2
 269
IGLV5_37_TARGET_GENES 1.10e-04 6.23 2.52 2.36e-02 1.25e-01
8LMNA, FGFR1, PRICKLE2, NFATC1, ADAMTS1, EGFR, OSMR, MYOF
 636
HNF3_Q6 1.17e-03 9.50 2.46 5.75e-02 1.00e+00
4FOSB, NR4A1, CCN1, ERRFI1
 192
TGAYRTCA_ATF3_Q6 2.91e-04 6.17 2.33 2.36e-02 3.30e-01
7HAS1, PRICKLE2, NFATC1, STAT3, ABI3BP, EGFR, FOS
 549
CTTTAAR_UNKNOWN 7.86e-05 5.22 2.32 2.36e-02 8.91e-02
10LMNA, HAS2, EMP1, B4GALT1, SIK3, PRRX1, AXL, CCN1, ADGRD1, ERRFI1
 994

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GO Biological Processes:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
GOBP_OVULATION_FROM_OVARIAN_FOLLICLE 8.61e-05 211.61 18.81 2.30e-02 6.44e-01
2MMP19, ADAMTS1
 6
GOBP_NEGATIVE_REGULATION_OF_CARDIAC_MUSCLE_ADAPTATION 1.60e-04 141.92 13.68 3.75e-02 1.00e+00
2LMNA, ERRFI1
 8
GOBP_RESPONSE_TO_PLATELET_DERIVED_GROWTH_FACTOR 1.73e-05 72.60 13.27 6.48e-03 1.30e-01
3HAS2, HAS1, ERRFI1
 21
GOBP_REGULATION_OF_NITRIC_OXIDE_MEDIATED_SIGNAL_TRANSDUCTION 2.06e-04 121.74 12.04 4.27e-02 1.00e+00
2EGFR, THBS1
 9
GOBP_OVULATION_CYCLE 3.95e-07 39.98 11.95 4.23e-04 2.96e-03
5HAS2, MMP19, ADAMTS1, EGFR, AXL
 62
GOBP_UDP_N_ACETYLGLUCOSAMINE_BIOSYNTHETIC_PROCESS 3.13e-04 94.83 9.72 5.72e-02 1.00e+00
2GFPT2, UAP1
 11
GOBP_REGULATION_OF_TYPE_B_PANCREATIC_CELL_PROLIFERATION 3.75e-04 85.24 8.86 6.52e-02 1.00e+00
2NR4A1, ERRFI1
 12
GOBP_ENDOTHELIAL_CELL_CHEMOTAXIS 6.33e-05 45.10 8.51 1.76e-02 4.74e-01
3FGFR1, NR4A1, THBS1
 32
GOBP_NEGATIVE_REGULATION_OF_MUSCLE_ADAPTATION 4.43e-04 77.52 8.14 6.52e-02 1.00e+00
2LMNA, ERRFI1
 13
GOBP_AMINO_SUGAR_BIOSYNTHETIC_PROCESS 4.43e-04 77.52 8.14 6.52e-02 1.00e+00
2GFPT2, UAP1
 13
GOBP_NEGATIVE_REGULATION_OF_VASCULAR_ASSOCIATED_SMOOTH_MUSCLE_CELL_DIFFERENTIATION 4.43e-04 77.52 8.14 6.52e-02 1.00e+00
2NFATC2, NFATC1
 13
GOBP_NEGATIVE_REGULATION_OF_EPIDERMAL_GROWTH_FACTOR_ACTIVATED_RECEPTOR_ACTIVITY 5.16e-04 71.02 7.54 6.77e-02 1.00e+00
2GPRC5A, ERRFI1
 14
GOBP_HYALURONAN_BIOSYNTHETIC_PROCESS 5.16e-04 71.02 7.54 6.77e-02 1.00e+00
2HAS2, HAS1
 14
GOBP_REGULATION_OF_KERATINOCYTE_MIGRATION 5.16e-04 71.02 7.54 6.77e-02 1.00e+00
2HAS2, FGF7
 14
GOBP_POSITIVE_REGULATION_OF_KERATINOCYTE_PROLIFERATION 5.94e-04 65.66 7.01 7.53e-02 1.00e+00
2HAS2, FGF7
 15
GOBP_UDP_N_ACETYLGLUCOSAMINE_METABOLIC_PROCESS 6.78e-04 60.98 6.55 7.68e-02 1.00e+00
2GFPT2, UAP1
 16
GOBP_OVULATION 6.78e-04 60.98 6.55 7.68e-02 1.00e+00
2MMP19, ADAMTS1
 16
GOBP_REGULATION_OF_CARDIAC_MUSCLE_ADAPTATION 7.67e-04 56.94 6.15 8.44e-02 1.00e+00
2LMNA, ERRFI1
 17
GOBP_RESPONSE_TO_PROGESTERONE 1.77e-04 31.17 5.97 3.89e-02 1.00e+00
3FOSB, FOS, THBS1
 45
GOBP_EXTERNAL_ENCAPSULATING_STRUCTURE_ORGANIZATION 2.68e-08 13.31 5.89 1.00e-04 2.01e-04
10CRISPLD2, HAS2, HAS1, MMP19, B4GALT1, ADAMTS1, COL4A4, CCN1, ADAMTS15, THBS1
 396

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Immunological Gene Sets:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
GSE37605_FOXP3_FUSION_GFP_VS_IRES_GFP_TREG_C57BL6_UP 2.87e-07 18.77 7.03 7.85e-04 1.40e-03
7FOSB, NR4A1, SVEP1, ADAMTS1, EGFR, FOS, THBS1
 185
GSE45365_NK_CELL_VS_CD11B_DC_DN 4.68e-07 17.41 6.52 7.85e-04 2.28e-03
7TWIST2, HAS1, GPRC5A, UAP1, OSMR, FOS, SLC2A3
 199
GSE12392_IFNAR_KO_VS_IFNB_KO_CD8_NEG_SPLEEN_DC_DN 4.84e-07 17.32 6.49 7.85e-04 2.36e-03
7LMNA, FOSB, EMP1, NR4A1, ADAMTS1, THBS1, ERRFI1
 200
GSE9988_ANTI_TREM1_VS_CTRL_TREATED_MONOCYTES_UP 7.77e-06 14.58 5.02 5.01e-03 3.78e-02
6ESYT2, MMP19, NR4A1, GPRC5A, IL1R1, SLC2A3
 198
GSE45365_NK_CELL_VS_BCELL_UP 7.77e-06 14.58 5.02 5.01e-03 3.78e-02
6FOSB, ESYT2, HAS1, FOS, CCN1, THBS1
 198
GSE4748_CTRL_VS_LPS_STIM_DC_3H_UP 8.22e-06 14.43 4.97 5.01e-03 4.01e-02
6HAS2, EMP1, ADAMTS1, DPYSL3, CCN1, ERRFI1
 200
GSE22196_HEALTHY_VS_OBESE_MOUSE_SKIN_GAMMADELTA_TCELL_DN 8.22e-06 14.43 4.97 5.01e-03 4.01e-02
6LMNA, FOSB, EMP1, UAP1, DPYSL3, THBS1
 200
GSE22935_WT_VS_MYD88_KO_MACROPHAGE_12H_MBOVIS_BCG_STIM_UP 8.22e-06 14.43 4.97 5.01e-03 4.01e-02
6HAS1, NR4A1, ADAMTS1, MEDAG, SPSB1, THBS1
 200
GSE37605_TREG_VS_TCONV_NOD_FOXP3_FUSION_GFP_UP 3.02e-05 15.73 4.80 1.63e-02 1.47e-01
5FOSB, NR4A1, ADAMTS1, FOS, ADAMTS15
 150
GSE9988_ANTI_TREM1_VS_VEHICLE_TREATED_MONOCYTES_UP 1.01e-04 12.07 3.70 1.84e-02 4.94e-01
5ESYT2, MMP19, GPRC5A, UAP1, IL1R1
 194
GSE9988_ANTI_TREM1_AND_LPS_VS_CTRL_TREATED_MONOCYTES_UP 1.01e-04 12.07 3.70 1.84e-02 4.94e-01
5NR4A1, GPRC5A, SLC19A2, SLC2A3, ERRFI1
 194
GSE29617_CTRL_VS_DAY7_TIV_FLU_VACCINE_PBMC_2008_UP 1.06e-04 11.94 3.66 1.84e-02 5.19e-01
5FOSB, NR4A1, TACC1, FOS, SLC2A3
 196
GSE20152_HTNFA_OVERXPRESS_ANKLE_VS_CTRL_SPHK1_KO_ANKLE_UP 1.06e-04 11.94 3.66 1.84e-02 5.19e-01
5B4GALT1, GPRC5A, FGF7, SVEP1, OSMR
 196
GSE2128_C57BL6_VS_NOD_CD4CD8_DP_THYMOCYTE_UP 1.09e-04 11.88 3.64 1.84e-02 5.31e-01
5EMP1, ERCC1, SLC19A2, SLC2A3, ERRFI1
 197
GSE23321_EFFECTOR_MEMORY_VS_NAIVE_CD8_TCELL_DN 1.09e-04 11.88 3.64 1.84e-02 5.31e-01
5LMNA, NFATC1, UAP1, SLC19A2, FOS
 197
GSE1460_DP_THYMOCYTE_VS_NAIVE_CD4_TCELL_CORD_BLOOD_DN 1.12e-04 11.82 3.62 1.84e-02 5.44e-01
5EMP1, RFX2, B4GALT1, SIK3, SIK2
 198
GSE15930_NAIVE_VS_48H_IN_VITRO_STIM_IFNAB_CD8_TCELL_UP 1.12e-04 11.82 3.62 1.84e-02 5.44e-01
5RFX2, B4GALT1, FGF7, SEMA4A, FOS
 198
GSE21546_UNSTIM_VS_ANTI_CD3_STIM_SAP1A_KO_DP_THYMOCYTES_UP 1.12e-04 11.82 3.62 1.84e-02 5.44e-01
5GPRC5A, ABI3BP, CCN1, ADAMTS15, ADGRD1
 198
GSE5455_HEALTHY_VS_TUMOR_BEARING_MOUSE_SPLEEN_MONOCYTE_DN 1.14e-04 11.76 3.60 1.84e-02 5.57e-01
5LMNA, EMP1, SPON1, AXL, SLC2A3
 199
GSE5589_WT_VS_IL6_KO_LPS_AND_IL6_STIM_MACROPHAGE_45MIN_DN 1.14e-04 11.76 3.60 1.84e-02 5.57e-01
5FGFR1, PRICKLE2, FGF7, SAMD4A, OSMR
 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
FOSB 4 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
TWIST2 7 Yes Known motif Monomer or homomultimer 100 perc ID - in vitro None None
RFX2 9 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
NFATC2 12 Yes Known motif Monomer or homomultimer High-throughput in vitro None PDB:1A02 has NFAT, Fos and Jun trimeric complex with non-consensus bZIP target site
NR4A1 15 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
NFATC1 19 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
SEMA4A 24 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None None
STAT3 28 Yes Known motif Monomer or homomultimer In vivo/Misc source None None
FOS 35 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
PRRX1 37 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
TSC22D2 51 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None There is some evidence that a related protein (TSC22D1) binds DNA specifically - thus, it is possible this is also a TF.
EGR1 53 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
ZFP36 58 No ssDNA/RNA binding Not a DNA binding protein No motif None RNA binding protein (PMID: 10330172).
NR4A3 60 Yes Known motif Monomer or homomultimer In vivo/Misc source Only known motifs are from Transfac or HocoMoco - origin is uncertain None
MAFF 65 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
IL6 67 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None None
JUNB 73 Yes Known motif Monomer or homomultimer High-throughput in vitro None Prefers forming heterodimers with FOS; FOSB; FOSL1 and FOSL2 over homodimers (PMID:12805554); but, clearly can bind DNA specifically in vitro.
KLF9 75 Yes Known motif Monomer or homomultimer 100 perc ID - in vitro None None
ZBTB16 80 Yes Known motif Monomer or homomultimer In vivo/Misc source Only known motifs are from Transfac or HocoMoco - origin is uncertain None
PER1 81 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None Protein that associates with CLOCK-ARNTL heterodimers to silence the expression of their target genes (PMID: 16987893)

Druggable Genes for this Gene Expression Program:

Gene Symbol Gene Loading Rank Drug Names Drug Category GTEx DepMap
FGFR1 10
3REGORAFENIB, PAZOPANIB, NINTEDANIB
 Small molecule GTEx DepMap
EGFR 33
6ERLOTINIB, AFATINIB, OSIMERTINIB, LAPATINIB, VANDETANIB, GEFITINIB
 Small molecule GTEx DepMap
EGFR 33
3PANITUMUMAB, NECITUMUMAB, CETUXIMAB
 Antibody GTEx DepMap
AXL 38
2R428, BGB324
 Small molecule GTEx DepMap
TUBB6 57
9VINORELBINE BASE, VINCRISTINE, ERIBULIN, CABAZITAXEL, IXABEPILONE, DOCETAXEL, COLCHICINE, PACLITAXEL, VINBLASTINE
 Small molecule GTEx DepMap
TUBB6 57
2BRENTUXIMAB VEDOTIN, TRASTUZUMAB EMTANSINE
 Antibody GTEx DepMap
IL6 67
1SILTUXIMAB
 Antibody GTEx DepMap
CDK17 105
2Roniciclib, AT-7519
 Small molecule GTEx DepMap
MCL1 108
1AMG176
 Small molecule GTEx DepMap
EPHA3 111
1VANDETANIB
 Small molecule GTEx DepMap
NTRK2 144
5AZD-6918, PLX-7486, CEP-2563, LOXO-101, AZD-7451
 Small molecule GTEx DepMap
ABL1 151
6IMATINIB, REGORAFENIB, NILOTINIB, PONATINIB, BOSUTINIB, DASATINIB
 Small molecule GTEx DepMap
MAPKAPK2 173
1AT-13148
 Small molecule GTEx DepMap
PDE3A 180
9THEOPHYLLINE SODIUM GLYCINATE, ANAGRELIDE, PENTOXIFYLLINE, THEOPHYLLINE, DYPHYLLINE, INAMRINONE, MILRINONE, CILOSTAZOL, DIPYRIDAMOLE
 Small molecule GTEx DepMap
IL4R 243
1DUPILUMAB
 Antibody GTEx DepMap
CDK14 291
2Roniciclib, AT-7519
 Small molecule GTEx DepMap
HDAC4 311
3ROMIDEPSIN, PANOBINOSTAT, BELINOSTAT
 Small molecule GTEx DepMap
TOP1 319
1IRINOTECAN
 Small molecule GTEx DepMap
VEGFA 357
2RANIBIZUMAB, BEVACIZUMAB
 Antibody GTEx DepMap
PPARD 377
1MBX-8025
 Small molecule GTEx DepMap
ESR1 397
23DIETHYLSTILBESTROL DIPHOSPHATE, TAMOXIFEN, TOREMIFENE, ESTRADIOL ACETATE, ESTROGENS, ESTERIFIED, SYNTHETIC CONJUGATED ESTROGENS, B, ESTROGENS, CONJUGATED, ESTROGENS, CONJUGATED SYNTHETIC A, BAZEDOXIFENE, CLOMIPHENE CITRATE, OSPEMIFENE, ESTRONE SULFURIC ACID, ESTRADIOL CYPIONATE, POLYESTRADIOL PHOSPHATE, MESTRANOL, QUINESTROL, ETHINYL ESTRADIOL, ESTRADIOL, DIETHYLSTILBESTROL, FULVESTRANT, ESTRADIOL VALERATE, ESTRONE, DIENESTROL
 Small molecule GTEx DepMap
JAK1 427
2RUXOLITINIB, TOFACITINIB
 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
CTCAATTAGGATACGC-1_HTA4_1021_4082 Fibroblasts 0.29 3070.77
Raw ScoresFibroblasts: 0.46, Smooth_muscle_cells: 0.44, Chondrocytes: 0.44, Osteoblasts: 0.43, Tissue_stem_cells: 0.42, iPS_cells: 0.4, MSC: 0.4, Astrocyte: 0.36, Neurons: 0.35, Neuroepithelial_cell: 0.35
CAACAGTGTTTGGGTT-1_HTA4_1020_4077 Smooth_muscle_cells 0.17 2692.88
Raw ScoresSmooth_muscle_cells: 0.28, Fibroblasts: 0.28, Osteoblasts: 0.27, Tissue_stem_cells: 0.27, Chondrocytes: 0.26, MSC: 0.25, iPS_cells: 0.25, Neurons: 0.22, Astrocyte: 0.22, Neuroepithelial_cell: 0.21
ATTATCCCATCTGGGC-1_HTA4_1012_4045 Tissue_stem_cells 0.21 2628.37
Raw ScoresFibroblasts: 0.36, Smooth_muscle_cells: 0.35, Tissue_stem_cells: 0.34, Chondrocytes: 0.33, Osteoblasts: 0.33, iPS_cells: 0.31, MSC: 0.3, Neurons: 0.26, Endothelial_cells: 0.24, Embryonic_stem_cells: 0.22
TAACTTCGTATCGTAC-1_HTA4_1009_4031 Fibroblasts 0.26 2595.25
Raw ScoresFibroblasts: 0.38, Smooth_muscle_cells: 0.36, Osteoblasts: 0.36, Chondrocytes: 0.35, Tissue_stem_cells: 0.33, iPS_cells: 0.32, MSC: 0.31, Neurons: 0.26, Astrocyte: 0.25, Endothelial_cells: 0.23
CTCAACCCACTTGTCC-1_HTA4_1009_4031 Smooth_muscle_cells 0.20 2349.01
Raw ScoresFibroblasts: 0.32, Osteoblasts: 0.3, Smooth_muscle_cells: 0.3, Tissue_stem_cells: 0.3, Chondrocytes: 0.29, iPS_cells: 0.27, MSC: 0.27, Endothelial_cells: 0.22, Neurons: 0.21, Astrocyte: 0.21
AGTTCCCGTGTTTGCA-1_HTA4_1009_4032 Smooth_muscle_cells 0.21 2151.14
Raw ScoresFibroblasts: 0.34, Osteoblasts: 0.33, Smooth_muscle_cells: 0.32, Chondrocytes: 0.31, Tissue_stem_cells: 0.3, MSC: 0.29, iPS_cells: 0.29, Neurons: 0.26, Astrocyte: 0.26, Endothelial_cells: 0.24
CCGGACATCGCTGATA-1_HTA4_1009_4031 Smooth_muscle_cells 0.16 2090.99
Raw ScoresFibroblasts: 0.36, Osteoblasts: 0.35, Smooth_muscle_cells: 0.34, Astrocyte: 0.34, Chondrocytes: 0.32, Tissue_stem_cells: 0.31, MSC: 0.31, Neurons: 0.31, iPS_cells: 0.3, Neuroepithelial_cell: 0.28
TCCTTCTTCCGCATAA-1_HTA4_1012_4046 Smooth_muscle_cells 0.29 2081.39
Raw ScoresFibroblasts: 0.5, Smooth_muscle_cells: 0.48, Chondrocytes: 0.48, Osteoblasts: 0.47, Tissue_stem_cells: 0.46, iPS_cells: 0.44, MSC: 0.44, Neurons: 0.37, Endothelial_cells: 0.36, Embryonic_stem_cells: 0.34
CCTGTTGGTCCGGCAT-1_HTA4_1001_4003 Smooth_muscle_cells 0.24 1997.93
Raw ScoresFibroblasts: 0.42, Smooth_muscle_cells: 0.41, Osteoblasts: 0.39, Tissue_stem_cells: 0.39, Chondrocytes: 0.38, iPS_cells: 0.37, MSC: 0.36, Neurons: 0.31, Astrocyte: 0.3, Endothelial_cells: 0.3
GGTGATTGTACAAGCG-1_HTA4_1009_4031 Fibroblasts 0.26 1982.83
Raw ScoresFibroblasts: 0.36, Osteoblasts: 0.34, Smooth_muscle_cells: 0.32, Chondrocytes: 0.31, Tissue_stem_cells: 0.31, MSC: 0.3, iPS_cells: 0.3, Neurons: 0.25, Astrocyte: 0.23, Neuroepithelial_cell: 0.23
TCTCCGAGTATCGTTG-1_HTA4_1009_4031 Fibroblasts 0.26 1975.32
Raw ScoresFibroblasts: 0.37, Chondrocytes: 0.35, Osteoblasts: 0.35, Smooth_muscle_cells: 0.35, Tissue_stem_cells: 0.34, iPS_cells: 0.32, MSC: 0.32, Neurons: 0.27, Astrocyte: 0.24, Endothelial_cells: 0.23
TTGACCCGTACCCAGC-1_HTA4_1009_4032 Fibroblasts 0.19 1918.76
Raw ScoresFibroblasts: 0.26, Smooth_muscle_cells: 0.24, Osteoblasts: 0.24, Tissue_stem_cells: 0.24, Chondrocytes: 0.24, MSC: 0.21, iPS_cells: 0.21, Neurons: 0.18, Endothelial_cells: 0.16, Astrocyte: 0.15
GCTACCTAGGAACATT-1_HTA4_1009_4031 Smooth_muscle_cells 0.23 1859.16
Raw ScoresFibroblasts: 0.36, Smooth_muscle_cells: 0.36, Osteoblasts: 0.36, Chondrocytes: 0.34, Tissue_stem_cells: 0.33, MSC: 0.32, iPS_cells: 0.32, Neurons: 0.27, Astrocyte: 0.26, Endothelial_cells: 0.25
AGCTCAACACGCGGTT-1_HTA4_1009_4031 Fibroblasts 0.24 1830.62
Raw ScoresFibroblasts: 0.35, Osteoblasts: 0.34, Smooth_muscle_cells: 0.33, Chondrocytes: 0.33, Tissue_stem_cells: 0.32, MSC: 0.3, iPS_cells: 0.3, Neurons: 0.24, Endothelial_cells: 0.23, Astrocyte: 0.22
CCTACGTCACATGACT-1_HTA4_1020_4077 Tissue_stem_cells 0.18 1727.28
Raw ScoresFibroblasts: 0.31, Osteoblasts: 0.31, Smooth_muscle_cells: 0.31, Tissue_stem_cells: 0.3, Chondrocytes: 0.3, MSC: 0.28, iPS_cells: 0.27, Neurons: 0.24, Astrocyte: 0.23, Endothelial_cells: 0.23
TCAGTGATCACTGAAC-1_HTA4_1009_4032 Smooth_muscle_cells 0.23 1711.73
Raw ScoresFibroblasts: 0.33, Smooth_muscle_cells: 0.32, Osteoblasts: 0.3, Chondrocytes: 0.29, Tissue_stem_cells: 0.28, iPS_cells: 0.28, MSC: 0.27, Neurons: 0.23, Endothelial_cells: 0.23, Astrocyte: 0.23
TGCACGGGTATGCTTG-1_HTA4_1020_4077 Smooth_muscle_cells 0.20 1709.41
Raw ScoresFibroblasts: 0.32, Smooth_muscle_cells: 0.31, Osteoblasts: 0.31, Chondrocytes: 0.29, Tissue_stem_cells: 0.29, MSC: 0.28, iPS_cells: 0.27, Neurons: 0.23, Astrocyte: 0.22, Endothelial_cells: 0.22
CCTGCATGTGTCCATA-1_HTA4_1009_4033 Smooth_muscle_cells 0.15 1686.84
Raw ScoresFibroblasts: 0.33, Smooth_muscle_cells: 0.33, Osteoblasts: 0.32, Chondrocytes: 0.3, Tissue_stem_cells: 0.3, iPS_cells: 0.29, MSC: 0.28, Astrocyte: 0.26, Neurons: 0.25, Endothelial_cells: 0.24
TAAGCACCATGCCATA-1_HTA4_1009_4031 Smooth_muscle_cells 0.22 1673.99
Raw ScoresFibroblasts: 0.3, Osteoblasts: 0.29, Smooth_muscle_cells: 0.28, Chondrocytes: 0.28, Tissue_stem_cells: 0.26, iPS_cells: 0.25, MSC: 0.25, Astrocyte: 0.22, Neurons: 0.2, Neuroepithelial_cell: 0.18
TGAGGTTGTGGAACCA-1_HTA4_1009_4031 Fibroblasts 0.25 1660.51
Raw ScoresFibroblasts: 0.35, Osteoblasts: 0.33, Chondrocytes: 0.33, Smooth_muscle_cells: 0.32, Tissue_stem_cells: 0.31, iPS_cells: 0.3, MSC: 0.3, Neurons: 0.24, Endothelial_cells: 0.22, Astrocyte: 0.21
CTTCTCTGTGTCCACG-1_HTA4_1009_4031 Fibroblasts 0.25 1654.35
Raw ScoresFibroblasts: 0.4, Osteoblasts: 0.39, Chondrocytes: 0.38, Tissue_stem_cells: 0.38, Smooth_muscle_cells: 0.37, MSC: 0.35, iPS_cells: 0.35, Neurons: 0.29, Endothelial_cells: 0.26, Astrocyte: 0.26
ATCCGTCTCACTTGGA-1_HTA4_1009_4031 Fibroblasts 0.23 1630.55
Raw ScoresFibroblasts: 0.3, Smooth_muscle_cells: 0.29, Osteoblasts: 0.28, Chondrocytes: 0.27, Tissue_stem_cells: 0.27, iPS_cells: 0.26, MSC: 0.25, Astrocyte: 0.21, Neurons: 0.2, Neuroepithelial_cell: 0.19
CTACAGAGTTGCCAAT-1_HTA4_1020_4077 Fibroblasts 0.20 1618.69
Raw ScoresFibroblasts: 0.31, Smooth_muscle_cells: 0.29, Osteoblasts: 0.29, Chondrocytes: 0.28, Tissue_stem_cells: 0.28, MSC: 0.25, iPS_cells: 0.25, Endothelial_cells: 0.22, Neurons: 0.22, Astrocyte: 0.2
AGGCATTCACCCTTAC-1_HTA4_1009_4031 Smooth_muscle_cells 0.18 1614.69
Raw ScoresFibroblasts: 0.31, Osteoblasts: 0.3, Smooth_muscle_cells: 0.3, Chondrocytes: 0.29, Tissue_stem_cells: 0.29, MSC: 0.27, iPS_cells: 0.27, Neurons: 0.22, Astrocyte: 0.21, Endothelial_cells: 0.21
CACGAATAGGTATCTC-1_HTA4_1012_4045 Tissue_stem_cells 0.16 1607.33
Raw ScoresTissue_stem_cells: 0.31, Fibroblasts: 0.31, Smooth_muscle_cells: 0.3, Osteoblasts: 0.3, Chondrocytes: 0.3, iPS_cells: 0.27, MSC: 0.27, Astrocyte: 0.26, Neurons: 0.24, Endothelial_cells: 0.24
GACTTCCTCGGCATCG-1_HTA4_1020_4077 Smooth_muscle_cells 0.24 1606.69
Raw ScoresFibroblasts: 0.34, Smooth_muscle_cells: 0.33, Osteoblasts: 0.31, Chondrocytes: 0.31, Tissue_stem_cells: 0.3, MSC: 0.29, iPS_cells: 0.29, Neurons: 0.24, Astrocyte: 0.24, Neuroepithelial_cell: 0.22
TGATCAGAGTCCGCGT-1_HTA4_1009_4031 Fibroblasts 0.34 1576.56
Raw ScoresFibroblasts: 0.48, Osteoblasts: 0.47, Chondrocytes: 0.45, Smooth_muscle_cells: 0.45, Tissue_stem_cells: 0.44, iPS_cells: 0.42, MSC: 0.42, Neurons: 0.36, Astrocyte: 0.33, Endothelial_cells: 0.32
CTCCTTTCAACCTAAC-1_HTA4_1009_4033 Smooth_muscle_cells 0.19 1556.87
Raw ScoresSmooth_muscle_cells: 0.3, Fibroblasts: 0.28, Osteoblasts: 0.27, MSC: 0.27, Chondrocytes: 0.27, iPS_cells: 0.27, Tissue_stem_cells: 0.27, Astrocyte: 0.25, Neuroepithelial_cell: 0.25, Neurons: 0.24
CCAATGATCATCGACA-1_HTA4_1009_4031 Fibroblasts 0.28 1523.41
Raw ScoresFibroblasts: 0.42, Osteoblasts: 0.4, Smooth_muscle_cells: 0.4, Chondrocytes: 0.39, Tissue_stem_cells: 0.39, iPS_cells: 0.37, MSC: 0.36, Neurons: 0.3, Astrocyte: 0.26, Endothelial_cells: 0.26
ATCACTTCACCATAAC-1_HTA4_1012_4046 Chondrocytes 0.26 1481.29
Raw ScoresChondrocytes: 0.41, Fibroblasts: 0.4, Smooth_muscle_cells: 0.39, Osteoblasts: 0.39, Tissue_stem_cells: 0.38, MSC: 0.36, iPS_cells: 0.35, Neurons: 0.29, Endothelial_cells: 0.27, Astrocyte: 0.26
CCTAACCGTGACCGAA-1_HTA4_1012_4046 Tissue_stem_cells 0.23 1455.50
Raw ScoresFibroblasts: 0.41, Smooth_muscle_cells: 0.4, Osteoblasts: 0.39, Chondrocytes: 0.38, Tissue_stem_cells: 0.38, iPS_cells: 0.37, MSC: 0.36, Neurons: 0.32, Endothelial_cells: 0.31, Astrocyte: 0.29
CCCATTGAGCCTCTCT-1_HTA4_1009_4031 Fibroblasts 0.23 1423.94
Raw ScoresFibroblasts: 0.32, Smooth_muscle_cells: 0.31, Osteoblasts: 0.3, Chondrocytes: 0.3, Tissue_stem_cells: 0.3, MSC: 0.27, iPS_cells: 0.27, Neurons: 0.23, Astrocyte: 0.21, Endothelial_cells: 0.21
ACTATCTGTCCACTCT-1_HTA4_1009_4033 Fibroblasts 0.20 1422.71
Raw ScoresFibroblasts: 0.34, Osteoblasts: 0.33, Smooth_muscle_cells: 0.33, MSC: 0.32, Tissue_stem_cells: 0.32, Chondrocytes: 0.32, iPS_cells: 0.31, Astrocyte: 0.28, Neurons: 0.28, Neuroepithelial_cell: 0.27
GTTGCGGCACTCCACT-1_HTA4_1017_4062 Smooth_muscle_cells 0.24 1416.47
Raw ScoresFibroblasts: 0.35, Smooth_muscle_cells: 0.34, Osteoblasts: 0.33, Chondrocytes: 0.32, Tissue_stem_cells: 0.31, iPS_cells: 0.3, MSC: 0.3, Neurons: 0.25, Endothelial_cells: 0.24, Astrocyte: 0.22
ATCACGAGTAGTGATA-1_HTA4_1020_4077 Smooth_muscle_cells 0.14 1409.46
Raw ScoresFibroblasts: 0.25, Smooth_muscle_cells: 0.24, Tissue_stem_cells: 0.24, Osteoblasts: 0.23, Chondrocytes: 0.23, MSC: 0.22, iPS_cells: 0.22, Neurons: 0.19, Astrocyte: 0.18, Neuroepithelial_cell: 0.18
CTCATGCCACCCTGTT-1_HTA4_1009_4032 Fibroblasts 0.21 1406.35
Raw ScoresFibroblasts: 0.28, Smooth_muscle_cells: 0.27, Osteoblasts: 0.26, Chondrocytes: 0.25, Tissue_stem_cells: 0.24, iPS_cells: 0.22, MSC: 0.22, Neurons: 0.19, Astrocyte: 0.19, Neuroepithelial_cell: 0.17
CGTTCTGCATCTATCT-1_HTA4_1009_4032 Tissue_stem_cells 0.18 1393.02
Raw ScoresFibroblasts: 0.34, Osteoblasts: 0.34, Smooth_muscle_cells: 0.32, Chondrocytes: 0.32, Tissue_stem_cells: 0.31, iPS_cells: 0.29, MSC: 0.29, Neurons: 0.27, Astrocyte: 0.27, Endothelial_cells: 0.24
TAGCACAAGACTTCAC-1_HTA4_1009_4032 Fibroblasts 0.23 1392.28
Raw ScoresFibroblasts: 0.34, Smooth_muscle_cells: 0.33, Osteoblasts: 0.32, Chondrocytes: 0.31, Tissue_stem_cells: 0.3, iPS_cells: 0.29, MSC: 0.28, Neurons: 0.25, Endothelial_cells: 0.23, Astrocyte: 0.23
TCCTTTCTCGCAACAT-1_HTA4_1020_4077 Fibroblasts 0.19 1382.54
Raw ScoresFibroblasts: 0.28, Smooth_muscle_cells: 0.27, Osteoblasts: 0.26, Chondrocytes: 0.26, Tissue_stem_cells: 0.25, MSC: 0.25, iPS_cells: 0.23, Astrocyte: 0.22, Neurons: 0.21, Endothelial_cells: 0.21
CTTCCGATCTTCTTCC-1_HTA4_1020_4077 Fibroblasts 0.18 1372.13
Raw ScoresFibroblasts: 0.28, Smooth_muscle_cells: 0.27, Osteoblasts: 0.26, Chondrocytes: 0.26, Tissue_stem_cells: 0.26, MSC: 0.26, iPS_cells: 0.24, Neuroepithelial_cell: 0.22, Endothelial_cells: 0.21, Astrocyte: 0.21
GACTCTCAGAATCCCT-1_HTA4_1020_4077 Smooth_muscle_cells 0.19 1359.22
Raw ScoresFibroblasts: 0.31, Smooth_muscle_cells: 0.31, Osteoblasts: 0.29, Chondrocytes: 0.28, Tissue_stem_cells: 0.28, iPS_cells: 0.27, MSC: 0.26, Neurons: 0.23, Astrocyte: 0.22, Endothelial_cells: 0.22
AGACACTGTTCCACGG-1_HTA4_1009_4032 Osteoblasts 0.23 1359.12
Raw ScoresFibroblasts: 0.33, Osteoblasts: 0.33, Chondrocytes: 0.3, Smooth_muscle_cells: 0.29, Tissue_stem_cells: 0.29, MSC: 0.28, iPS_cells: 0.27, Neurons: 0.26, Astrocyte: 0.25, Neuroepithelial_cell: 0.23
AACCACACAAGCGCTC-1_HTA4_1009_4031 Fibroblasts 0.25 1357.81
Raw ScoresFibroblasts: 0.36, Osteoblasts: 0.35, Smooth_muscle_cells: 0.35, Chondrocytes: 0.34, Tissue_stem_cells: 0.33, MSC: 0.32, iPS_cells: 0.31, Neurons: 0.26, Astrocyte: 0.26, Endothelial_cells: 0.24
GGGACAACAAATAGCA-1_HTA4_1009_4031 Smooth_muscle_cells 0.20 1356.50
Raw ScoresFibroblasts: 0.32, Osteoblasts: 0.31, Smooth_muscle_cells: 0.3, Tissue_stem_cells: 0.29, Chondrocytes: 0.28, MSC: 0.28, Neurons: 0.28, iPS_cells: 0.28, Astrocyte: 0.26, Neuroepithelial_cell: 0.24
CACGTGGGTCCGGACT-1_HTA4_1009_4031 Smooth_muscle_cells 0.15 1350.30
Raw ScoresFibroblasts: 0.36, Osteoblasts: 0.36, Smooth_muscle_cells: 0.35, Astrocyte: 0.34, Tissue_stem_cells: 0.32, Chondrocytes: 0.32, Neurons: 0.32, MSC: 0.31, iPS_cells: 0.31, Neuroepithelial_cell: 0.3
GGGCCATGTTGGTAGG-1_HTA4_1020_4077 Smooth_muscle_cells 0.18 1347.30
Raw ScoresFibroblasts: 0.3, Smooth_muscle_cells: 0.3, Tissue_stem_cells: 0.29, Osteoblasts: 0.29, Chondrocytes: 0.28, MSC: 0.27, iPS_cells: 0.26, Neurons: 0.24, Endothelial_cells: 0.23, Astrocyte: 0.23
GTAACCAGTCTCGACG-1_HTA4_1009_4031 Smooth_muscle_cells 0.17 1335.84
Raw ScoresFibroblasts: 0.39, Smooth_muscle_cells: 0.37, Osteoblasts: 0.37, Astrocyte: 0.36, Chondrocytes: 0.35, Tissue_stem_cells: 0.35, Endothelial_cells: 0.35, MSC: 0.34, Neurons: 0.34, iPS_cells: 0.34
GTCTACCCACGAAGAC-1_HTA4_1009_4031 Smooth_muscle_cells 0.20 1330.71
Raw ScoresFibroblasts: 0.3, Osteoblasts: 0.29, Smooth_muscle_cells: 0.28, Chondrocytes: 0.27, Tissue_stem_cells: 0.26, MSC: 0.25, iPS_cells: 0.25, Neurons: 0.23, Astrocyte: 0.21, Endothelial_cells: 0.19
TCCCACATCCGAGTGC-1_HTA4_1009_4032 Fibroblasts 0.23 1328.86
Raw ScoresFibroblasts: 0.32, Smooth_muscle_cells: 0.31, Osteoblasts: 0.29, Tissue_stem_cells: 0.28, Chondrocytes: 0.28, iPS_cells: 0.26, MSC: 0.25, Neurons: 0.21, Astrocyte: 0.21, Endothelial_cells: 0.21
GTGGGAATCTTAGCCC-1_HTA4_1009_4032 Smooth_muscle_cells 0.19 1327.61
Raw ScoresFibroblasts: 0.3, Smooth_muscle_cells: 0.28, Osteoblasts: 0.28, Chondrocytes: 0.27, Tissue_stem_cells: 0.26, iPS_cells: 0.26, MSC: 0.25, Neurons: 0.21, Endothelial_cells: 0.2, Astrocyte: 0.2


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: 2.01e-16
Mean rank of genes in gene set: 2654.22
Rank on gene expression program of genes in gene set:
Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
IL1R1 0.0053024 23 GTEx DepMap Descartes 2.47 378.89
IL6 0.0035210 67 GTEx DepMap Descartes 0.16 93.60
CCL2 0.0027366 132 GTEx DepMap Descartes 0.84 651.59
CFD 0.0023247 166 GTEx DepMap Descartes 0.16 135.33
C7 0.0020133 209 GTEx DepMap Descartes 3.17 416.76
CXCL14 0.0019637 220 GTEx DepMap Descartes 0.21 108.74
CXCL2 0.0017104 271 GTEx DepMap Descartes 0.58 268.62
C3 0.0015218 314 GTEx DepMap Descartes 4.11 335.41
C1R 0.0014796 325 GTEx DepMap Descartes 0.71 132.68
C1S 0.0014392 337 GTEx DepMap Descartes 1.25 258.28
PDPN 0.0012221 429 GTEx DepMap Descartes 0.15 36.40
IGF1 0.0011718 456 GTEx DepMap Descartes 0.65 62.50
CXCL12 0.0011286 481 GTEx DepMap Descartes 0.41 85.73
SCARA5 0.0010717 510 GTEx DepMap Descartes 0.03 7.00
LIF 0.0010293 532 GTEx DepMap Descartes 0.07 12.45
IL33 0.0009806 566 GTEx DepMap Descartes 0.28 82.98
PDGFD 0.0009610 580 GTEx DepMap Descartes 1.36 177.85
RGMA 0.0008989 640 GTEx DepMap Descartes 0.13 8.42
PDGFRB 0.0007031 795 GTEx DepMap Descartes 0.79 99.38
SERPING1 0.0006437 858 GTEx DepMap Descartes 0.83 183.25
PDGFRA 0.0004345 1193 GTEx DepMap Descartes 0.16 17.02
SOD2 0.0002805 1555 GTEx DepMap Descartes 0.06 1.92
SAA1 0.0002419 1681 GTEx DepMap Descartes 0.06 31.84
HGF 0.0001725 1964 GTEx DepMap Descartes 0.39 39.23
CXCL1 0.0001665 2001 GTEx DepMap Descartes 0.04 17.40
IGFBP6 0.0001420 2133 GTEx DepMap Descartes 0.13 81.22
CCL21 0.0001399 2144 GTEx DepMap Descartes 0.47 358.20
SCARA3 0.0001397 2145 GTEx DepMap Descartes 0.09 14.76
CCL8 0.0001240 2234 GTEx DepMap Descartes 0.02 11.55
GPX3 0.0001174 2277 GTEx DepMap Descartes 0.23 70.95
ADH1B 0.0001124 2317 GTEx DepMap Descartes 0.92 75.78
CFB 0.0000996 2433 GTEx DepMap Descartes 0.04 6.00
CXCL9 0.0000391 3094 GTEx DepMap Descartes 0.02 5.20
CCL7 0.0000298 3248 GTEx DepMap Descartes 0.00 1.02
IL10 -0.0000098 6291 GTEx DepMap Descartes 0.01 1.88
C4B -0.0000218 7572 GTEx DepMap Descartes 0.01 0.41
CXCL10 -0.0000504 9668 GTEx DepMap Descartes 0.03 11.35
CXCL13 -0.0001327 13880 GTEx DepMap Descartes 0.02 9.76
C1QC -0.0001483 14564 GTEx DepMap Descartes 0.06 29.74
C1QA -0.0001825 15864 GTEx DepMap Descartes 0.11 63.94


Stroma (Hanemaaijer)
Marker genes obtained from Supplementary Table SD of Hanemaaijer et al (PMID 33500353). The authors generated single-cell RNA-seq data (sort-seq, 2,229 cells total) from mouse adrenal glads at E13.5, E14.5, E17.5, E18.5, P1 and P5. These were marker genes that matched with a similar dataset generated by Furlan et al (PMID 28684471). This particular set of markers are for the broad Stroma cluster:
Wilcoxon ranksum test P-value for gene set overrepresentation: 2.66e-04
Mean rank of genes in gene set: 1087.4
Rank on gene expression program of genes in gene set:

Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
GPC3 0.0015370 309 GTEx DepMap Descartes 0.63 240.52
COL6A1 0.0009909 559 GTEx DepMap Descartes 1.16 188.71
COL5A1 0.0009332 607 GTEx DepMap Descartes 1.57 132.45
FN1 0.0002499 1654 GTEx DepMap Descartes 7.97 506.91
COL3A1 0.0001135 2308 GTEx DepMap Descartes 5.38 584.38


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: 3.64e-04
Mean rank of genes in gene set: 7428.2
Rank on gene expression program of genes in gene set:

Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
THBS1 0.0040045 49 GTEx DepMap Descartes 5.13 501.17
COL5A2 0.0035144 68 GTEx DepMap Descartes 3.37 374.12
COL4A1 0.0031169 93 GTEx DepMap Descartes 8.07 953.18
TNC 0.0029182 110 GTEx DepMap Descartes 3.35 326.56
COL14A1 0.0024358 155 GTEx DepMap Descartes 1.52 136.20
VCAN 0.0020448 205 GTEx DepMap Descartes 3.44 184.38
COL12A1 0.0020241 208 GTEx DepMap Descartes 2.23 141.98
THBS2 0.0014910 321 GTEx DepMap Descartes 1.68 192.53
VEGFA 0.0013846 357 GTEx DepMap Descartes 1.26 58.38
IGFBP7 0.0013663 363 GTEx DepMap Descartes 8.25 4186.75
MMP2 0.0011523 471 GTEx DepMap Descartes 0.34 72.52
COL5A1 0.0009332 607 GTEx DepMap Descartes 1.57 132.45
DCN 0.0006219 879 GTEx DepMap Descartes 1.41 144.64
TAGLN 0.0005131 1044 GTEx DepMap Descartes 1.03 200.95
CNN3 0.0004893 1089 GTEx DepMap Descartes 1.18 405.92
TGFBR2 0.0004884 1092 GTEx DepMap Descartes 2.25 226.51
ITGA7 0.0004603 1133 GTEx DepMap Descartes 0.23 37.85
CNN2 0.0003805 1292 GTEx DepMap Descartes 0.19 55.60
IGFBP3 0.0003702 1311 GTEx DepMap Descartes 0.35 80.02
TGFB1 0.0003377 1388 GTEx DepMap Descartes 0.58 139.23
TPM1 0.0002873 1535 GTEx DepMap Descartes 2.78 434.52
LUM 0.0002728 1576 GTEx DepMap Descartes 0.92 228.00
FN1 0.0002499 1654 GTEx DepMap Descartes 7.97 506.91
WNT5A 0.0002261 1740 GTEx DepMap Descartes 0.04 5.73
TGFBR1 0.0001441 2120 GTEx DepMap Descartes 0.83 73.14
COL3A1 0.0001135 2308 GTEx DepMap Descartes 5.38 584.38
TPM2 0.0001087 2349 GTEx DepMap Descartes 0.40 169.62
MYL9 0.0000874 2539 GTEx DepMap Descartes 0.47 117.16
COL15A1 0.0000583 2843 GTEx DepMap Descartes 1.19 109.51
TMEM119 0.0000050 4011 GTEx DepMap Descartes 0.07 15.75
TGFB2 -0.0000616 10314 GTEx DepMap Descartes 0.28 30.28
COL13A1 -0.0000738 11016 GTEx DepMap Descartes 0.03 5.45
ACTG2 -0.0001269 13611 GTEx DepMap Descartes 0.03 11.22
THY1 -0.0001326 13878 GTEx DepMap Descartes 0.67 77.93
BGN -0.0001617 15093 GTEx DepMap Descartes 0.60 160.56
HOPX -0.0001748 15588 GTEx DepMap Descartes 0.18 21.12
PGF -0.0002042 16560 GTEx DepMap Descartes 0.05 8.26
COL8A1 -0.0002239 17112 GTEx DepMap Descartes 1.48 164.10
COL1A2 -0.0002336 17374 GTEx DepMap Descartes 5.55 556.81
MYH11 -0.0002849 18481 GTEx DepMap Descartes 0.38 38.60
MYLK -0.0003278 19074 GTEx DepMap Descartes 0.53 30.68
COL1A1 -0.0003563 19387 GTEx DepMap Descartes 5.07 486.77
MMP11 -0.0003668 19471 GTEx DepMap Descartes 0.08 10.78
MEF2C -0.0004534 20018 GTEx DepMap Descartes 1.28 95.55
COL10A1 -0.0004972 20167 GTEx DepMap Descartes 0.12 14.05
COL11A1 -0.0005490 20288 GTEx DepMap Descartes 0.46 30.90
RGS5 -0.0007252 20510 GTEx DepMap Descartes 1.09 92.27
ACTA2 -0.0008446 20558 GTEx DepMap Descartes 0.73 336.28
POSTN -0.0009171 20572 GTEx DepMap Descartes 1.06 162.87




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: 15734.02
Median rank of genes in gene set: 17750
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
DPYSL3 0.0043736 39 GTEx DepMap Descartes 2.80 357.64
FOXO3 0.0027897 124 GTEx DepMap Descartes 5.59 513.54
CELF2 0.0025269 150 GTEx DepMap Descartes 4.01 410.73
NFIL3 0.0022116 182 GTEx DepMap Descartes 0.96 254.83
AKAP12 0.0019096 232 GTEx DepMap Descartes 5.87 470.60
NCS1 0.0016572 284 GTEx DepMap Descartes 0.83 106.66
EML4 0.0012681 406 GTEx DepMap Descartes 4.66 431.81
SLIT3 0.0011853 448 GTEx DepMap Descartes 6.71 430.61
RBMS3 0.0010260 536 GTEx DepMap Descartes 4.45 349.31
TENM4 0.0009434 600 GTEx DepMap Descartes 2.80 NA
KLF13 0.0009164 623 GTEx DepMap Descartes 0.89 77.48
GCH1 0.0008924 648 GTEx DepMap Descartes 1.70 268.07
GNB1 0.0007829 725 GTEx DepMap Descartes 3.64 664.83
ANK2 0.0006988 800 GTEx DepMap Descartes 8.40 301.37
ABLIM1 0.0006476 855 GTEx DepMap Descartes 4.92 279.00
TIAM1 0.0005029 1067 GTEx DepMap Descartes 1.55 141.24
HK2 0.0004896 1088 GTEx DepMap Descartes 0.19 22.49
PTS 0.0003961 1263 GTEx DepMap Descartes 0.79 365.34
KLC1 0.0003106 1463 GTEx DepMap Descartes 1.06 42.61
TACC2 0.0002948 1511 GTEx DepMap Descartes 0.90 49.40
GRB10 0.0002420 1679 GTEx DepMap Descartes 2.29 230.04
BMP7 0.0002406 1686 GTEx DepMap Descartes 0.43 48.79
GNG4 0.0002201 1762 GTEx DepMap Descartes 1.51 128.27
STXBP1 0.0001833 1913 GTEx DepMap Descartes 1.43 139.10
NCOA7 0.0001814 1922 GTEx DepMap Descartes 2.48 NA
DNAJB1 0.0001698 1981 GTEx DepMap Descartes 0.26 62.67
EVL 0.0001560 2048 GTEx DepMap Descartes 2.28 319.54
RUFY3 0.0000768 2643 GTEx DepMap Descartes 2.61 306.53
MAGI3 0.0000607 2815 GTEx DepMap Descartes 2.24 160.79
NPTX2 0.0000380 3115 GTEx DepMap Descartes 0.07 12.88


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: 3.95e-41
Mean rank of genes in gene set: 6667.87
Median rank of genes in gene set: 2445
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
LMNA 0.0084675 2 GTEx DepMap Descartes 6.62 1852.26
EMP1 0.0073940 6 GTEx DepMap Descartes 6.85 1059.63
FGFR1 0.0063647 10 GTEx DepMap Descartes 2.30 322.99
UAP1 0.0054367 21 GTEx DepMap Descartes 1.06 310.86
STAT3 0.0051113 28 GTEx DepMap Descartes 6.62 822.99
EGFR 0.0048645 33 GTEx DepMap Descartes 3.98 301.96
PRRX1 0.0044597 37 GTEx DepMap Descartes 1.66 335.61
THBS1 0.0040045 49 GTEx DepMap Descartes 5.13 501.17
ERRFI1 0.0039704 50 GTEx DepMap Descartes 2.93 551.92
TSC22D2 0.0039197 51 GTEx DepMap Descartes 3.61 194.77
EGR1 0.0038581 53 GTEx DepMap Descartes 2.99 662.65
TUBB6 0.0037511 57 GTEx DepMap Descartes 0.98 369.51
CBLB 0.0037253 59 GTEx DepMap Descartes 6.64 706.89
COL5A2 0.0035144 68 GTEx DepMap Descartes 3.37 374.12
HIPK3 0.0034959 69 GTEx DepMap Descartes 3.10 279.70
EPS8 0.0034951 70 GTEx DepMap Descartes 4.17 651.47
CCDC80 0.0033400 74 GTEx DepMap Descartes 1.07 63.97
COL4A2 0.0032710 79 GTEx DepMap Descartes 7.02 857.28
FSTL1 0.0032112 83 GTEx DepMap Descartes 1.60 224.34
COL6A2 0.0031832 85 GTEx DepMap Descartes 2.00 465.37
LATS2 0.0031779 86 GTEx DepMap Descartes 1.44 189.94
ALDH1A3 0.0031729 88 GTEx DepMap Descartes 0.64 145.93
HOMER1 0.0031574 89 GTEx DepMap Descartes 2.48 244.43
COL4A1 0.0031169 93 GTEx DepMap Descartes 8.07 953.18
ZFP36L1 0.0030922 95 GTEx DepMap Descartes 1.70 396.29
BNC2 0.0030624 100 GTEx DepMap Descartes 4.20 288.21
ANXA1 0.0030476 102 GTEx DepMap Descartes 1.73 644.13
CFH 0.0029780 106 GTEx DepMap Descartes 3.95 318.10
TNC 0.0029182 110 GTEx DepMap Descartes 3.35 326.56
EPHA3 0.0029169 111 GTEx DepMap Descartes 1.63 233.73


Descartes adrenocortical markers
Top 50 marker genes of adrenocortical cells in the Decartes fetal adrenal single cell map (https://atlas.brotmanbaty.org/bbi/human-gene-expression-during-development/cell/adrenocortical/in/adrenal)
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.00e+00
Mean rank of genes in gene set: 14116.11
Median rank of genes in gene set: 16858
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
SH3PXD2B 0.0028176 118 GTEx DepMap Descartes 1.43 135.34
LDLR 0.0004912 1083 GTEx DepMap Descartes 2.51 214.48
PAPSS2 0.0003980 1259 GTEx DepMap Descartes 2.00 266.54
SH3BP5 0.0002866 1538 GTEx DepMap Descartes 2.44 423.20
PDE10A 0.0001223 2247 GTEx DepMap Descartes 4.27 268.28
ERN1 0.0000428 3043 GTEx DepMap Descartes 1.68 85.15
APOC1 0.0000030 4126 GTEx DepMap Descartes 1.22 793.76
IGF1R -0.0000346 8613 GTEx DepMap Descartes 4.44 191.24
SLC2A14 -0.0000380 8859 GTEx DepMap Descartes 0.07 7.26
PEG3 -0.0000419 9129 GTEx DepMap Descartes 0.01 NA
FREM2 -0.0000743 11050 GTEx DepMap Descartes 0.05 1.64
SULT2A1 -0.0000815 11410 GTEx DepMap Descartes 0.77 130.57
INHA -0.0000869 11668 GTEx DepMap Descartes 0.03 8.20
HMGCS1 -0.0001117 12900 GTEx DepMap Descartes 1.23 98.06
HSPD1 -0.0001120 12917 GTEx DepMap Descartes 2.01 388.94
CLU -0.0001179 13193 GTEx DepMap Descartes 2.12 284.74
FDXR -0.0001571 14909 GTEx DepMap Descartes 0.09 15.12
TM7SF2 -0.0001596 15008 GTEx DepMap Descartes 0.13 29.07
POR -0.0001661 15286 GTEx DepMap Descartes 2.63 370.63
DHCR7 -0.0001668 15303 GTEx DepMap Descartes 0.09 14.62
MSMO1 -0.0001736 15539 GTEx DepMap Descartes 0.55 109.58
HMGCR -0.0001931 16199 GTEx DepMap Descartes 0.58 58.11
SGCZ -0.0002152 16858 GTEx DepMap Descartes 3.72 221.86
NPC1 -0.0002155 16866 GTEx DepMap Descartes 1.02 103.04
CYP17A1 -0.0002195 16988 GTEx DepMap Descartes 0.27 69.42
STAR -0.0002352 17415 GTEx DepMap Descartes 0.54 61.78
CYP21A2 -0.0002581 17979 GTEx DepMap Descartes 0.38 58.17
CYP11A1 -0.0002617 18039 GTEx DepMap Descartes 0.48 77.12
BAIAP2L1 -0.0002654 18098 GTEx DepMap Descartes 0.84 76.05
DHCR24 -0.0002658 18109 GTEx DepMap Descartes 0.85 60.19


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: 17845.3
Median rank of genes in gene set: 18985
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
PTCHD1 0.0002978 1501 GTEx DepMap Descartes 0.72 23.93
GREM1 0.0000751 2661 GTEx DepMap Descartes 0.36 15.33
PLXNA4 -0.0000582 10133 GTEx DepMap Descartes 1.23 41.12
CNTFR -0.0001010 12362 GTEx DepMap Descartes 0.32 65.32
NTRK1 -0.0001533 14766 GTEx DepMap Descartes 0.30 30.04
TUBB2A -0.0001801 15785 GTEx DepMap Descartes 0.73 225.55
MLLT11 -0.0002060 16601 GTEx DepMap Descartes 0.49 104.88
RPH3A -0.0002141 16823 GTEx DepMap Descartes 0.13 8.51
PRPH -0.0002243 17124 GTEx DepMap Descartes 0.82 174.52
BASP1 -0.0002551 17913 GTEx DepMap Descartes 1.42 399.25
STMN4 -0.0002559 17938 GTEx DepMap Descartes 0.51 105.49
RGMB -0.0002574 17966 GTEx DepMap Descartes 0.29 32.04
MAP1B -0.0002650 18092 GTEx DepMap Descartes 5.60 232.38
SYNPO2 -0.0002862 18500 GTEx DepMap Descartes 1.72 73.75
FAT3 -0.0002896 18547 GTEx DepMap Descartes 0.42 10.94
EYA4 -0.0002933 18612 GTEx DepMap Descartes 0.56 38.51
HMX1 -0.0002947 18638 GTEx DepMap Descartes 0.40 72.33
MAB21L1 -0.0002969 18684 GTEx DepMap Descartes 0.07 12.23
TMEFF2 -0.0002996 18730 GTEx DepMap Descartes 0.80 96.82
MAB21L2 -0.0003022 18768 GTEx DepMap Descartes 0.04 7.37
GAP43 -0.0003089 18869 GTEx DepMap Descartes 1.85 390.45
IL7 -0.0003191 18985 GTEx DepMap Descartes 1.88 350.72
REEP1 -0.0003257 19051 GTEx DepMap Descartes 0.66 57.98
ANKFN1 -0.0003361 19179 GTEx DepMap Descartes 0.98 84.38
TUBA1A -0.0003401 19232 GTEx DepMap Descartes 3.47 1008.85
GAL -0.0003492 19329 GTEx DepMap Descartes 0.39 250.33
SLC6A2 -0.0003567 19391 GTEx DepMap Descartes 0.22 27.02
RYR2 -0.0003843 19607 GTEx DepMap Descartes 5.64 128.79
EPHA6 -0.0003866 19625 GTEx DepMap Descartes 1.66 153.24
TUBB2B -0.0003893 19646 GTEx DepMap Descartes 1.02 292.00


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: 9.71e-01
Mean rank of genes in gene set: 11991.2
Median rank of genes in gene set: 13176.5
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
TMEM88 0.0007259 768 GTEx DepMap Descartes 0.09 61.51
NPR1 0.0001913 1884 GTEx DepMap Descartes 0.04 5.48
CHRM3 0.0001243 2232 GTEx DepMap Descartes 1.19 76.06
BTNL9 0.0000372 3126 GTEx DepMap Descartes 0.08 12.56
APLNR 0.0000341 3169 GTEx DepMap Descartes 0.05 8.42
ESM1 0.0000126 3697 GTEx DepMap Descartes 0.03 7.09
CLDN5 0.0000106 3765 GTEx DepMap Descartes 0.11 25.38
PLVAP 0.0000090 3835 GTEx DepMap Descartes 0.16 38.83
RASIP1 0.0000064 3948 GTEx DepMap Descartes 0.10 18.57
CYP26B1 -0.0000147 6857 GTEx DepMap Descartes 0.03 3.28
ID1 -0.0000165 7053 GTEx DepMap Descartes 0.29 104.15
NOTCH4 -0.0000233 7688 GTEx DepMap Descartes 0.07 5.57
ECSCR -0.0000311 8337 GTEx DepMap Descartes 0.00 0.04
MMRN2 -0.0000440 9265 GTEx DepMap Descartes 0.09 11.81
CDH5 -0.0000591 10185 GTEx DepMap Descartes 0.14 19.88
CRHBP -0.0000687 10715 GTEx DepMap Descartes 0.04 11.58
IRX3 -0.0000849 11563 GTEx DepMap Descartes 0.01 1.55
SOX18 -0.0000901 11846 GTEx DepMap Descartes 0.06 15.24
SHE -0.0000909 11881 GTEx DepMap Descartes 0.07 5.42
KDR -0.0001050 12564 GTEx DepMap Descartes 0.07 6.09
TM4SF18 -0.0001141 13005 GTEx DepMap Descartes 0.03 4.45
GALNT15 -0.0001159 13092 GTEx DepMap Descartes 0.08 NA
F8 -0.0001196 13261 GTEx DepMap Descartes 0.14 8.01
TIE1 -0.0001213 13342 GTEx DepMap Descartes 0.09 12.68
KANK3 -0.0001357 14013 GTEx DepMap Descartes 0.08 17.60
FLT4 -0.0001358 14014 GTEx DepMap Descartes 0.06 6.03
HYAL2 -0.0001369 14060 GTEx DepMap Descartes 0.12 14.96
ROBO4 -0.0001379 14100 GTEx DepMap Descartes 0.05 5.83
RAMP2 -0.0001557 14864 GTEx DepMap Descartes 0.08 52.29
FCGR2B -0.0001580 14945 GTEx DepMap Descartes 0.02 2.55


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: 2.86e-09
Mean rank of genes in gene set: 5354.53
Median rank of genes in gene set: 1455
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
PRRX1 0.0044597 37 GTEx DepMap Descartes 1.66 335.61
CCDC80 0.0033400 74 GTEx DepMap Descartes 1.07 63.97
BICC1 0.0027636 128 GTEx DepMap Descartes 5.50 655.33
GLI2 0.0027046 134 GTEx DepMap Descartes 0.82 104.18
COL12A1 0.0020241 208 GTEx DepMap Descartes 2.23 141.98
C7 0.0020133 209 GTEx DepMap Descartes 3.17 416.76
COL6A3 0.0017676 261 GTEx DepMap Descartes 2.70 187.94
COL27A1 0.0014141 350 GTEx DepMap Descartes 0.75 68.16
HHIP 0.0013064 388 GTEx DepMap Descartes 0.29 24.21
FREM1 0.0012914 395 GTEx DepMap Descartes 0.68 54.03
MGP 0.0012038 437 GTEx DepMap Descartes 2.62 1018.63
ADAMTSL3 0.0011502 472 GTEx DepMap Descartes 1.76 142.68
SCARA5 0.0010717 510 GTEx DepMap Descartes 0.03 7.00
CCDC102B 0.0009901 562 GTEx DepMap Descartes 3.38 863.94
CDH11 0.0009003 639 GTEx DepMap Descartes 2.10 213.12
ADAMTS2 0.0008316 696 GTEx DepMap Descartes 1.09 110.91
ABCA6 0.0008167 709 GTEx DepMap Descartes 1.25 112.95
SFRP2 0.0007488 748 GTEx DepMap Descartes 0.44 120.21
ABCC9 0.0006507 849 GTEx DepMap Descartes 0.32 24.82
DCN 0.0006219 879 GTEx DepMap Descartes 1.41 144.64
ELN 0.0005801 937 GTEx DepMap Descartes 0.60 108.48
CD248 0.0005393 1002 GTEx DepMap Descartes 0.07 21.78
PDGFRA 0.0004345 1193 GTEx DepMap Descartes 0.16 17.02
IGFBP3 0.0003702 1311 GTEx DepMap Descartes 0.35 80.02
ZNF385D 0.0003130 1455 GTEx DepMap Descartes 0.69 40.32
LUM 0.0002728 1576 GTEx DepMap Descartes 0.92 228.00
ISLR 0.0002420 1680 GTEx DepMap Descartes 0.14 42.89
OGN 0.0002152 1784 GTEx DepMap Descartes 0.18 37.57
LOX 0.0002093 1797 GTEx DepMap Descartes 0.11 13.30
MXRA5 0.0001804 1925 GTEx DepMap Descartes 0.16 9.60


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: 13960.3
Median rank of genes in gene set: 15917
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
GRM7 0.0013112 387 GTEx DepMap Descartes 0.75 118.12
GCH1 0.0008924 648 GTEx DepMap Descartes 1.70 268.07
ARC 0.0007271 767 GTEx DepMap Descartes 0.45 74.04
TIAM1 0.0005029 1067 GTEx DepMap Descartes 1.55 141.24
LAMA3 0.0003583 1334 GTEx DepMap Descartes 0.54 30.65
PENK 0.0001730 1962 GTEx DepMap Descartes 0.05 39.67
MGAT4C 0.0000850 2567 GTEx DepMap Descartes 1.46 36.31
PCSK2 0.0000072 3916 GTEx DepMap Descartes 0.49 64.79
PNMT -0.0000263 7951 GTEx DepMap Descartes 0.02 7.15
NTNG1 -0.0000367 8761 GTEx DepMap Descartes 1.22 118.47
EML6 -0.0000676 10649 GTEx DepMap Descartes 1.48 58.86
DGKK -0.0000722 10924 GTEx DepMap Descartes 0.18 9.24
GALNTL6 -0.0000926 11963 GTEx DepMap Descartes 1.18 145.26
HTATSF1 -0.0001355 13998 GTEx DepMap Descartes 0.20 38.10
SORCS3 -0.0001485 14574 GTEx DepMap Descartes 0.25 18.34
PCSK1N -0.0001490 14600 GTEx DepMap Descartes 1.21 584.14
SLC24A2 -0.0001549 14830 GTEx DepMap Descartes 0.20 5.85
SLC18A1 -0.0001557 14865 GTEx DepMap Descartes 0.13 16.27
C1QL1 -0.0001672 15321 GTEx DepMap Descartes 0.06 19.28
PACRG -0.0001819 15843 GTEx DepMap Descartes 1.10 248.05
TBX20 -0.0001837 15901 GTEx DepMap Descartes 0.34 80.61
CHGA -0.0001843 15917 GTEx DepMap Descartes 0.42 116.75
INSM1 -0.0002000 16419 GTEx DepMap Descartes 0.08 11.49
CHGB -0.0002060 16602 GTEx DepMap Descartes 2.10 467.95
TENM1 -0.0002248 17135 GTEx DepMap Descartes 1.10 NA
CNTN3 -0.0002287 17241 GTEx DepMap Descartes 0.20 17.54
TMEM130 -0.0002312 17307 GTEx DepMap Descartes 0.39 40.80
GRID2 -0.0002720 18244 GTEx DepMap Descartes 1.24 72.63
CNTNAP5 -0.0002825 18427 GTEx DepMap Descartes 0.54 33.05
SCG2 -0.0002829 18432 GTEx DepMap Descartes 2.34 418.30


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: 6.68e-01
Mean rank of genes in gene set: 10674.28
Median rank of genes in gene set: 11103.5
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
MICAL2 0.0011874 447 GTEx DepMap Descartes 1.67 173.19
RAPGEF2 0.0011355 477 GTEx DepMap Descartes 3.44 284.33
DENND4A 0.0008012 717 GTEx DepMap Descartes 4.55 247.51
SELENBP1 0.0003455 1368 GTEx DepMap Descartes 0.05 11.00
SLC25A21 0.0001180 2271 GTEx DepMap Descartes 0.14 18.36
SLC25A37 0.0000882 2533 GTEx DepMap Descartes 0.77 83.51
TSPAN5 0.0000690 2725 GTEx DepMap Descartes 1.64 251.98
HBA2 0.0000100 3785 GTEx DepMap Descartes 0.08 98.23
HEMGN 0.0000033 4097 GTEx DepMap Descartes 0.00 0.88
HBG2 0.0000000 4705 GTEx DepMap Descartes 0.00 0.00
HBA1 -0.0000001 4933 GTEx DepMap Descartes 0.03 36.45
HBB -0.0000047 5553 GTEx DepMap Descartes 0.15 151.48
HBG1 -0.0000079 6027 GTEx DepMap Descartes 0.00 0.00
GCLC -0.0000152 6897 GTEx DepMap Descartes 1.68 155.32
HBZ -0.0000247 7828 GTEx DepMap Descartes 0.00 3.18
AHSP -0.0000306 8289 GTEx DepMap Descartes 0.00 1.76
SPTA1 -0.0000358 8700 GTEx DepMap Descartes 0.01 0.39
HBM -0.0000440 9263 GTEx DepMap Descartes 0.00 2.99
ALAS2 -0.0000450 9338 GTEx DepMap Descartes 0.00 0.68
EPB42 -0.0000510 9702 GTEx DepMap Descartes 0.00 0.36
GYPA -0.0000548 9939 GTEx DepMap Descartes 0.00 0.62
SLC4A1 -0.0000674 10634 GTEx DepMap Descartes 0.01 0.68
GYPB -0.0000736 11004 GTEx DepMap Descartes 0.01 4.62
RHCE -0.0000775 11203 GTEx DepMap Descartes 0.04 8.12
SPECC1 -0.0000792 11303 GTEx DepMap Descartes 0.87 76.49
RHAG -0.0000804 11355 GTEx DepMap Descartes 0.01 1.33
GYPC -0.0000880 11733 GTEx DepMap Descartes 0.12 41.60
BLVRB -0.0000891 11794 GTEx DepMap Descartes 0.18 66.59
GYPE -0.0000916 11913 GTEx DepMap Descartes 0.03 8.35
SPTB -0.0000969 12159 GTEx DepMap Descartes 0.20 8.10


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: 9.99e-01
Mean rank of genes in gene set: 12892.06
Median rank of genes in gene set: 15511
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
AXL 0.0044290 38 GTEx DepMap Descartes 1.29 243.26
CTSC 0.0016633 283 GTEx DepMap Descartes 0.55 65.57
HRH1 0.0008719 667 GTEx DepMap Descartes 0.96 122.89
ABCA1 0.0006824 814 GTEx DepMap Descartes 2.05 110.50
SLC9A9 0.0006495 851 GTEx DepMap Descartes 1.61 305.31
FGL2 0.0003111 1459 GTEx DepMap Descartes 0.14 26.96
SLC1A3 0.0002913 1522 GTEx DepMap Descartes 0.51 72.00
HLA-DRB1 0.0000016 4224 GTEx DepMap Descartes 0.10 57.28
LGMN 0.0000015 4235 GTEx DepMap Descartes 0.58 154.96
CTSD -0.0000093 6215 GTEx DepMap Descartes 0.00 0.06
RNASE1 -0.0000141 6794 GTEx DepMap Descartes 0.07 46.20
CSF1R -0.0000648 10496 GTEx DepMap Descartes 0.11 18.04
CYBB -0.0000734 10995 GTEx DepMap Descartes 0.01 0.76
MS4A7 -0.0000862 11639 GTEx DepMap Descartes 0.02 3.09
IFNGR1 -0.0000893 11807 GTEx DepMap Descartes 0.54 108.31
CST3 -0.0000931 11980 GTEx DepMap Descartes 0.70 135.70
VSIG4 -0.0000967 12145 GTEx DepMap Descartes 0.02 4.43
MPEG1 -0.0001002 12323 GTEx DepMap Descartes 0.04 6.23
PTPRE -0.0001176 13185 GTEx DepMap Descartes 1.97 217.48
CD14 -0.0001199 13283 GTEx DepMap Descartes 0.13 44.80
C1QC -0.0001483 14564 GTEx DepMap Descartes 0.06 29.74
SPP1 -0.0001631 15143 GTEx DepMap Descartes 0.64 210.40
ITPR2 -0.0001639 15178 GTEx DepMap Descartes 3.96 137.46
MS4A4A -0.0001672 15319 GTEx DepMap Descartes 0.10 28.65
CD163 -0.0001730 15511 GTEx DepMap Descartes 0.12 11.70
RBPJ -0.0001773 15675 GTEx DepMap Descartes 1.77 162.55
CD163L1 -0.0001790 15735 GTEx DepMap Descartes 0.34 28.58
C1QA -0.0001825 15864 GTEx DepMap Descartes 0.11 63.94
SLCO2B1 -0.0001901 16109 GTEx DepMap Descartes 0.66 49.20
FGD2 -0.0002029 16520 GTEx DepMap Descartes 0.05 4.49


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: 2.59e-01
Mean rank of genes in gene set: 9745.24
Median rank of genes in gene set: 11170
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
COL5A2 0.0035144 68 GTEx DepMap Descartes 3.37 374.12
GAS7 0.0030890 96 GTEx DepMap Descartes 2.48 276.58
COL18A1 0.0020762 202 GTEx DepMap Descartes 2.52 276.73
VCAN 0.0020448 205 GTEx DepMap Descartes 3.44 184.38
LAMC1 0.0018036 254 GTEx DepMap Descartes 2.28 204.73
VIM 0.0017931 255 GTEx DepMap Descartes 2.76 742.58
ABCA8 0.0013144 385 GTEx DepMap Descartes 1.62 214.78
FIGN 0.0008294 700 GTEx DepMap Descartes 1.38 108.12
LAMB1 0.0007750 734 GTEx DepMap Descartes 1.87 246.93
CDH19 0.0005681 951 GTEx DepMap Descartes 2.17 318.90
LAMA4 0.0005448 992 GTEx DepMap Descartes 2.02 196.99
XKR4 0.0003665 1322 GTEx DepMap Descartes 2.17 100.24
COL25A1 0.0003107 1462 GTEx DepMap Descartes 0.46 38.93
IL1RAPL1 0.0003032 1488 GTEx DepMap Descartes 1.42 319.88
STARD13 0.0002810 1549 GTEx DepMap Descartes 3.80 455.87
PLCE1 0.0002763 1568 GTEx DepMap Descartes 0.59 33.98
EDNRB 0.0002522 1645 GTEx DepMap Descartes 0.21 32.04
PMP22 0.0001657 2007 GTEx DepMap Descartes 1.06 328.36
GRIK3 0.0001092 2345 GTEx DepMap Descartes 0.36 33.73
ADAMTS5 0.0000872 2543 GTEx DepMap Descartes 0.14 9.45
IL1RAPL2 0.0000740 2679 GTEx DepMap Descartes 1.46 307.54
KCTD12 0.0000304 3232 GTEx DepMap Descartes 0.25 25.50
PLP1 -0.0000281 8085 GTEx DepMap Descartes 0.09 24.43
GFRA3 -0.0000491 9585 GTEx DepMap Descartes 0.08 31.74
EGFLAM -0.0000768 11170 GTEx DepMap Descartes 0.46 55.07
SFRP1 -0.0000939 12019 GTEx DepMap Descartes 0.41 45.74
MPZ -0.0001008 12352 GTEx DepMap Descartes 0.07 22.96
DST -0.0001185 13212 GTEx DepMap Descartes 10.01 217.26
SOX10 -0.0001251 13527 GTEx DepMap Descartes 0.06 15.95
ZNF536 -0.0001296 13744 GTEx DepMap Descartes 1.64 187.22


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: 1.95e-03
Mean rank of genes in gene set: 7846.51
Median rank of genes in gene set: 4024
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
SLC2A3 0.0040398 47 GTEx DepMap Descartes 3.01 544.69
THBS1 0.0040045 49 GTEx DepMap Descartes 5.13 501.17
PDE3A 0.0022140 180 GTEx DepMap Descartes 5.43 497.63
VCL 0.0021447 194 GTEx DepMap Descartes 3.45 285.81
TPM4 0.0019656 219 GTEx DepMap Descartes 2.71 392.46
GSN 0.0017465 266 GTEx DepMap Descartes 1.59 192.71
STOM 0.0016108 292 GTEx DepMap Descartes 0.97 179.24
ACTN1 0.0012427 416 GTEx DepMap Descartes 2.57 342.55
ARHGAP6 0.0011829 450 GTEx DepMap Descartes 0.82 102.19
LIMS1 0.0011666 461 GTEx DepMap Descartes 3.07 416.11
RAP1B 0.0011030 496 GTEx DepMap Descartes 2.65 120.77
UBASH3B 0.0008689 669 GTEx DepMap Descartes 1.09 115.94
ZYX 0.0007167 774 GTEx DepMap Descartes 0.39 103.13
FLNA 0.0006293 872 GTEx DepMap Descartes 0.80 63.24
SLC24A3 0.0005725 946 GTEx DepMap Descartes 1.12 185.06
STON2 0.0005667 956 GTEx DepMap Descartes 0.44 61.42
HIPK2 0.0005656 958 GTEx DepMap Descartes 2.55 95.38
TGFB1 0.0003377 1388 GTEx DepMap Descartes 0.58 139.23
MYH9 0.0002255 1743 GTEx DepMap Descartes 3.13 217.20
TLN1 0.0001604 2027 GTEx DepMap Descartes 0.62 38.49
DOK6 0.0001071 2362 GTEx DepMap Descartes 1.13 67.71
PPBP 0.0000188 3521 GTEx DepMap Descartes 0.00 0.69
CD9 0.0000153 3622 GTEx DepMap Descartes 0.89 260.44
GP9 0.0000146 3636 GTEx DepMap Descartes 0.00 0.04
GP1BA 0.0000047 4024 GTEx DepMap Descartes 0.01 3.12
TUBB1 0.0000028 4134 GTEx DepMap Descartes 0.02 2.33
SPN 0.0000005 4309 GTEx DepMap Descartes 0.00 0.01
PF4 -0.0000160 6996 GTEx DepMap Descartes 0.00 0.19
ITGB3 -0.0000502 9654 GTEx DepMap Descartes 0.00 0.03
ANGPT1 -0.0000579 10114 GTEx DepMap Descartes 0.22 32.37


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: 9.61e-01
Mean rank of genes in gene set: 11817.57
Median rank of genes in gene set: 14948
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
NCALD 0.0031868 84 GTEx DepMap Descartes 1.69 334.68
ARID5B 0.0030242 103 GTEx DepMap Descartes 3.18 282.33
CELF2 0.0025269 150 GTEx DepMap Descartes 4.01 410.73
MBNL1 0.0014335 340 GTEx DepMap Descartes 8.27 809.80
BACH2 0.0011114 489 GTEx DepMap Descartes 4.83 296.21
CD44 0.0010842 503 GTEx DepMap Descartes 3.01 341.30
PITPNC1 0.0009122 627 GTEx DepMap Descartes 5.11 499.41
ABLIM1 0.0006476 855 GTEx DepMap Descartes 4.92 279.00
MSN 0.0006186 885 GTEx DepMap Descartes 1.11 185.21
IFI16 0.0006078 892 GTEx DepMap Descartes 0.81 138.03
FYN 0.0002367 1699 GTEx DepMap Descartes 2.72 401.49
FOXP1 0.0001984 1849 GTEx DepMap Descartes 0.39 25.03
ITPKB 0.0001945 1869 GTEx DepMap Descartes 0.57 68.33
EVL 0.0001560 2048 GTEx DepMap Descartes 2.28 319.54
ETS1 0.0000882 2532 GTEx DepMap Descartes 1.05 137.79
BCL2 0.0000743 2676 GTEx DepMap Descartes 5.35 383.92
SAMD3 0.0000270 3323 GTEx DepMap Descartes 0.34 57.20
NKG7 -0.0000751 11088 GTEx DepMap Descartes 0.01 10.58
WIPF1 -0.0000957 12093 GTEx DepMap Descartes 1.09 155.14
SP100 -0.0001205 13307 GTEx DepMap Descartes 1.23 124.85
PLEKHA2 -0.0001274 13638 GTEx DepMap Descartes 0.74 88.49
CCL5 -0.0001310 13806 GTEx DepMap Descartes 0.04 22.40
ARHGAP15 -0.0001382 14116 GTEx DepMap Descartes 1.61 378.89
HLA-A -0.0001581 14948 GTEx DepMap Descartes 0.77 81.34
ARHGDIB -0.0002096 16703 GTEx DepMap Descartes 0.09 49.23
PRKCH -0.0002109 16741 GTEx DepMap Descartes 1.09 180.15
HLA-C -0.0002117 16758 GTEx DepMap Descartes 0.32 95.18
MCTP2 -0.0002349 17406 GTEx DepMap Descartes 0.39 24.33
HLA-B -0.0002381 17485 GTEx DepMap Descartes 0.55 198.26
CCND3 -0.0003173 18967 GTEx DepMap Descartes 1.01 237.18


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: 6.68e-01
Mean rank of genes in gene set: 10995.79
Median rank of genes in gene set: 12829
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
YPEL2 0.0006626 839 GTEx DepMap Descartes 0.90 91.93
SPRY1 0.0003414 1378 GTEx DepMap Descartes 0.46 113.18
CTSL 0.0000926 2493 GTEx DepMap Descartes 0.57 NA
ACSS1 0.0000386 3107 GTEx DepMap Descartes 0.10 14.82
LY6G6E 0.0000000 4798 GTEx DepMap Descartes 0.00 0.00
HEXA -0.0000604 10249 GTEx DepMap Descartes 0.04 2.87
ALDH6A1 -0.0001073 12674 GTEx DepMap Descartes 0.15 12.69
HEXB -0.0001136 12984 GTEx DepMap Descartes 0.39 93.97
APOE -0.0001655 15257 GTEx DepMap Descartes 1.80 823.62
RENBP -0.0001738 15547 GTEx DepMap Descartes 0.06 21.66
CCNG2 -0.0002581 17978 GTEx DepMap Descartes 0.20 19.59
DPP7 -0.0002606 18021 GTEx DepMap Descartes 0.23 70.79
PDCD4 -0.0003072 18849 GTEx DepMap Descartes 0.70 94.67
AUH -0.0004088 19767 GTEx DepMap Descartes 1.40 385.82


Embryonic Pausing Signatures Down
Embryonic pausing signature downregulated genes from Supplementary Table 6 of Rehman et al. Cell 2021. These genes are downregulated in paused ESCs and diapaused embryos.
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.00e+00
Mean rank of genes in gene set: 12952.85
Median rank of genes in gene set: 14326
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
DUSP14 0.0006712 829 GTEx DepMap Descartes 0.20 47.41
SMS 0.0006653 836 GTEx DepMap Descartes 1.00 345.61
LDHA 0.0003985 1258 GTEx DepMap Descartes 0.71 168.92
EIF3B 0.0003122 1456 GTEx DepMap Descartes 0.78 114.20
PPA1 0.0002045 1819 GTEx DepMap Descartes 1.04 149.57
HDLBP 0.0001877 1892 GTEx DepMap Descartes 1.30 110.86
ANKRD37 0.0001872 1897 GTEx DepMap Descartes 0.08 32.59
MGMT 0.0001583 2036 GTEx DepMap Descartes 1.13 121.09
MRPL12 0.0000343 3167 GTEx DepMap Descartes 0.00 0.02
HILPDA 0.0000218 3442 GTEx DepMap Descartes 0.07 28.24
TOMM40 0.0000154 3619 GTEx DepMap Descartes 0.19 28.30
PMF1 0.0000151 3628 GTEx DepMap Descartes 0.00 0.29
TMEM109 0.0000067 3935 GTEx DepMap Descartes 0.07 19.30
SEC13 0.0000031 4110 GTEx DepMap Descartes 0.35 81.47
DGCR6 -0.0000049 5589 GTEx DepMap Descartes 0.00 0.05
BYSL -0.0000059 5742 GTEx DepMap Descartes 0.04 12.84
NUDC -0.0000193 7342 GTEx DepMap Descartes 0.38 108.38
CITED1 -0.0000196 7367 GTEx DepMap Descartes 0.00 0.08
UBE2V1 -0.0000276 8053 GTEx DepMap Descartes 0.02 3.11
TOMM40L -0.0000339 8553 GTEx DepMap Descartes 0.04 6.73
GNG10 -0.0000422 9155 GTEx DepMap Descartes 0.00 1.19
PELO -0.0000432 9219 GTEx DepMap Descartes 0.00 0.03
PSMB10 -0.0000507 9685 GTEx DepMap Descartes 0.02 9.01
DPH3 -0.0000522 9782 GTEx DepMap Descartes 0.07 8.72
BRMS1 -0.0000589 10174 GTEx DepMap Descartes 0.06 17.73
DRG2 -0.0000661 10570 GTEx DepMap Descartes 0.11 10.69
NAA10 -0.0000744 11053 GTEx DepMap Descartes 0.03 10.09
ID3 -0.0000775 11204 GTEx DepMap Descartes 0.30 167.50
YKT6 -0.0000810 11380 GTEx DepMap Descartes 0.14 24.60
EXOSC2 -0.0000811 11382 GTEx DepMap Descartes 0.09 16.29


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


Fibroblasts: Fibroblasts (model markers)
the most common cells of connective tissues which synthesize the extracellular matrix and collagen to maintain tissue homeostasis:
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.08e-04
Mean rank of genes in gene set: 3340.9
Rank on gene expression program of genes in gene set:
Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
PRRX1 0.0044597 37 GTEx DepMap Descartes 1.66 335.61
NTRK2 0.0026102 144 GTEx DepMap Descartes 0.90 75.75
SMOC2 0.0016188 290 GTEx DepMap Descartes 0.92 225.60
EBF2 0.0009593 583 GTEx DepMap Descartes 1.33 233.77
PDGFRA 0.0004345 1193 GTEx DepMap Descartes 0.16 17.02
MXRA5 0.0001804 1925 GTEx DepMap Descartes 0.16 9.60
ANGPTL1 0.0001034 2394 GTEx DepMap Descartes 0.17 25.90
F10 0.0000834 2579 GTEx DepMap Descartes 0.07 19.68
SFRP1 -0.0000939 12019 GTEx DepMap Descartes 0.41 45.74
OLFML1 -0.0000986 12245 GTEx DepMap Descartes 0.03 6.46


ILC: ILC (curated markers)
specialised innate immune cells from the lymphoid lineage but without antigen-specific T-cell receptors on the surface:
Wilcoxon ranksum test P-value for gene set overrepresentation: 5.37e-03
Mean rank of genes in gene set: 1541.67
Rank on gene expression program of genes in gene set:

Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
TLE1 0.0008481 681 GTEx DepMap Descartes 1.22 176.48
AREG 0.0002052 1813 GTEx DepMap Descartes 0.10 65.45
S100A13 0.0001422 2131 GTEx DepMap Descartes 0.12 32.75


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: 1.16e-02
Mean rank of genes in gene set: 2502.67
Rank on gene expression program of genes in gene set:

Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
CD99 0.0003021 1492 GTEx DepMap Descartes 0.77 379.12
HES1 0.0000834 2580 GTEx DepMap Descartes 0.19 63.08
FXYD2 0.0000222 3436 GTEx DepMap Descartes 0.00 0.76