Program: 8. NB Cell Line #8 (SKNAS Mesenchymal).

Program: 8. NB Cell Line #8 (SKNAS Mesenchymal).

Program description and justification of annotation: 8.
Submit a comment on this gene expression program’s interpretation: CLICK

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

Interactive QQ Plot

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

Gene Loading Gene.Name GTEx DepMap Descartes Mean.Counts Mean.Tpm
1 IFITM3 0.0204881 interferon induced transmembrane protein 3 GTEx DepMap Descartes 7.66 560.37
2 SH3BGRL3 0.0192947 SH3 domain binding glutamate rich protein like 3 GTEx DepMap Descartes 40.90 2637.64
3 FTH1 0.0189562 ferritin heavy chain 1 GTEx DepMap Descartes 222.31 9126.40
4 S100A11 0.0187302 S100 calcium binding protein A11 GTEx DepMap Descartes 80.30 7360.19
5 SPRY1 0.0183860 sprouty RTK signaling antagonist 1 GTEx DepMap Descartes 7.85 164.08
6 S100A4 0.0183527 S100 calcium binding protein A4 GTEx DepMap Descartes 80.72 5366.38
7 IER3 0.0181730 immediate early response 3 GTEx DepMap Descartes 17.03 697.85
8 S100A16 0.0175113 S100 calcium binding protein A16 GTEx DepMap Descartes 20.28 893.20
9 RGS13 0.0173778 regulator of G protein signaling 13 GTEx DepMap Descartes 2.41 24.90
10 PTPRC 0.0166774 protein tyrosine phosphatase receptor type C GTEx DepMap Descartes 4.20 43.46
11 IL13RA2 0.0166232 interleukin 13 receptor subunit alpha 2 GTEx DepMap Descartes 10.85 388.85
12 S100A3 0.0164179 S100 calcium binding protein A3 GTEx DepMap Descartes 2.52 155.19
13 HGF 0.0162934 hepatocyte growth factor GTEx DepMap Descartes 17.90 168.94
14 CYGB 0.0162670 cytoglobin GTEx DepMap Descartes 9.77 259.09
15 PSMB9 0.0159216 proteasome 20S subunit beta 9 GTEx DepMap Descartes 2.72 53.18
16 SSR2 0.0157984 signal sequence receptor subunit 2 GTEx DepMap Descartes 36.44 358.87
17 LUM 0.0154739 lumican GTEx DepMap Descartes 13.33 277.64
18 LTBR 0.0152213 lymphotoxin beta receptor GTEx DepMap Descartes 0.93 20.79
19 CFI 0.0148760 complement factor I GTEx DepMap Descartes 2.15 53.82
20 VAMP5 0.0148288 vesicle associated membrane protein 5 GTEx DepMap Descartes 5.31 422.96
21 ID3 0.0147730 inhibitor of DNA binding 3, HLH protein GTEx DepMap Descartes 35.14 1904.52
22 TIMP1 0.0146998 TIMP metallopeptidase inhibitor 1 GTEx DepMap Descartes 22.86 1063.43
23 GSDMD 0.0145873 gasdermin D GTEx DepMap Descartes 2.38 37.72
24 CRABP2 0.0143381 cellular retinoic acid binding protein 2 GTEx DepMap Descartes 15.45 825.78
25 PPIC 0.0142090 peptidylprolyl isomerase C GTEx DepMap Descartes 3.96 150.71
26 ID1 0.0138930 inhibitor of DNA binding 1, HLH protein GTEx DepMap Descartes 28.65 1238.69
27 GUK1 0.0138597 guanylate kinase 1 GTEx DepMap Descartes 37.20 733.74
28 UBL5 0.0138189 ubiquitin like 5 GTEx DepMap Descartes 51.16 1728.17
29 FERMT3 0.0137798 FERM domain containing kindlin 3 GTEx DepMap Descartes 1.56 34.99
30 PSMB8 0.0137062 proteasome 20S subunit beta 8 GTEx DepMap Descartes 3.34 75.87
31 NDUFB9 0.0137016 NADH:ubiquinone oxidoreductase subunit B9 GTEx DepMap Descartes 29.63 523.17
32 CD81 0.0136508 CD81 molecule GTEx DepMap Descartes 22.40 221.33
33 COL6A2 0.0133682 collagen type VI alpha 2 chain GTEx DepMap Descartes 5.67 89.04
34 PPIA 0.0132197 peptidylprolyl isomerase A GTEx DepMap Descartes 108.15 2525.97
35 PYCARD 0.0128863 PYD and CARD domain containing GTEx DepMap Descartes 1.28 61.86
36 FXYD5 0.0128574 FXYD domain containing ion transport regulator 5 GTEx DepMap Descartes 3.55 108.11
37 LAMTOR2 0.0128194 late endosomal/lysosomal adaptor, MAPK and MTOR activator 2 GTEx DepMap Descartes 16.15 936.72
38 UQCRQ 0.0125722 ubiquinol-cytochrome c reductase complex III subunit VII GTEx DepMap Descartes 41.12 1289.51
39 PPP1R14B 0.0125299 protein phosphatase 1 regulatory inhibitor subunit 14B GTEx DepMap Descartes 54.89 2756.93
40 APOE 0.0124783 apolipoprotein E GTEx DepMap Descartes 11.85 580.18
41 UQCRH 0.0124570 ubiquinol-cytochrome c reductase hinge protein GTEx DepMap Descartes 74.58 5366.34
42 GAS1 0.0124027 growth arrest specific 1 GTEx DepMap Descartes 2.87 50.74
43 LYPD6B 0.0124005 LY6/PLAUR domain containing 6B GTEx DepMap Descartes 1.34 40.02
44 EVA1B 0.0123684 eva-1 homolog B GTEx DepMap Descartes 3.52 NA
45 OST4 0.0123572 oligosaccharyltransferase complex subunit 4, non-catalytic GTEx DepMap Descartes 41.96 3741.42
46 ARPC1B 0.0122888 actin related protein ⅔ complex subunit 1B GTEx DepMap Descartes 13.27 386.45
47 TWIST2 0.0122221 twist family bHLH transcription factor 2 GTEx DepMap Descartes 1.16 46.42
48 ASS1 0.0121539 argininosuccinate synthase 1 GTEx DepMap Descartes 18.12 499.44
49 SEC61G 0.0121511 SEC61 translocon subunit gamma GTEx DepMap Descartes 33.31 1336.89
50 QSOX1 0.0121332 quiescin sulfhydryl oxidase 1 GTEx DepMap Descartes 6.05 32.17


Dowload full table

UMAP plots showing activity of gene expression program identified in community:8. NB Cell Line #8 (SKNAS Mesenchymal)

Interactive UMAP Plot
Interactive Boxplot

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

Interactive BioCircos Plot

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


mSigDB Cell Types Gene Set:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
FAN_EMBRYONIC_CTX_BIG_GROUPS_BRAIN_IMMUNE 2.35e-10 22.64 9.89 5.63e-08 1.58e-07
10IFITM3, SH3BGRL3, S100A11, S100A4, PTPRC, PSMB9, FERMT3, PSMB8, FXYD5, ARPC1B
 148
DURANTE_ADULT_OLFACTORY_NEUROEPITHELIUM_FIBROBLASTS_STROMAL_CELLS 7.87e-07 22.40 7.58 3.52e-05 5.28e-04
6IFITM3, HGF, LUM, TIMP1, CRABP2, COL6A2
 82
RUBENSTEIN_SKELETAL_MUSCLE_MYELOID_CELLS 3.14e-11 14.60 7.20 2.10e-08 2.10e-08
14SH3BGRL3, FTH1, S100A11, S100A4, IER3, PTPRC, SSR2, TIMP1, PYCARD, FXYD5, LAMTOR2, UQCRH, OST4, ARPC1B
 347
FAN_OVARY_CL12_T_LYMPHOCYTE_NK_CELL_2 1.90e-07 15.56 6.20 1.16e-05 1.28e-04
8SH3BGRL3, FTH1, S100A11, S100A4, PTPRC, FXYD5, OST4, ARPC1B
 161
TRAVAGLINI_LUNG_CAPILLARY_INTERMEDIATE_2_CELL 2.52e-10 12.34 6.10 5.63e-08 1.69e-07
14IFITM3, SH3BGRL3, FTH1, S100A4, S100A3, PSMB9, VAMP5, GUK1, UBL5, NDUFB9, PPIA, UQCRQ, OST4, SEC61G
 408
FAN_EMBRYONIC_CTX_BIG_GROUPS_BRAIN_ENDOTHELIAL 8.18e-10 12.48 6.03 1.37e-07 5.49e-07
13IFITM3, S100A16, LTBR, VAMP5, ID3, TIMP1, GSDMD, PPIC, ID1, PSMB8, COL6A2, FXYD5, EVA1B
 365
FAN_OVARY_CL7_ANGEIOGENIC_ENDOTHELIAL_CELL 3.62e-08 12.96 5.71 4.05e-06 2.43e-05
10IFITM3, S100A16, PSMB9, VAMP5, ID3, ID1, GUK1, PSMB8, FXYD5, ARPC1B
 251
RUBENSTEIN_SKELETAL_MUSCLE_FAP_CELLS 4.24e-07 13.93 5.56 2.19e-05 2.85e-04
8S100A11, SPRY1, S100A4, SSR2, LUM, TIMP1, CD81, COL6A2
 179
MENON_FETAL_KIDNEY_10_IMMUNE_CELLS 1.82e-05 17.79 5.37 4.57e-04 1.22e-02
5SH3BGRL3, S100A11, S100A4, PTPRC, ARPC1B
 83
DURANTE_ADULT_OLFACTORY_NEUROEPITHELIUM_DENDRITIC_CELLS 6.23e-06 15.35 5.24 1.90e-04 4.18e-03
6SH3BGRL3, FTH1, S100A4, PTPRC, TIMP1, PYCARD
 117
AIZARANI_LIVER_C21_STELLATE_CELLS_1 7.76e-07 12.80 5.12 3.52e-05 5.20e-04
8IFITM3, IER3, HGF, LUM, TIMP1, CD81, COL6A2, QSOX1
 194
RUBENSTEIN_SKELETAL_MUSCLE_FBN1_FAP_CELLS 1.33e-07 11.20 4.94 1.07e-05 8.90e-05
10SH3BGRL3, FTH1, S100A11, S100A4, TIMP1, PPIC, COL6A2, GAS1, OST4, SEC61G
 289
FAN_OVARY_CL4_T_LYMPHOCYTE_NK_CELL_1 3.91e-07 11.58 4.89 2.19e-05 2.62e-04
9SH3BGRL3, FTH1, S100A11, S100A4, PTPRC, PSMB9, GUK1, FXYD5, ARPC1B
 246
FAN_OVARY_CL13_MONOCYTE_MACROPHAGE 1.17e-08 9.87 4.78 1.56e-06 7.82e-06
13SH3BGRL3, FTH1, S100A11, S100A4, IER3, PTPRC, PSMB9, TIMP1, FERMT3, PYCARD, FXYD5, LAMTOR2, ARPC1B
 458
FAN_OVARY_CL2_PUTATIVE_EARLY_ATRETIC_FOLLICLE_THECAL_CELL_1 4.05e-05 14.93 4.52 8.50e-04 2.72e-02
5IFITM3, LUM, COL6A2, APOE, OST4
 98
RUBENSTEIN_SKELETAL_MUSCLE_ENDOTHELIAL_CELLS 1.53e-05 13.01 4.45 4.46e-04 1.03e-02
6IFITM3, S100A16, VAMP5, ID3, PPIC, ID1
 137
FAN_EMBRYONIC_CTX_BRAIN_MYELOID 1.66e-05 12.81 4.39 4.57e-04 1.11e-02
6IFITM3, S100A11, S100A4, PSMB9, TIMP1, FXYD5
 139
RUBENSTEIN_SKELETAL_MUSCLE_NK_CELLS 2.40e-06 10.92 4.38 8.47e-05 1.61e-03
8SH3BGRL3, S100A4, PTPRC, PSMB9, SSR2, UBL5, OST4, ARPC1B
 226
HU_FETAL_RETINA_FIBROBLAST 1.85e-07 9.43 4.32 1.16e-05 1.24e-04
11IFITM3, S100A11, LUM, CFI, ID3, TIMP1, ID1, CD81, COL6A2, FXYD5, EVA1B
 385
FAN_OVARY_CL16_LYMPHATIC_ENDOTHELIAL_CELL 2.91e-06 10.63 4.26 9.75e-05 1.95e-03
8IFITM3, SH3BGRL3, S100A16, CFI, PPIC, GUK1, FXYD5, ARPC1B
 232

Dowload full table

mSigDB Hallmark Gene Sets:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
HALLMARK_ANGIOGENESIS 3.84e-04 24.16 4.58 1.02e-02 1.92e-02
3S100A4, LUM, TIMP1
 36
HALLMARK_APOPTOSIS 4.10e-04 8.90 2.72 1.02e-02 2.05e-02
5IFITM3, IER3, HGF, LUM, TIMP1
 161
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION 1.08e-03 7.12 2.18 1.80e-02 5.40e-02
5LUM, TIMP1, COL6A2, GAS1, QSOX1
 200
HALLMARK_INTERFERON_ALPHA_RESPONSE 6.61e-03 8.48 1.66 7.71e-02 3.30e-01
3IFITM3, PSMB9, PSMB8
 97
HALLMARK_INTERFERON_GAMMA_RESPONSE 7.71e-03 5.55 1.44 7.71e-02 3.85e-01
4IFITM3, PSMB9, VAMP5, PSMB8
 200
HALLMARK_TGF_BETA_SIGNALING 1.94e-02 10.01 1.15 1.61e-01 9.68e-01
2ID3, ID1
 54
HALLMARK_GLYCOLYSIS 4.35e-02 4.05 0.80 2.72e-01 1.00e+00
3IER3, PPIA, QSOX1
 200
HALLMARK_P53_PATHWAY 4.35e-02 4.05 0.80 2.72e-01 1.00e+00
3S100A4, IER3, CD81
 200
HALLMARK_COAGULATION 1.03e-01 3.83 0.45 5.71e-01 1.00e+00
2CFI, TIMP1
 138
HALLMARK_IL2_STAT5_SIGNALING 1.83e-01 2.64 0.31 5.78e-01 1.00e+00
2IFITM3, CD81
 199
HALLMARK_HYPOXIA 1.85e-01 2.63 0.31 5.78e-01 1.00e+00
2S100A4, IER3
 200
HALLMARK_ADIPOGENESIS 1.85e-01 2.63 0.31 5.78e-01 1.00e+00
2UQCRQ, APOE
 200
HALLMARK_COMPLEMENT 1.85e-01 2.63 0.31 5.78e-01 1.00e+00
2PSMB9, TIMP1
 200
HALLMARK_OXIDATIVE_PHOSPHORYLATION 1.85e-01 2.63 0.31 5.78e-01 1.00e+00
2UQCRQ, UQCRH
 200
HALLMARK_ALLOGRAFT_REJECTION 1.85e-01 2.63 0.31 5.78e-01 1.00e+00
2PTPRC, TIMP1
 200
HALLMARK_APICAL_SURFACE 1.61e-01 5.93 0.14 5.78e-01 1.00e+00
1GAS1
 44
HALLMARK_CHOLESTEROL_HOMEOSTASIS 2.55e-01 3.49 0.09 7.50e-01 1.00e+00
1S100A11
 74
HALLMARK_IL6_JAK_STAT3_SIGNALING 2.93e-01 2.97 0.07 8.13e-01 1.00e+00
1LTBR
 87
HALLMARK_PEROXISOME 3.39e-01 2.48 0.06 8.82e-01 1.00e+00
1CRABP2
 104
HALLMARK_SPERMATOGENESIS 4.15e-01 1.90 0.05 8.82e-01 1.00e+00
1IL13RA2
 135

Dowload full table

KEGG Pathways:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
KEGG_ALZHEIMERS_DISEASE 4.04e-03 6.71 1.73 7.04e-01 7.52e-01
4NDUFB9, UQCRQ, APOE, UQCRH
 166
KEGG_PROTEASOME 1.43e-02 11.83 1.35 7.04e-01 1.00e+00
2PSMB9, PSMB8
 46
KEGG_PARKINSONS_DISEASE 1.45e-02 6.28 1.23 7.04e-01 1.00e+00
3NDUFB9, UQCRQ, UQCRH
 130
KEGG_OXIDATIVE_PHOSPHORYLATION 1.51e-02 6.18 1.22 7.04e-01 1.00e+00
3NDUFB9, UQCRQ, UQCRH
 132
KEGG_HUNTINGTONS_DISEASE 3.45e-02 4.46 0.88 1.00e+00 1.00e+00
3NDUFB9, UQCRQ, UQCRH
 182
KEGG_CARDIAC_MUSCLE_CONTRACTION 3.90e-02 6.76 0.78 1.00e+00 1.00e+00
2UQCRQ, UQCRH
 79
KEGG_TGF_BETA_SIGNALING_PATHWAY 4.54e-02 6.20 0.72 1.00e+00 1.00e+00
2ID3, ID1
 86
KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS 5.52e-02 5.54 0.64 1.00e+00 1.00e+00
2PTPRC, ARPC1B
 96
KEGG_JAK_STAT_SIGNALING_PATHWAY 1.24e-01 3.40 0.40 1.00e+00 1.00e+00
2SPRY1, IL13RA2
 155
KEGG_FOCAL_ADHESION 1.83e-01 2.64 0.31 1.00e+00 1.00e+00
2HGF, COL6A2
 199
KEGG_PROTEIN_EXPORT 9.13e-02 11.08 0.26 1.00e+00 1.00e+00
1SEC61G
 24
KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION 2.77e-01 1.98 0.23 1.00e+00 1.00e+00
2HGF, LTBR
 265
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM 1.20e-01 8.23 0.20 1.00e+00 1.00e+00
1ASS1
 32
KEGG_PRIMARY_IMMUNODEFICIENCY 1.30e-01 7.50 0.18 1.00e+00 1.00e+00
1PTPRC
 35
KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT 1.41e-01 6.89 0.17 1.00e+00 1.00e+00
1VAMP5
 38
KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM 1.51e-01 6.37 0.15 1.00e+00 1.00e+00
1FTH1
 41
KEGG_INTESTINAL_IMMUNE_NETWORK_FOR_IGA_PRODUCTION 1.74e-01 5.43 0.13 1.00e+00 1.00e+00
1LTBR
 48
KEGG_ARGININE_AND_PROLINE_METABOLISM 1.94e-01 4.81 0.12 1.00e+00 1.00e+00
1ASS1
 54
KEGG_VIBRIO_CHOLERAE_INFECTION 1.94e-01 4.81 0.12 1.00e+00 1.00e+00
1SEC61G
 54
KEGG_CYTOSOLIC_DNA_SENSING_PATHWAY 1.97e-01 4.72 0.12 1.00e+00 1.00e+00
1PYCARD
 55

Dowload full table

CHR Positional Gene Sets:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
chr1q22 3.13e-02 7.66 0.88 1.00e+00 1.00e+00
2SSR2, LAMTOR2
 70
chr1q31 3.21e-02 7.55 0.87 1.00e+00 1.00e+00
2RGS13, PTPRC
 71
chr1q21 6.42e-02 2.80 0.73 1.00e+00 1.00e+00
4S100A11, S100A4, S100A16, S100A3
 392
chr6p21 4.27e-01 1.72 0.34 1.00e+00 1.00e+00
3IER3, PSMB9, PSMB8
 467
chr8q24 3.56e-01 1.63 0.19 1.00e+00 1.00e+00
2GSDMD, NDUFB9
 321
chr11q13 6.78e-01 1.24 0.15 1.00e+00 1.00e+00
2FERMT3, PPP1R14B
 421
chr7p13 1.81e-01 5.21 0.13 1.00e+00 1.00e+00
1PPIA
 50
chr2q23 1.84e-01 5.10 0.12 1.00e+00 1.00e+00
1LYPD6B
 51
chr1p33 2.13e-01 4.32 0.11 1.00e+00 1.00e+00
1UQCRH
 60
chr1p36 1.00e+00 0.80 0.09 1.00e+00 1.00e+00
2SH3BGRL3, ID3
 656
chr7p11 2.78e-01 3.15 0.08 1.00e+00 1.00e+00
1SEC61G
 82
chr4q25 2.93e-01 2.97 0.07 1.00e+00 1.00e+00
1CFI
 87
chrXq23 2.98e-01 2.90 0.07 1.00e+00 1.00e+00
1IL13RA2
 89
chr5q23 3.57e-01 2.32 0.06 1.00e+00 1.00e+00
1PPIC
 111
chr19q13 4.39e-01 0.45 0.05 1.00e+00 1.00e+00
2FXYD5, APOE
 1165
chr12q21 3.99e-01 2.01 0.05 1.00e+00 1.00e+00
1LUM
 128
chr2p23 4.38e-01 1.77 0.04 1.00e+00 1.00e+00
1OST4
 145
chr1q25 4.70e-01 1.60 0.04 1.00e+00 1.00e+00
1QSOX1
 160
chr7q21 4.78e-01 1.56 0.04 1.00e+00 1.00e+00
1HGF
 164
chr9q21 5.25e-01 1.36 0.03 1.00e+00 1.00e+00
1GAS1
 188

Dowload full table

Transcription Factor Targets:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
STTTCRNTTT_IRF_Q6 9.02e-04 7.43 2.27 6.20e-01 1.00e+00
5HGF, PSMB9, VAMP5, GSDMD, PSMB8
 192
IRF2_01 1.64e-03 8.69 2.24 6.20e-01 1.00e+00
4PSMB9, GSDMD, PSMB8, FXYD5
 129
ZBED4_TARGET_GENES 4.49e-03 6.51 1.68 1.00e+00 1.00e+00
4IER3, S100A16, UQCRQ, SEC61G
 171
TEAD2_TARGET_GENES 5.24e-03 2.67 1.27 1.00e+00 1.00e+00
12S100A11, S100A16, PSMB9, GUK1, PSMB8, NDUFB9, PPIA, LAMTOR2, UQCRQ, PPP1R14B, UQCRH, SEC61G
 1494
ZMYM2_TARGET_GENES 1.42e-02 6.33 1.24 1.00e+00 1.00e+00
3PPIC, PPIA, PPP1R14B
 129
IRF1_01 1.73e-02 4.33 1.12 1.00e+00 1.00e+00
4PSMB9, GSDMD, PSMB8, FXYD5
 255
RYTTCCTG_ETS2_B 1.83e-02 2.49 1.06 1.00e+00 1.00e+00
9FTH1, PTPRC, HGF, LTBR, VAMP5, ID3, TIMP1, FERMT3, FXYD5
 1112
DLX6_TARGET_GENES 2.48e-02 2.89 1.00 1.00e+00 1.00e+00
6FTH1, LTBR, ID1, UQCRQ, PPP1R14B, UQCRH
 596
PSMB5_TARGET_GENES 3.11e-02 3.59 0.93 1.00e+00 1.00e+00
4FTH1, IER3, ID1, PPP1R14B
 307
FOXJ2_01 3.69e-02 4.34 0.86 1.00e+00 1.00e+00
3IER3, ID1, TWIST2
 187
ZNF92_TARGET_GENES 9.61e-02 1.92 0.82 1.00e+00 1.00e+00
9CYGB, VAMP5, FERMT3, CD81, PPIA, FXYD5, PPP1R14B, EVA1B, ASS1
 1440
WGTTNNNNNAAA_UNKNOWN 5.91e-02 2.53 0.78 1.00e+00 1.00e+00
5IER3, RGS13, CYGB, CFI, UBL5
 554
HNF3B_01 5.65e-02 3.63 0.72 1.00e+00 1.00e+00
3IER3, ID1, TWIST2
 223
SFMBT1_TARGET_GENES 1.81e-01 1.66 0.71 1.00e+00 1.00e+00
9SH3BGRL3, S100A16, RGS13, PSMB9, ID3, PPIC, ASS1, SEC61G, QSOX1
 1661
CREB3L4_TARGET_GENES 1.61e-01 1.69 0.68 1.00e+00 1.00e+00
8SH3BGRL3, SPRY1, IER3, S100A16, PPIC, GUK1, PPIA, UQCRQ
 1418
ETS_Q4 7.52e-02 3.20 0.63 1.00e+00 1.00e+00
3LTBR, FXYD5, ARPC1B
 252
ICSBP_Q6 7.59e-02 3.19 0.63 1.00e+00 1.00e+00
3PSMB9, GSDMD, PSMB8
 253
CREL_01 7.87e-02 3.14 0.62 1.00e+00 1.00e+00
3IER3, HGF, NDUFB9
 257
UBP1_TARGET_GENES 2.98e-01 1.44 0.61 1.00e+00 1.00e+00
9S100A11, SPRY1, PSMB9, LTBR, GUK1, PSMB8, PPIA, FXYD5, UQCRQ
 1915
PEA3_Q6 8.29e-02 3.07 0.61 1.00e+00 1.00e+00
3PTPRC, LTBR, FERMT3
 263

Dowload full table

GO Biological Processes:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
GOBP_MITOCHONDRIAL_ELECTRON_TRANSPORT_UBIQUINOL_TO_CYTOCHROME_C 1.37e-03 43.30 4.59 8.47e-01 1.00e+00
2UQCRQ, UQCRH
 14
GOBP_POSITIVE_REGULATION_OF_EXTRINSIC_APOPTOTIC_SIGNALING_PATHWAY 8.97e-04 17.71 3.40 6.71e-01 1.00e+00
3PTPRC, LTBR, PYCARD
 48
GOBP_POSITIVE_REGULATION_OF_ALPHA_BETA_T_CELL_PROLIFERATION 3.10e-03 27.37 3.01 1.00e+00 1.00e+00
2PTPRC, CD81
 21
GOBP_PROTEASOMAL_UBIQUITIN_INDEPENDENT_PROTEIN_CATABOLIC_PROCESS 3.40e-03 26.01 2.87 1.00e+00 1.00e+00
2PSMB9, PSMB8
 22
GOBP_POSITIVE_REGULATION_OF_ANTIGEN_RECEPTOR_MEDIATED_SIGNALING_PATHWAY 3.72e-03 24.78 2.74 1.00e+00 1.00e+00
2PTPRC, CD81
 23
GOBP_REGULATION_OF_MEMBRANE_PROTEIN_ECTODOMAIN_PROTEOLYSIS 3.72e-03 24.78 2.74 1.00e+00 1.00e+00
2TIMP1, APOE
 23
GOBP_NEGATIVE_REGULATION_OF_VIRAL_LIFE_CYCLE 4.05e-03 23.65 2.62 1.00e+00 1.00e+00
2IFITM3, PPIA
 24
GOBP_PLATELET_DEGRANULATION 1.59e-03 8.76 2.26 8.52e-01 1.00e+00
4HGF, TIMP1, FERMT3, QSOX1
 128
GOBP_MYELOID_DENDRITIC_CELL_ACTIVATION 5.87e-03 19.27 2.16 1.00e+00 1.00e+00
2LTBR, PYCARD
 29
GOBP_MYELOID_LEUKOCYTE_MEDIATED_IMMUNITY 2.04e-04 5.07 2.16 4.52e-01 1.00e+00
9FTH1, S100A11, PTPRC, IL13RA2, GSDMD, PPIA, PYCARD, LAMTOR2, QSOX1
 550
GOBP_LOCALIZATION_WITHIN_MEMBRANE 3.23e-03 11.08 2.16 1.00e+00 1.00e+00
3PTPRC, CD81, APOE
 75
GOBP_MYELOID_LEUKOCYTE_ACTIVATION 1.50e-04 4.82 2.14 4.52e-01 1.00e+00
10FTH1, S100A11, PTPRC, IL13RA2, LTBR, GSDMD, PPIA, PYCARD, LAMTOR2, QSOX1
 659
GOBP_EXOCYTOSIS 7.77e-05 4.49 2.13 4.52e-01 5.81e-01
12FTH1, S100A11, PTPRC, IL13RA2, HGF, TIMP1, GSDMD, FERMT3, PPIA, PYCARD, LAMTOR2, QSOX1
 891
GOBP_REGULATION_OF_MAP_KINASE_ACTIVITY 1.16e-03 5.66 1.96 7.88e-01 1.00e+00
6SPRY1, PTPRC, HGF, CD81, PPIA, APOE
 307
GOBP_CELL_ACTIVATION_INVOLVED_IN_IMMUNE_RESPONSE 3.02e-04 4.39 1.95 4.52e-01 1.00e+00
10FTH1, S100A11, PTPRC, IL13RA2, GSDMD, CD81, PPIA, PYCARD, LAMTOR2, QSOX1
 722
GOBP_LEUKOCYTE_MEDIATED_IMMUNITY 2.96e-04 4.09 1.88 4.52e-01 1.00e+00
11FTH1, S100A11, PTPRC, IL13RA2, CFI, GSDMD, CD81, PPIA, PYCARD, LAMTOR2, QSOX1
 873
GOBP_ACTIVATION_OF_MAPK_ACTIVITY 3.10e-03 7.25 1.87 1.00e+00 1.00e+00
4PTPRC, HGF, CD81, PPIA
 154
GOBP_REGULATION_OF_EXTRINSIC_APOPTOTIC_SIGNALING_PATHWAY 3.10e-03 7.25 1.87 1.00e+00 1.00e+00
4PTPRC, HGF, LTBR, PYCARD
 154
GOBP_CELLULAR_RESPONSE_TO_LIPOPROTEIN_PARTICLE_STIMULUS 8.00e-03 16.26 1.84 1.00e+00 1.00e+00
2CD81, APOE
 34
GOBP_MAPK_CASCADE 4.21e-04 3.91 1.80 4.56e-01 1.00e+00
11SPRY1, PTPRC, HGF, PSMB9, LTBR, PSMB8, CD81, PPIA, PYCARD, LAMTOR2, APOE
 912

Dowload full table

Immunological Gene Sets:

P-value OR Lower 95% CI FDR FWER Genes Found Gene Set Size
GSE19888_ADENOSINE_A3R_INH_PRETREAT_AND_ACT_BY_A3R_VS_TCELL_MEMBRANES_ACT_MAST_CELL_UP 1.19e-05 10.54 3.95 5.79e-02 5.79e-02
7IFITM3, PTPRC, PSMB9, TIMP1, GSDMD, PSMB8, FXYD5
 200
GSE24026_PD1_LIGATION_VS_CTRL_IN_ACT_TCELL_LINE_UP 1.14e-04 8.92 3.07 8.61e-02 5.55e-01
6SH3BGRL3, PTPRC, PSMB9, TIMP1, PSMB8, SEC61G
 197
GSE37534_UNTREATED_VS_PIOGLITAZONE_TREATED_CD4_TCELL_PPARG1_AND_FOXP3_TRASDUCED_DN 1.20e-04 8.83 3.04 8.61e-02 5.86e-01
6IFITM3, PSMB9, VAMP5, ID3, GSDMD, PSMB8
 199
GSE339_CD4POS_VS_CD8POS_DC_IN_CULTURE_DN 1.24e-04 8.78 3.02 8.61e-02 6.03e-01
6IL13RA2, CRABP2, PSMB8, CD81, PPP1R14B, SEC61G
 200
GSE5960_TH1_VS_ANERGIC_TH1_DN 1.24e-04 8.78 3.02 8.61e-02 6.03e-01
6IER3, S100A3, VAMP5, ID1, CD81, ASS1
 200
GSE1925_CTRL_VS_IFNG_PRIMED_MACROPHAGE_24H_IFNG_STIM_DN 1.24e-04 8.78 3.02 8.61e-02 6.03e-01
6IFITM3, S100A11, S100A16, PPIA, APOE, QSOX1
 200
GSE24726_WT_VS_E2_2_KO_PDC_DAY4_POST_DELETION_UP 1.24e-04 8.78 3.02 8.61e-02 6.03e-01
6IFITM3, S100A11, PSMB9, PSMB8, UQCRQ, PPP1R14B
 200
GSE3720_UNSTIM_VS_PMA_STIM_VD1_GAMMADELTA_TCELL_UP 6.12e-04 8.12 2.49 1.31e-01 1.00e+00
5S100A11, GSDMD, PSMB8, NDUFB9, UQCRQ
 176
GSE21360_NAIVE_VS_SECONDARY_MEMORY_CD8_TCELL_UP 7.29e-04 7.80 2.39 1.31e-01 1.00e+00
5IER3, PPIC, PPP1R14B, EVA1B, QSOX1
 183
GSE22886_NAIVE_VS_IGG_IGA_MEMORY_BCELL_DN 9.88e-04 7.27 2.23 1.31e-01 1.00e+00
5S100A4, PSMB9, PYCARD, UQCRH, ARPC1B
 196
GSE21546_WT_VS_SAP1A_KO_DP_THYMOCYTES_UP 9.88e-04 7.27 2.23 1.31e-01 1.00e+00
5IFITM3, IL13RA2, PSMB9, VAMP5, PSMB8
 196
GSE1925_3H_VS_24H_IFNG_STIM_MACROPHAGE_DN 1.01e-03 7.23 2.22 1.31e-01 1.00e+00
5IFITM3, S100A11, S100A4, ID3, ARPC1B
 197
GSE11057_NAIVE_VS_MEMORY_CD4_TCELL_DN 1.03e-03 7.19 2.20 1.31e-01 1.00e+00
5SH3BGRL3, S100A11, S100A4, TIMP1, ARPC1B
 198
GSE22886_CD4_TCELL_VS_BCELL_NAIVE_UP 1.03e-03 7.19 2.20 1.31e-01 1.00e+00
5IFITM3, S100A4, TIMP1, GUK1, PPP1R14B
 198
GSE2585_THYMIC_DC_VS_THYMIC_MACROPHAGE_DN 1.03e-03 7.19 2.20 1.31e-01 1.00e+00
5S100A4, ID3, GSDMD, GUK1, LAMTOR2
 198
GSE45382_UNTREATED_VS_TGFB_TREATED_MACROPHAGES_UP 1.03e-03 7.19 2.20 1.31e-01 1.00e+00
5SH3BGRL3, S100A4, FERMT3, CD81, PYCARD
 198
GSE17721_POLYIC_VS_PAM3CSK4_6H_BMDC_DN 1.06e-03 7.16 2.19 1.31e-01 1.00e+00
5FTH1, UBL5, FERMT3, UQCRQ, PPP1R14B
 199
GSE29618_MONOCYTE_VS_PDC_UP 1.06e-03 7.16 2.19 1.31e-01 1.00e+00
5S100A11, S100A4, IER3, PTPRC, TIMP1
 199
GSE360_CTRL_VS_L_MAJOR_DC_DN 1.06e-03 7.16 2.19 1.31e-01 1.00e+00
5IFITM3, IER3, PSMB9, VAMP5, TIMP1
 199
GSE41978_ID2_KO_VS_BIM_KO_KLRG1_LOW_EFFECTOR_CD8_TCELL_UP 1.06e-03 7.16 2.19 1.31e-01 1.00e+00
5IFITM3, PTPRC, PSMB9, LTBR, PSMB8
 199

Dowload full table

Top Ranked Transcription Factors for this Gene Expression Program:

Gene Symbol TF Rank DNA Binding Domain Motif Status IUPAC PWM GTEx DepMap Decartes
ID3 21 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
ID1 26 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
PYCARD 35 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None None
TWIST2 47 Yes Known motif Monomer or homomultimer 100 perc ID - in vitro None None
NR2F1 53 Yes Known motif Monomer or homomultimer High-throughput in vitro None None
TAF10 54 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None General transcription factor
POLR2L 90 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None Does not contact DNA in the structure (PDB: 5FLM)
POLR2J 97 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None Does not contact DNA in the structure (PDB: 5FLM)
ZFP36 104 No ssDNA/RNA binding Not a DNA binding protein No motif None RNA binding protein (PMID: 10330172).
EIF3K 107 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None None
ATOH8 117 Yes Inferred motif Monomer or homomultimer High-throughput in vitro None None
NFKBIA 118 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None This is I kappa B alpha, which interacts with NFkappaB. No DBD, and evidence indicates that it is not a TF.
JUNB 121 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.
NME2 123 Yes Likely to be sequence specific TF Monomer or homomultimer No motif None Binds to telomeres (PMID: 22135295). Binds specific sequences by gel-shift, and binding is impacted by a SNP (PMID: 23368879)
DRAP1 133 Yes Likely to be sequence specific TF Obligate heteromer No motif None Based on structure (PDB: 1JFI), it forms the obligate heterodimer DR1-DRAP1 that furthermore contacts TBP. Only makes contact with the minor groove in a histone-like interaction, which is probably non-specific (PMID: 11461703)
PPARG 151 Yes Known motif Monomer or homomultimer 100 perc ID - in vitro None Also heterodimerizes.
PSMA6 173 No Unlikely to be sequence specific TF Not a DNA binding protein No motif None None
SP100 179 Yes Likely to be sequence specific TF Monomer or homomultimer No motif None Gel-shift experiments using human SP100 have shown binding to specific TTCG half sites (PMID: 11427895).
SP110 182 Yes Likely to be sequence specific TF Monomer or homomultimer No motif None None
MSC 190 Yes Known motif Monomer or homomultimer High-throughput in vitro None None

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

Interactive QQ-plot of gene loadings:

Interactive QQ Plot

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

Interactive QQ-plot:

Interactive QQ Plot

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


Cell ID Singler label Singler Delta Activity Score Top Singler Raw Scores
SKNAS_ATCGATGAGGAGTCTG-1 MSC 0.17 1253.20
Raw ScoresSmooth_muscle_cells:umbilical_vein: 0.57, MSC: 0.57, Neurons:adrenal_medulla_cell_line: 0.56, Tissue_stem_cells:lipoma-derived_MSC: 0.56, Fibroblasts:foreskin: 0.55, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.55, Smooth_muscle_cells:vascular: 0.55, iPS_cells:foreskin_fibrobasts: 0.55, iPS_cells:skin_fibroblast: 0.54, Tissue_stem_cells:dental_pulp: 0.53
SKNAS_CTGCATCCAATTGCTG-1 Smooth_muscle_cells 0.13 529.65
Raw ScoresSmooth_muscle_cells:umbilical_vein: 0.51, MSC: 0.5, Smooth_muscle_cells:vascular: 0.49, Tissue_stem_cells:lipoma-derived_MSC: 0.49, iPS_cells:foreskin_fibrobasts: 0.49, Fibroblasts:foreskin: 0.49, Smooth_muscle_cells:vascular:IL-17: 0.48, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.48, iPS_cells:skin_fibroblast: 0.48, Neurons:Schwann_cell: 0.48
SKNAS_TAAGCCATCGACGATT-1 Neurons 0.14 420.29
Raw ScoresSmooth_muscle_cells:umbilical_vein: 0.53, MSC: 0.52, Neurons:adrenal_medulla_cell_line: 0.51, Fibroblasts:foreskin: 0.51, Tissue_stem_cells:lipoma-derived_MSC: 0.51, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.51, Smooth_muscle_cells:vascular: 0.51, iPS_cells:foreskin_fibrobasts: 0.5, iPS_cells:skin_fibroblast: 0.5, Fibroblasts:breast: 0.5
SKNAS_TTACCGCGTAGCGTAG-1 Smooth_muscle_cells 0.16 338.89
Raw ScoresSmooth_muscle_cells:umbilical_vein: 0.49, MSC: 0.49, Smooth_muscle_cells:vascular: 0.48, Smooth_muscle_cells:vascular:IL-17: 0.48, iPS_cells:skin_fibroblast: 0.48, iPS_cells:foreskin_fibrobasts: 0.48, Fibroblasts:breast: 0.48, Tissue_stem_cells:lipoma-derived_MSC: 0.47, iPS_cells:adipose_stem_cells: 0.47, Fibroblasts:foreskin: 0.47
SKNAS_GGTGAAGCAGGTCCCA-1 MSC 0.20 333.52
Raw ScoresMSC: 0.55, Smooth_muscle_cells:umbilical_vein: 0.54, Fibroblasts:foreskin: 0.53, iPS_cells:foreskin_fibrobasts: 0.53, Smooth_muscle_cells:vascular: 0.53, iPS_cells:skin_fibroblast: 0.53, Tissue_stem_cells:lipoma-derived_MSC: 0.53, Tissue_stem_cells:dental_pulp: 0.52, iPS_cells:CRL2097_foreskin: 0.52, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.52
SKNAS_CGAGTGCCACGTAGAG-1 Neurons 0.14 300.66
Raw ScoresMSC: 0.55, Smooth_muscle_cells:umbilical_vein: 0.54, Neurons:adrenal_medulla_cell_line: 0.54, Tissue_stem_cells:lipoma-derived_MSC: 0.54, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.53, Fibroblasts:foreskin: 0.53, iPS_cells:skin_fibroblast: 0.52, Smooth_muscle_cells:vascular: 0.52, Tissue_stem_cells:CD326-CD56+: 0.52, iPS_cells:foreskin_fibrobasts: 0.52
SKNAS_AGTCATGAGCAAGCCA-1 Neurons 0.15 287.28
Raw ScoresMSC: 0.53, Neurons:adrenal_medulla_cell_line: 0.53, Smooth_muscle_cells:umbilical_vein: 0.52, Tissue_stem_cells:lipoma-derived_MSC: 0.52, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.51, Fibroblasts:foreskin: 0.51, Smooth_muscle_cells:vascular: 0.51, Tissue_stem_cells:CD326-CD56+: 0.5, Endothelial_cells:HUVEC:FPV-infected: 0.5, iPS_cells:skin_fibroblast: 0.5
SKNAS_TGGAGAGTCACACCCT-1 Neurons 0.12 278.37
Raw ScoresMSC: 0.54, Neurons:adrenal_medulla_cell_line: 0.53, Smooth_muscle_cells:umbilical_vein: 0.52, Tissue_stem_cells:lipoma-derived_MSC: 0.52, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.51, Smooth_muscle_cells:vascular: 0.51, Fibroblasts:foreskin: 0.51, Endothelial_cells:HUVEC: 0.51, iPS_cells:skin_fibroblast: 0.5, Tissue_stem_cells:CD326-CD56+: 0.5
SKNAS_GAAGGACGTATGACAA-1 MSC 0.16 271.94
Raw ScoresMSC: 0.53, Tissue_stem_cells:lipoma-derived_MSC: 0.53, Smooth_muscle_cells:umbilical_vein: 0.53, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.52, Fibroblasts:foreskin: 0.51, Smooth_muscle_cells:vascular: 0.51, iPS_cells:foreskin_fibrobasts: 0.51, iPS_cells:skin_fibroblast: 0.51, Neurons:adrenal_medulla_cell_line: 0.51, Tissue_stem_cells:dental_pulp: 0.5
SKNAS_GGGAAGTGTGCTAGCC-1 Neurons 0.13 269.86
Raw ScoresMSC: 0.52, Smooth_muscle_cells:umbilical_vein: 0.51, Neurons:adrenal_medulla_cell_line: 0.51, Tissue_stem_cells:lipoma-derived_MSC: 0.5, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.5, Smooth_muscle_cells:vascular: 0.5, Fibroblasts:foreskin: 0.5, iPS_cells:skin_fibroblast: 0.49, Tissue_stem_cells:CD326-CD56+: 0.49, iPS_cells:foreskin_fibrobasts: 0.49
SKNAS_TCATGGACAATGCTCA-1 Smooth_muscle_cells 0.16 269.41
Raw ScoresSmooth_muscle_cells:umbilical_vein: 0.49, MSC: 0.48, Smooth_muscle_cells:vascular: 0.48, Smooth_muscle_cells:vascular:IL-17: 0.47, Fibroblasts:breast: 0.47, iPS_cells:foreskin_fibrobasts: 0.47, iPS_cells:skin_fibroblast: 0.47, Fibroblasts:foreskin: 0.47, iPS_cells:adipose_stem_cells: 0.47, iPS_cells:CRL2097_foreskin: 0.47
SKNAS_GGGACTCGTGCGCTCA-1 Smooth_muscle_cells 0.15 261.85
Raw ScoresMSC: 0.49, Smooth_muscle_cells:umbilical_vein: 0.49, Fibroblasts:foreskin: 0.48, iPS_cells:skin_fibroblast: 0.48, Smooth_muscle_cells:vascular: 0.48, iPS_cells:foreskin_fibrobasts: 0.48, Fibroblasts:breast: 0.48, Smooth_muscle_cells:vascular:IL-17: 0.47, iPS_cells:CRL2097_foreskin: 0.47, iPS_cells:adipose_stem_cells: 0.47
SKNAS_GGGATGATCGCTGTCT-1 MSC 0.16 258.20
Raw ScoresMSC: 0.5, Smooth_muscle_cells:umbilical_vein: 0.49, Smooth_muscle_cells:vascular: 0.48, Tissue_stem_cells:lipoma-derived_MSC: 0.48, Smooth_muscle_cells:vascular:IL-17: 0.48, Fibroblasts:foreskin: 0.48, iPS_cells:foreskin_fibrobasts: 0.47, iPS_cells:skin_fibroblast: 0.47, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.47, Fibroblasts:breast: 0.47
SKNAS_TTGCATTTCAACACCA-1 Neurons 0.13 257.87
Raw ScoresSmooth_muscle_cells:umbilical_vein: 0.51, MSC: 0.51, Smooth_muscle_cells:vascular: 0.5, iPS_cells:foreskin_fibrobasts: 0.5, iPS_cells:skin_fibroblast: 0.5, Tissue_stem_cells:lipoma-derived_MSC: 0.5, Fibroblasts:foreskin: 0.49, Neurons:Schwann_cell: 0.49, Smooth_muscle_cells:vascular:IL-17: 0.49, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.49
SKNAS_AGCCACGCACTCATAG-1 Smooth_muscle_cells 0.17 257.47
Raw ScoresSmooth_muscle_cells:umbilical_vein: 0.5, MSC: 0.5, Smooth_muscle_cells:vascular: 0.49, Smooth_muscle_cells:vascular:IL-17: 0.49, Fibroblasts:breast: 0.49, iPS_cells:foreskin_fibrobasts: 0.48, Fibroblasts:foreskin: 0.48, iPS_cells:adipose_stem_cells: 0.48, Tissue_stem_cells:lipoma-derived_MSC: 0.48, iPS_cells:skin_fibroblast: 0.48
SKNAS_GGGTGAAAGATGGCGT-1 MSC 0.17 249.26
Raw ScoresMSC: 0.53, Smooth_muscle_cells:umbilical_vein: 0.52, Neurons:adrenal_medulla_cell_line: 0.52, Tissue_stem_cells:lipoma-derived_MSC: 0.52, Smooth_muscle_cells:vascular: 0.52, Fibroblasts:foreskin: 0.52, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.51, iPS_cells:foreskin_fibrobasts: 0.51, iPS_cells:skin_fibroblast: 0.51, Tissue_stem_cells:dental_pulp: 0.5
SKNAS_CTACCTGGTACAATAG-1 Smooth_muscle_cells 0.16 238.15
Raw ScoresSmooth_muscle_cells:umbilical_vein: 0.49, Smooth_muscle_cells:vascular: 0.49, MSC: 0.49, Smooth_muscle_cells:vascular:IL-17: 0.49, Fibroblasts:breast: 0.48, iPS_cells:skin_fibroblast: 0.48, iPS_cells:adipose_stem_cells: 0.48, iPS_cells:foreskin_fibrobasts: 0.48, Fibroblasts:foreskin: 0.48, Tissue_stem_cells:iliac_MSC: 0.48
SKNAS_GTGAGTTCATATAGCC-1 MSC 0.17 234.85
Raw ScoresMSC: 0.56, Smooth_muscle_cells:umbilical_vein: 0.54, Tissue_stem_cells:lipoma-derived_MSC: 0.54, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.54, Neurons:adrenal_medulla_cell_line: 0.53, Fibroblasts:foreskin: 0.53, iPS_cells:skin_fibroblast: 0.52, Neurons:Schwann_cell: 0.52, Smooth_muscle_cells:vascular: 0.52, Tissue_stem_cells:CD326-CD56+: 0.52
SKNAS_ATCAGGTCATGACCCG-1 Smooth_muscle_cells 0.15 233.72
Raw ScoresSmooth_muscle_cells:umbilical_vein: 0.51, MSC: 0.51, Neurons:adrenal_medulla_cell_line: 0.5, Tissue_stem_cells:lipoma-derived_MSC: 0.49, Smooth_muscle_cells:vascular: 0.49, iPS_cells:skin_fibroblast: 0.49, iPS_cells:foreskin_fibrobasts: 0.49, Fibroblasts:foreskin: 0.49, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.48, Smooth_muscle_cells:vascular:IL-17: 0.48
SKNAS_TTGGGCGTCAGGACAG-1 MSC 0.19 232.13
Raw ScoresMSC: 0.59, Tissue_stem_cells:lipoma-derived_MSC: 0.57, Smooth_muscle_cells:umbilical_vein: 0.57, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.57, iPS_cells:skin_fibroblast: 0.56, Fibroblasts:foreskin: 0.56, Neurons:adrenal_medulla_cell_line: 0.56, Smooth_muscle_cells:vascular: 0.55, iPS_cells:foreskin_fibrobasts: 0.55, Tissue_stem_cells:dental_pulp: 0.54
SKNAS_CTACCTGCATCCTATT-1 Neurons 0.16 230.32
Raw ScoresMSC: 0.54, Neurons:adrenal_medulla_cell_line: 0.53, Smooth_muscle_cells:umbilical_vein: 0.53, Smooth_muscle_cells:vascular: 0.52, Tissue_stem_cells:lipoma-derived_MSC: 0.52, Fibroblasts:foreskin: 0.52, iPS_cells:skin_fibroblast: 0.52, iPS_cells:foreskin_fibrobasts: 0.52, Neurons:Schwann_cell: 0.52, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.51
SKNAS_TGGGATTCAACACACT-1 MSC 0.16 228.57
Raw ScoresMSC: 0.52, Smooth_muscle_cells:umbilical_vein: 0.51, Tissue_stem_cells:lipoma-derived_MSC: 0.51, Fibroblasts:foreskin: 0.51, iPS_cells:skin_fibroblast: 0.51, Neurons:adrenal_medulla_cell_line: 0.51, iPS_cells:foreskin_fibrobasts: 0.5, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.5, Smooth_muscle_cells:vascular: 0.5, Tissue_stem_cells:CD326-CD56+: 0.49
SKNAS_ATCACGACAAATCAAG-1 Neurons 0.15 226.65
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.53, MSC: 0.52, Smooth_muscle_cells:umbilical_vein: 0.52, Tissue_stem_cells:lipoma-derived_MSC: 0.51, Smooth_muscle_cells:vascular: 0.51, Fibroblasts:foreskin: 0.51, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.51, iPS_cells:skin_fibroblast: 0.5, iPS_cells:foreskin_fibrobasts: 0.5, Neurons:Schwann_cell: 0.5
SKNAS_GTCATCCTCCCTCAAC-1 Smooth_muscle_cells 0.17 222.93
Raw ScoresMSC: 0.5, Smooth_muscle_cells:umbilical_vein: 0.49, Smooth_muscle_cells:vascular: 0.49, iPS_cells:CRL2097_foreskin: 0.49, Tissue_stem_cells:lipoma-derived_MSC: 0.49, Smooth_muscle_cells:vascular:IL-17: 0.49, Neurons:adrenal_medulla_cell_line: 0.49, iPS_cells:skin_fibroblast: 0.48, iPS_cells:foreskin_fibrobasts: 0.48, Fibroblasts:breast: 0.48
SKNAS_CGTAGTACAGAGCTAG-1 Neurons 0.15 220.94
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.53, MSC: 0.5, Smooth_muscle_cells:umbilical_vein: 0.49, Tissue_stem_cells:lipoma-derived_MSC: 0.49, Tissue_stem_cells:CD326-CD56+: 0.49, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.49, Fibroblasts:foreskin: 0.48, Smooth_muscle_cells:vascular: 0.47, Endothelial_cells:HUVEC: 0.47, iPS_cells:skin_fibroblast: 0.47
SKNAS_CGCATAATCGAGTGGA-1 Neurons 0.15 219.73
Raw ScoresMSC: 0.51, Neurons:adrenal_medulla_cell_line: 0.51, Smooth_muscle_cells:umbilical_vein: 0.5, Tissue_stem_cells:lipoma-derived_MSC: 0.5, Smooth_muscle_cells:vascular: 0.5, Fibroblasts:foreskin: 0.49, iPS_cells:foreskin_fibrobasts: 0.49, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.49, iPS_cells:skin_fibroblast: 0.49, Neurons:Schwann_cell: 0.49
SKNAS_GGATCTAGTGAGTAGC-1 MSC 0.20 218.06
Raw ScoresMSC: 0.57, Neurons:adrenal_medulla_cell_line: 0.57, Tissue_stem_cells:CD326-CD56+: 0.55, Tissue_stem_cells:lipoma-derived_MSC: 0.54, Smooth_muscle_cells:umbilical_vein: 0.54, Fibroblasts:foreskin: 0.54, iPS_cells:skin_fibroblast: 0.54, Neuroepithelial_cell:ESC-derived: 0.54, iPS_cells:foreskin_fibrobasts: 0.54, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.54
SKNAS_ACCGTTCAGTTACTCG-1 Smooth_muscle_cells 0.20 217.35
Raw ScoresMSC: 0.53, Smooth_muscle_cells:umbilical_vein: 0.53, Smooth_muscle_cells:vascular: 0.52, Tissue_stem_cells:lipoma-derived_MSC: 0.52, Smooth_muscle_cells:vascular:IL-17: 0.51, iPS_cells:skin_fibroblast: 0.51, iPS_cells:foreskin_fibrobasts: 0.51, Fibroblasts:foreskin: 0.51, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.51, iPS_cells:CRL2097_foreskin: 0.5
SKNAS_TTAGGGTGTTAACCTG-1 Neurons 0.13 216.99
Raw ScoresSmooth_muscle_cells:umbilical_vein: 0.53, MSC: 0.53, Neurons:adrenal_medulla_cell_line: 0.52, Tissue_stem_cells:lipoma-derived_MSC: 0.52, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.51, Smooth_muscle_cells:vascular: 0.51, iPS_cells:foreskin_fibrobasts: 0.51, iPS_cells:skin_fibroblast: 0.51, Fibroblasts:foreskin: 0.51, Endothelial_cells:HUVEC: 0.5
SKNAS_TTCACCGCAGGCCCTA-1 Neurons 0.13 215.86
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.53, MSC: 0.51, Smooth_muscle_cells:umbilical_vein: 0.51, Fibroblasts:foreskin: 0.5, Tissue_stem_cells:lipoma-derived_MSC: 0.5, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.49, Smooth_muscle_cells:vascular: 0.49, iPS_cells:foreskin_fibrobasts: 0.49, iPS_cells:skin_fibroblast: 0.49, Tissue_stem_cells:CD326-CD56+: 0.49
SKNAS_GCTACAAAGCTGAAGC-1 Neurons 0.15 215.32
Raw ScoresSmooth_muscle_cells:umbilical_vein: 0.51, MSC: 0.51, Neurons:adrenal_medulla_cell_line: 0.51, Tissue_stem_cells:lipoma-derived_MSC: 0.49, Fibroblasts:foreskin: 0.49, iPS_cells:foreskin_fibrobasts: 0.49, Smooth_muscle_cells:vascular: 0.49, iPS_cells:skin_fibroblast: 0.49, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.49, Tissue_stem_cells:dental_pulp: 0.48
SKNAS_ATGACCAAGTTGTAAG-1 Neurons 0.12 214.96
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.46, MSC: 0.45, Smooth_muscle_cells:umbilical_vein: 0.45, Smooth_muscle_cells:vascular: 0.44, Fibroblasts:foreskin: 0.44, Tissue_stem_cells:dental_pulp: 0.44, iPS_cells:foreskin_fibrobasts: 0.44, Smooth_muscle_cells:vascular:IL-17: 0.44, Tissue_stem_cells:lipoma-derived_MSC: 0.44, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.44
SKNAS_ACAAAGACATCAGCGC-1 Neurons 0.16 214.53
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.52, MSC: 0.51, Smooth_muscle_cells:umbilical_vein: 0.51, Tissue_stem_cells:lipoma-derived_MSC: 0.5, iPS_cells:skin_fibroblast: 0.5, iPS_cells:foreskin_fibrobasts: 0.5, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.49, Fibroblasts:foreskin: 0.49, Smooth_muscle_cells:vascular: 0.49, iPS_cells:CRL2097_foreskin: 0.49
SKNAS_TGCAGTATCGAGAGCA-1 Neurons 0.14 212.29
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.53, MSC: 0.52, Smooth_muscle_cells:umbilical_vein: 0.5, Tissue_stem_cells:CD326-CD56+: 0.5, Smooth_muscle_cells:vascular: 0.49, Tissue_stem_cells:lipoma-derived_MSC: 0.49, Fibroblasts:foreskin: 0.49, iPS_cells:skin_fibroblast: 0.49, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.49, Neurons:Schwann_cell: 0.49
SKNAS_GATAGAACAGCTTCCT-1 MSC 0.20 211.86
Raw ScoresMSC: 0.57, Tissue_stem_cells:lipoma-derived_MSC: 0.55, Smooth_muscle_cells:umbilical_vein: 0.54, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.54, Neurons:adrenal_medulla_cell_line: 0.54, iPS_cells:skin_fibroblast: 0.53, Fibroblasts:foreskin: 0.53, Smooth_muscle_cells:vascular: 0.53, iPS_cells:foreskin_fibrobasts: 0.52, Neurons:Schwann_cell: 0.52
SKNAS_ATTATCCTCTCTATGT-1 Neurons 0.15 211.01
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.53, MSC: 0.53, Tissue_stem_cells:lipoma-derived_MSC: 0.52, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.51, Smooth_muscle_cells:umbilical_vein: 0.5, Fibroblasts:foreskin: 0.5, Smooth_muscle_cells:vascular: 0.5, iPS_cells:skin_fibroblast: 0.49, Endothelial_cells:HUVEC: 0.49, iPS_cells:foreskin_fibrobasts: 0.49
SKNAS_ATCAGGTCAAATGAAC-1 Neurons 0.11 208.62
Raw ScoresMSC: 0.53, Smooth_muscle_cells:umbilical_vein: 0.51, Tissue_stem_cells:lipoma-derived_MSC: 0.51, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.51, Tissue_stem_cells:CD326-CD56+: 0.5, Fibroblasts:foreskin: 0.5, Neurons:Schwann_cell: 0.49, Endothelial_cells:HUVEC: 0.49, Smooth_muscle_cells:vascular: 0.49, iPS_cells:skin_fibroblast: 0.49
SKNAS_GTCATCCTCCGCGGAT-1 Neurons 0.16 208.42
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.55, MSC: 0.54, Smooth_muscle_cells:umbilical_vein: 0.52, Tissue_stem_cells:lipoma-derived_MSC: 0.52, Tissue_stem_cells:CD326-CD56+: 0.52, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.51, Fibroblasts:foreskin: 0.51, iPS_cells:skin_fibroblast: 0.5, Neuroepithelial_cell:ESC-derived: 0.5, Smooth_muscle_cells:vascular: 0.5
SKNAS_TCTGGCTCAAAGCAAT-1 MSC 0.18 208.36
Raw ScoresMSC: 0.53, Smooth_muscle_cells:umbilical_vein: 0.53, Tissue_stem_cells:lipoma-derived_MSC: 0.51, Smooth_muscle_cells:vascular: 0.51, Fibroblasts:foreskin: 0.51, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.5, iPS_cells:skin_fibroblast: 0.5, iPS_cells:foreskin_fibrobasts: 0.5, Neurons:Schwann_cell: 0.5, Neurons:adrenal_medulla_cell_line: 0.49
SKNAS_TGTTTGTCAGAGGCTA-1 MSC 0.13 207.73
Raw ScoresMSC: 0.49, Tissue_stem_cells:lipoma-derived_MSC: 0.49, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.48, Smooth_muscle_cells:umbilical_vein: 0.48, Neurons:adrenal_medulla_cell_line: 0.48, Fibroblasts:foreskin: 0.47, Smooth_muscle_cells:vascular: 0.47, iPS_cells:skin_fibroblast: 0.47, iPS_cells:foreskin_fibrobasts: 0.46, Neurons:Schwann_cell: 0.46
SKNAS_GTGGTTATCCTTCGAC-1 Smooth_muscle_cells 0.14 206.84
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.48, Smooth_muscle_cells:umbilical_vein: 0.47, Smooth_muscle_cells:vascular: 0.47, MSC: 0.46, Smooth_muscle_cells:vascular:IL-17: 0.46, Fibroblasts:foreskin: 0.45, Fibroblasts:breast: 0.45, iPS_cells:foreskin_fibrobasts: 0.45, Tissue_stem_cells:lipoma-derived_MSC: 0.45, Smooth_muscle_cells:bronchial:vit_D: 0.45
SKNAS_ACCTACCGTCAGGTGA-1 MSC 0.19 206.39
Raw ScoresMSC: 0.55, Tissue_stem_cells:lipoma-derived_MSC: 0.53, Smooth_muscle_cells:umbilical_vein: 0.53, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.53, Smooth_muscle_cells:vascular: 0.52, Fibroblasts:foreskin: 0.52, Neurons:adrenal_medulla_cell_line: 0.52, iPS_cells:skin_fibroblast: 0.52, iPS_cells:foreskin_fibrobasts: 0.52, iPS_cells:CRL2097_foreskin: 0.51
SKNAS_CACCAAATCGCCATAA-1 MSC 0.17 203.85
Raw ScoresMSC: 0.56, Tissue_stem_cells:lipoma-derived_MSC: 0.55, Smooth_muscle_cells:umbilical_vein: 0.54, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.54, Smooth_muscle_cells:vascular: 0.54, Neurons:adrenal_medulla_cell_line: 0.54, Fibroblasts:foreskin: 0.54, iPS_cells:skin_fibroblast: 0.53, iPS_cells:foreskin_fibrobasts: 0.53, iPS_cells:CRL2097_foreskin: 0.52
SKNAS_CGTAAGTAGGCCTTGC-1 MSC 0.18 203.04
Raw ScoresMSC: 0.52, Smooth_muscle_cells:umbilical_vein: 0.51, iPS_cells:skin_fibroblast: 0.5, Tissue_stem_cells:lipoma-derived_MSC: 0.5, iPS_cells:foreskin_fibrobasts: 0.5, Fibroblasts:foreskin: 0.5, Smooth_muscle_cells:vascular: 0.5, iPS_cells:CRL2097_foreskin: 0.49, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.49, Smooth_muscle_cells:vascular:IL-17: 0.49
BE2C_GGGCCATGTCGCGGTT-1 Neurons 0.19 202.20
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.53, Endothelial_cells:HUVEC: 0.49, Endothelial_cells:HUVEC:B._anthracis_LT: 0.48, Endothelial_cells:HUVEC:IL-1b: 0.48, Endothelial_cells:HUVEC:VEGF: 0.48, Endothelial_cells:HUVEC:FPV-infected: 0.48, Endothelial_cells:HUVEC:H5N1-infected: 0.47, Endothelial_cells:HUVEC:Serum_Amyloid_A: 0.47, MSC: 0.47, Endothelial_cells:lymphatic: 0.47
SKNAS_CTAACTTTCACCTCGT-1 MSC 0.15 200.43
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.55, MSC: 0.54, Tissue_stem_cells:lipoma-derived_MSC: 0.53, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.53, Smooth_muscle_cells:umbilical_vein: 0.52, Fibroblasts:foreskin: 0.52, Smooth_muscle_cells:vascular: 0.51, iPS_cells:skin_fibroblast: 0.51, Endothelial_cells:HUVEC: 0.51, iPS_cells:foreskin_fibrobasts: 0.51
SKNAS_ACTTCGCCAGAATTCC-1 Smooth_muscle_cells 0.16 198.20
Raw ScoresMSC: 0.52, Smooth_muscle_cells:umbilical_vein: 0.52, Tissue_stem_cells:lipoma-derived_MSC: 0.51, Smooth_muscle_cells:vascular: 0.51, Neurons:adrenal_medulla_cell_line: 0.51, Fibroblasts:foreskin: 0.5, iPS_cells:skin_fibroblast: 0.5, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.5, iPS_cells:foreskin_fibrobasts: 0.5, Smooth_muscle_cells:vascular:IL-17: 0.5
SKNAS_CACTGTCGTTGTTTGG-1 Neurons 0.19 196.58
Raw ScoresNeurons:adrenal_medulla_cell_line: 0.53, MSC: 0.5, Smooth_muscle_cells:umbilical_vein: 0.49, Smooth_muscle_cells:vascular: 0.48, Tissue_stem_cells:lipoma-derived_MSC: 0.48, Fibroblasts:breast: 0.48, Tissue_stem_cells:CD326-CD56+: 0.48, Fibroblasts:foreskin: 0.48, iPS_cells:foreskin_fibrobasts: 0.48, iPS_cells:skin_fibroblast: 0.48
SKNAS_GAAACCTGTGTCATTG-1 Neurons 0.15 195.63
Raw ScoresMSC: 0.5, Neurons:adrenal_medulla_cell_line: 0.49, Tissue_stem_cells:lipoma-derived_MSC: 0.48, Smooth_muscle_cells:umbilical_vein: 0.48, iPS_cells:skin_fibroblast: 0.47, Tissue_stem_cells:CD326-CD56+: 0.47, iPS_cells:foreskin_fibrobasts: 0.47, Fibroblasts:foreskin: 0.47, Tissue_stem_cells:adipose-derived_MSC_AM3: 0.47, iPS_cells:CRL2097_foreskin: 0.46
SKNAS_AGGAATAAGGGTAATT-1 Smooth_muscle_cells 0.14 194.06
Raw ScoresMSC: 0.43, Smooth_muscle_cells:umbilical_vein: 0.43, Smooth_muscle_cells:vascular:IL-17: 0.43, Smooth_muscle_cells:vascular: 0.43, iPS_cells:foreskin_fibrobasts: 0.43, Fibroblasts:foreskin: 0.43, Fibroblasts:breast: 0.42, iPS_cells:adipose_stem_cells: 0.42, iPS_cells:skin_fibroblast: 0.42, iPS_cells:CRL2097_foreskin: 0.42


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.


Mesenchymal Fig 1D (Olsen)
Selected mesenchymal marker genes shown in Fig. 1D of Olsen et al. https://www.biorxiv.org/content/10.1101/2020.05.04.077057v1 - these are highly expressed in their mesenchymal cluster on their UMAP.:
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.37e-05
Mean rank of genes in gene set: 2063.31
Rank on gene expression program of genes in gene set:
Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
LUM 0.0154739 17 GTEx DepMap Descartes 13.33 277.64
COL6A2 0.0133682 33 GTEx DepMap Descartes 5.67 89.04
DCN 0.0117293 57 GTEx DepMap Descartes 4.66 37.46
SPARC 0.0111328 65 GTEx DepMap Descartes 10.09 147.85
MGP 0.0108435 69 GTEx DepMap Descartes 21.42 689.31
BGN 0.0080307 170 GTEx DepMap Descartes 3.43 77.82
COL3A1 0.0071373 223 GTEx DepMap Descartes 9.42 91.63
PDGFRA 0.0027722 950 GTEx DepMap Descartes 1.63 14.22
PRRX1 0.0022088 1202 GTEx DepMap Descartes 1.59 22.17
COL1A1 0.0021199 1251 GTEx DepMap Descartes 9.37 81.51
LEPR 0.0008598 2278 GTEx DepMap Descartes 0.24 1.62
CALD1 -0.0006560 8295 GTEx DepMap Descartes 10.19 103.34
COL1A2 -0.0026084 12213 GTEx DepMap Descartes 0.00 0.01


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: 7.13e-04
Mean rank of genes in gene set: 3966.4
Rank on gene expression program of genes in gene set:

Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
HGF 0.0162934 13 GTEx DepMap Descartes 17.90 168.94
CCL2 0.0117816 56 GTEx DepMap Descartes 8.80 519.45
C7 0.0066044 263 GTEx DepMap Descartes 8.82 90.80
IL1R1 0.0059854 324 GTEx DepMap Descartes 0.59 6.68
IGFBP6 0.0045407 505 GTEx DepMap Descartes 2.33 98.67
PDGFRA 0.0027722 950 GTEx DepMap Descartes 1.63 14.22
CXCL2 0.0022512 1180 GTEx DepMap Descartes 0.07 4.11
C3 0.0018970 1354 GTEx DepMap Descartes 0.03 0.37
CFB 0.0015108 1633 GTEx DepMap Descartes 0.04 1.04
LIF 0.0014576 1670 GTEx DepMap Descartes 0.11 1.54
IL33 0.0006612 2587 GTEx DepMap Descartes 0.04 0.83
CXCL14 0.0006160 2651 GTEx DepMap Descartes 0.06 1.16
SOD2 0.0003913 3103 GTEx DepMap Descartes 1.20 4.41
IGF1 0.0000215 4248 GTEx DepMap Descartes 0.01 0.06
IL10 -0.0000584 4624 GTEx DepMap Descartes 0.00 0.00
CXCL12 -0.0000995 4941 GTEx DepMap Descartes 0.41 6.55
PDPN -0.0001056 4987 GTEx DepMap Descartes 0.00 0.00
SCARA5 -0.0001672 5520 GTEx DepMap Descartes 0.00 0.00
PDGFD -0.0002418 6077 GTEx DepMap Descartes 0.07 0.90
GPX3 -0.0002878 6380 GTEx DepMap Descartes 0.11 2.93
CFD -0.0003116 6524 GTEx DepMap Descartes 0.02 0.53
RGMA -0.0006769 8402 GTEx DepMap Descartes 0.01 0.02
SERPING1 -0.0010342 9830 GTEx DepMap Descartes 0.05 1.20
PDGFRB -0.0012329 10441 GTEx DepMap Descartes 0.39 3.53
SCARA3 -0.0014120 10897 GTEx DepMap Descartes 0.11 1.37


Bridge region mesenchymal-SCP transition (Olsen)
As above but for cells in the mesenchymal transitioning to SCP region:
Wilcoxon ranksum test P-value for gene set overrepresentation: 1.53e-03
Mean rank of genes in gene set: 82.33
Rank on gene expression program of genes in gene set:

Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
IFITM3 0.0204881 1 GTEx DepMap Descartes 7.66 560.37
B2M 0.0108168 70 GTEx DepMap Descartes 44.73 970.70
S100A10 0.0079129 176 GTEx DepMap Descartes 34.84 2518.79




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: 9999.3
Median rank of genes in gene set: 11190
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
CYGB 0.0162670 14 GTEx DepMap Descartes 9.77 259.09
RGS5 0.0085898 143 GTEx DepMap Descartes 77.85 736.81
PKIA 0.0072684 211 GTEx DepMap Descartes 5.72 78.36
NSG1 0.0063219 291 GTEx DepMap Descartes 6.06 NA
CDKN2C 0.0051262 419 GTEx DepMap Descartes 4.81 86.52
INO80C 0.0032679 790 GTEx DepMap Descartes 1.73 29.35
NPY 0.0028863 900 GTEx DepMap Descartes 32.60 2317.76
AHSA1 0.0027526 961 GTEx DepMap Descartes 5.93 235.31
FBXO8 0.0022689 1175 GTEx DepMap Descartes 3.61 96.11
GGCT 0.0015036 1638 GTEx DepMap Descartes 7.09 294.14
LEPROTL1 0.0012155 1873 GTEx DepMap Descartes 3.58 55.40
TUBB4B 0.0011105 1986 GTEx DepMap Descartes 16.55 412.85
SYT4 0.0009434 2182 GTEx DepMap Descartes 3.15 40.57
ATP6V0E2 0.0008081 2356 GTEx DepMap Descartes 2.05 24.23
PRSS12 0.0007753 2404 GTEx DepMap Descartes 3.90 43.96
FAM167A 0.0007719 2407 GTEx DepMap Descartes 0.60 8.27
TMTC4 0.0007451 2447 GTEx DepMap Descartes 0.75 11.68
TBC1D30 0.0005214 2811 GTEx DepMap Descartes 0.16 1.10
CCDC167 0.0005012 2856 GTEx DepMap Descartes 4.58 387.48
HMGA1 0.0004224 3033 GTEx DepMap Descartes 10.45 230.76
BMPR1B 0.0003288 3259 GTEx DepMap Descartes 0.53 5.56
SEC11C 0.0003098 3305 GTEx DepMap Descartes 3.59 85.03
RGS17 0.0002526 3455 GTEx DepMap Descartes 0.55 3.61
NFIL3 0.0002319 3517 GTEx DepMap Descartes 0.38 9.77
TSPAN13 0.0002173 3559 GTEx DepMap Descartes 0.82 23.04
ST3GAL6 0.0001846 3664 GTEx DepMap Descartes 1.22 19.12
TBPL1 0.0001478 3775 GTEx DepMap Descartes 1.53 17.56
LSM4 0.0001444 3789 GTEx DepMap Descartes 13.94 387.31
SETD7 0.0001344 3819 GTEx DepMap Descartes 0.68 4.80
RET 0.0001287 3840 GTEx DepMap Descartes 1.97 19.35


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: 2.05e-28
Mean rank of genes in gene set: 4398.85
Median rank of genes in gene set: 2821
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
IFITM3 0.0204881 1 GTEx DepMap Descartes 7.66 560.37
SPRY1 0.0183860 5 GTEx DepMap Descartes 7.85 164.08
CFI 0.0148760 19 GTEx DepMap Descartes 2.15 53.82
ID3 0.0147730 21 GTEx DepMap Descartes 35.14 1904.52
TIMP1 0.0146998 22 GTEx DepMap Descartes 22.86 1063.43
CRABP2 0.0143381 24 GTEx DepMap Descartes 15.45 825.78
PPIC 0.0142090 25 GTEx DepMap Descartes 3.96 150.71
ID1 0.0138930 26 GTEx DepMap Descartes 28.65 1238.69
COL6A2 0.0133682 33 GTEx DepMap Descartes 5.67 89.04
APOE 0.0124783 40 GTEx DepMap Descartes 11.85 580.18
GAS1 0.0124027 42 GTEx DepMap Descartes 2.87 50.74
ARPC1B 0.0122888 46 GTEx DepMap Descartes 13.27 386.45
QSOX1 0.0121332 50 GTEx DepMap Descartes 6.05 32.17
SQSTM1 0.0119391 52 GTEx DepMap Descartes 11.22 197.93
OSTC 0.0118713 55 GTEx DepMap Descartes 17.53 870.48
RAB13 0.0112335 64 GTEx DepMap Descartes 14.66 370.04
SPARC 0.0111328 65 GTEx DepMap Descartes 10.09 147.85
MYL12A 0.0110297 66 GTEx DepMap Descartes 17.38 747.53
CD63 0.0108499 68 GTEx DepMap Descartes 41.88 1809.15
MGP 0.0108435 69 GTEx DepMap Descartes 21.42 689.31
B2M 0.0108168 70 GTEx DepMap Descartes 44.73 970.70
SRPX 0.0104297 78 GTEx DepMap Descartes 1.77 49.36
NQO1 0.0102715 86 GTEx DepMap Descartes 8.56 174.90
POLR2L 0.0100895 90 GTEx DepMap Descartes 22.49 1298.52
PRDX6 0.0096348 106 GTEx DepMap Descartes 27.86 848.81
EFEMP2 0.0095739 108 GTEx DepMap Descartes 2.99 69.71
MYL12B 0.0095206 112 GTEx DepMap Descartes 17.98 755.71
TNFRSF1A 0.0092874 122 GTEx DepMap Descartes 2.42 59.10
RHOC 0.0091516 127 GTEx DepMap Descartes 6.97 153.08
MEST 0.0090613 130 GTEx DepMap Descartes 4.56 78.95


Descartes adrenocortical markers
Top 50 marker genes of adrenocortical cells in the Decartes fetal adrenal single cell map (https://atlas.brotmanbaty.org/bbi/human-gene-expression-during-development/cell/adrenocortical/in/adrenal)
Wilcoxon ranksum test P-value for gene set overrepresentation: 8.72e-01
Mean rank of genes in gene set: 6959.69
Median rank of genes in gene set: 6966.5
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
BAIAP2L1 0.0028152 928 GTEx DepMap Descartes 0.20 2.73
FDPS 0.0016024 1556 GTEx DepMap Descartes 10.86 284.97
SH3BP5 0.0008317 2323 GTEx DepMap Descartes 1.18 19.11
PDE10A 0.0007931 2375 GTEx DepMap Descartes 0.44 2.84
DHCR7 0.0004785 2908 GTEx DepMap Descartes 0.83 16.26
MSMO1 0.0004036 3079 GTEx DepMap Descartes 1.78 45.74
TM7SF2 0.0003547 3187 GTEx DepMap Descartes 1.16 27.64
FDX1 0.0003538 3190 GTEx DepMap Descartes 1.51 22.84
APOC1 0.0002708 3409 GTEx DepMap Descartes 0.33 25.28
POR 0.0000102 4300 GTEx DepMap Descartes 0.81 17.06
INHA -0.0000130 4386 GTEx DepMap Descartes 0.01 0.45
GSTA4 -0.0000151 4397 GTEx DepMap Descartes 1.27 40.19
ERN1 -0.0001373 5262 GTEx DepMap Descartes 0.16 1.01
DNER -0.0001869 5687 GTEx DepMap Descartes 0.02 0.35
CYB5B -0.0002603 6206 GTEx DepMap Descartes 2.22 26.21
NPC1 -0.0002925 6411 GTEx DepMap Descartes 0.13 1.43
SGCZ -0.0003500 6757 GTEx DepMap Descartes 0.00 0.00
FRMD5 -0.0003780 6914 GTEx DepMap Descartes 0.14 1.44
STAR -0.0003967 7019 GTEx DepMap Descartes 0.00 0.03
FREM2 -0.0004082 7087 GTEx DepMap Descartes 0.00 0.00
LDLR -0.0005468 7802 GTEx DepMap Descartes 0.82 8.02
FDXR -0.0006855 8438 GTEx DepMap Descartes 0.54 11.22
SCAP -0.0007650 8810 GTEx DepMap Descartes 0.31 3.58
GRAMD1B -0.0008061 8997 GTEx DepMap Descartes 0.06 0.37
SLC16A9 -0.0008196 9054 GTEx DepMap Descartes 0.10 1.34
SCARB1 -0.0009203 9435 GTEx DepMap Descartes 0.47 4.17
SH3PXD2B -0.0010200 9786 GTEx DepMap Descartes 0.24 1.68
IGF1R -0.0010363 9841 GTEx DepMap Descartes 0.92 3.90
SLC1A2 -0.0010840 9989 GTEx DepMap Descartes 0.01 0.01
PEG3 -0.0013254 10698 GTEx DepMap Descartes 0.01 NA


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: 9299.51
Median rank of genes in gene set: 10751
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
NPY 0.0028863 900 GTEx DepMap Descartes 32.60 2317.76
MAB21L2 0.0017642 1455 GTEx DepMap Descartes 3.39 72.15
MLLT11 0.0007262 2488 GTEx DepMap Descartes 11.10 226.94
GREM1 0.0006868 2551 GTEx DepMap Descartes 0.48 1.55
NTRK1 0.0001078 3924 GTEx DepMap Descartes 0.46 8.59
IL7 0.0000958 3961 GTEx DepMap Descartes 0.23 6.08
SYNPO2 0.0000934 3968 GTEx DepMap Descartes 4.64 16.16
TMEM132C -0.0003061 6497 GTEx DepMap Descartes 0.00 0.00
ANKFN1 -0.0003170 6560 GTEx DepMap Descartes 0.00 0.00
EPHA6 -0.0005087 7617 GTEx DepMap Descartes 0.01 0.09
TUBB2A -0.0005289 7715 GTEx DepMap Descartes 2.30 68.79
PTCHD1 -0.0006759 8398 GTEx DepMap Descartes 0.01 0.04
REEP1 -0.0007926 8951 GTEx DepMap Descartes 0.01 0.13
RYR2 -0.0008717 9247 GTEx DepMap Descartes 0.10 0.34
EYA1 -0.0008772 9270 GTEx DepMap Descartes 0.35 4.22
TMEFF2 -0.0009252 9449 GTEx DepMap Descartes 0.02 0.17
SLC44A5 -0.0009645 9595 GTEx DepMap Descartes 0.03 0.35
KCNB2 -0.0010467 9873 GTEx DepMap Descartes 0.00 0.00
HS3ST5 -0.0011024 10046 GTEx DepMap Descartes 0.02 0.29
RBFOX1 -0.0012188 10404 GTEx DepMap Descartes 0.01 0.03
EYA4 -0.0013503 10751 GTEx DepMap Descartes 0.06 0.45
FAT3 -0.0013733 10816 GTEx DepMap Descartes 0.01 0.01
ALK -0.0013869 10847 GTEx DepMap Descartes 0.00 0.01
CNKSR2 -0.0014286 10934 GTEx DepMap Descartes 0.11 0.69
PLXNA4 -0.0014824 11056 GTEx DepMap Descartes 0.12 0.36
RGMB -0.0015548 11196 GTEx DepMap Descartes 0.29 3.01
CNTFR -0.0015980 11276 GTEx DepMap Descartes 0.47 11.04
RPH3A -0.0017293 11473 GTEx DepMap Descartes 0.03 0.27
MAB21L1 -0.0019111 11695 GTEx DepMap Descartes 3.17 60.36
MARCH11 -0.0019538 11746 GTEx DepMap Descartes 0.56 NA


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: 1.41e-01
Mean rank of genes in gene set: 5643.16
Median rank of genes in gene set: 5447
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
ID1 0.0138930 26 GTEx DepMap Descartes 28.65 1238.69
NPR1 0.0100816 91 GTEx DepMap Descartes 0.97 12.50
PLVAP 0.0027660 954 GTEx DepMap Descartes 0.02 0.50
KDR 0.0026646 999 GTEx DepMap Descartes 0.02 0.23
PODXL 0.0025867 1023 GTEx DepMap Descartes 0.68 5.31
CRHBP 0.0011616 1930 GTEx DepMap Descartes 0.00 0.20
F8 0.0002472 3475 GTEx DepMap Descartes 0.04 0.22
HYAL2 0.0002470 3477 GTEx DepMap Descartes 1.59 20.18
GALNT15 0.0002161 3562 GTEx DepMap Descartes 0.01 NA
RASIP1 0.0001092 3915 GTEx DepMap Descartes 0.02 0.38
CALCRL 0.0000787 4024 GTEx DepMap Descartes 0.04 0.31
BTNL9 0.0000116 4294 GTEx DepMap Descartes 0.00 0.03
ARHGAP29 0.0000054 4316 GTEx DepMap Descartes 1.59 9.57
KANK3 -0.0000877 4856 GTEx DepMap Descartes 0.00 0.02
SHE -0.0000911 4880 GTEx DepMap Descartes 0.00 0.00
TEK -0.0000954 4914 GTEx DepMap Descartes 0.00 0.01
MMRN2 -0.0001146 5064 GTEx DepMap Descartes 0.00 0.05
CEACAM1 -0.0001416 5304 GTEx DepMap Descartes 0.00 0.06
TIE1 -0.0001547 5416 GTEx DepMap Descartes 0.00 0.00
CYP26B1 -0.0001628 5478 GTEx DepMap Descartes 0.00 0.00
SLCO2A1 -0.0001722 5554 GTEx DepMap Descartes 0.00 0.03
ROBO4 -0.0001923 5721 GTEx DepMap Descartes 0.00 0.01
NR5A2 -0.0002141 5899 GTEx DepMap Descartes 0.00 0.00
CDH13 -0.0002308 6014 GTEx DepMap Descartes 0.04 0.26
FLT4 -0.0003559 6790 GTEx DepMap Descartes 0.00 0.01
CLDN5 -0.0004279 7179 GTEx DepMap Descartes 0.00 0.00
SHANK3 -0.0004359 7206 GTEx DepMap Descartes 0.03 0.17
ESM1 -0.0005140 7641 GTEx DepMap Descartes 0.00 0.00
CDH5 -0.0005504 7819 GTEx DepMap Descartes 0.00 0.00
EHD3 -0.0005667 7901 GTEx DepMap Descartes 0.14 1.45


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: 2.05e-05
Mean rank of genes in gene set: 4039.05
Median rank of genes in gene set: 2721.5
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
LUM 0.0154739 17 GTEx DepMap Descartes 13.33 277.64
DCN 0.0117293 57 GTEx DepMap Descartes 4.66 37.46
MGP 0.0108435 69 GTEx DepMap Descartes 21.42 689.31
ITGA11 0.0087714 139 GTEx DepMap Descartes 1.69 9.21
COL3A1 0.0071373 223 GTEx DepMap Descartes 9.42 91.63
PCOLCE 0.0071101 225 GTEx DepMap Descartes 16.57 607.02
C7 0.0066044 263 GTEx DepMap Descartes 8.82 90.80
CD248 0.0052130 411 GTEx DepMap Descartes 1.15 23.42
CDH11 0.0044669 521 GTEx DepMap Descartes 1.49 11.99
PDGFRA 0.0027722 950 GTEx DepMap Descartes 1.63 14.22
GLI2 0.0026021 1016 GTEx DepMap Descartes 0.55 4.20
PRRX1 0.0022088 1202 GTEx DepMap Descartes 1.59 22.17
COL1A1 0.0021199 1251 GTEx DepMap Descartes 9.37 81.51
ACTA2 0.0018812 1365 GTEx DepMap Descartes 0.72 25.76
IGFBP3 0.0018054 1429 GTEx DepMap Descartes 2.00 36.30
CCDC80 0.0011818 1914 GTEx DepMap Descartes 1.99 7.55
COL27A1 0.0010799 2020 GTEx DepMap Descartes 0.12 0.90
GAS2 0.0009126 2222 GTEx DepMap Descartes 0.16 3.57
LRRC17 0.0007911 2379 GTEx DepMap Descartes 2.42 61.13
COL6A3 0.0007739 2406 GTEx DepMap Descartes 0.53 2.90
ELN 0.0006717 2572 GTEx DepMap Descartes 0.18 2.53
PCDH18 0.0005719 2720 GTEx DepMap Descartes 0.33 3.06
CLDN11 0.0005707 2723 GTEx DepMap Descartes 0.07 1.29
DKK2 0.0003719 3143 GTEx DepMap Descartes 0.76 11.29
PAMR1 0.0002280 3534 GTEx DepMap Descartes 0.00 0.04
ADAMTS2 0.0002224 3548 GTEx DepMap Descartes 0.12 1.04
FREM1 0.0001650 3727 GTEx DepMap Descartes 0.07 0.40
OGN 0.0000476 4131 GTEx DepMap Descartes 0.01 0.21
ABCA6 -0.0000491 4558 GTEx DepMap Descartes 0.00 0.00
SFRP2 -0.0000669 4691 GTEx DepMap Descartes 0.00 0.00


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: 8223.74
Median rank of genes in gene set: 8501.5
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
SLC35F3 0.0038486 647 GTEx DepMap Descartes 0.60 10.29
ARC 0.0000444 4153 GTEx DepMap Descartes 0.20 3.53
PENK 0.0000373 4188 GTEx DepMap Descartes 0.01 0.18
NTNG1 -0.0000744 4746 GTEx DepMap Descartes 0.25 2.71
KCTD16 -0.0001118 5032 GTEx DepMap Descartes 0.15 0.59
LAMA3 -0.0001130 5046 GTEx DepMap Descartes 0.01 0.04
SLC24A2 -0.0002372 6048 GTEx DepMap Descartes 0.00 0.00
GALNTL6 -0.0002655 6235 GTEx DepMap Descartes 0.07 0.91
CDH12 -0.0002679 6257 GTEx DepMap Descartes 0.00 0.00
CDH18 -0.0002765 6326 GTEx DepMap Descartes 0.04 0.50
TENM1 -0.0002942 6422 GTEx DepMap Descartes 0.02 NA
SORCS3 -0.0003051 6485 GTEx DepMap Descartes 0.00 0.00
AGBL4 -0.0003359 6664 GTEx DepMap Descartes 0.03 0.44
PACRG -0.0003385 6683 GTEx DepMap Descartes 0.00 0.15
KSR2 -0.0003493 6754 GTEx DepMap Descartes 0.00 0.01
CNTN3 -0.0003744 6895 GTEx DepMap Descartes 0.00 0.04
TBX20 -0.0004590 7351 GTEx DepMap Descartes 0.03 1.03
ROBO1 -0.0006752 8392 GTEx DepMap Descartes 0.69 5.05
DGKK -0.0006958 8482 GTEx DepMap Descartes 0.00 0.00
ST18 -0.0007051 8521 GTEx DepMap Descartes 0.00 0.01
EML6 -0.0007055 8524 GTEx DepMap Descartes 0.37 2.17
FGF14 -0.0007957 8962 GTEx DepMap Descartes 0.65 2.75
PCSK2 -0.0008350 9113 GTEx DepMap Descartes 0.00 0.00
GRM7 -0.0008458 9158 GTEx DepMap Descartes 0.01 0.06
CCSER1 -0.0008467 9160 GTEx DepMap Descartes 0.01 NA
SPOCK3 -0.0008576 9202 GTEx DepMap Descartes 0.06 1.10
GCH1 -0.0009421 9521 GTEx DepMap Descartes 0.16 3.06
SLC18A1 -0.0011820 10299 GTEx DepMap Descartes 0.05 0.79
UNC80 -0.0011914 10326 GTEx DepMap Descartes 0.01 0.04
GRID2 -0.0012203 10409 GTEx DepMap Descartes 0.01 0.09


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: 4.77e-01
Mean rank of genes in gene set: 6236.24
Median rank of genes in gene set: 6360
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
BLVRB 0.0092240 125 GTEx DepMap Descartes 3.75 136.08
SELENBP1 0.0038511 645 GTEx DepMap Descartes 0.50 9.91
CAT 0.0025520 1038 GTEx DepMap Descartes 1.28 31.34
MICAL2 0.0023980 1108 GTEx DepMap Descartes 0.91 7.39
SNCA 0.0021294 1246 GTEx DepMap Descartes 1.14 17.97
MARCH3 0.0013459 1757 GTEx DepMap Descartes 0.62 NA
TSPAN5 0.0008329 2320 GTEx DepMap Descartes 2.02 25.41
SLC4A1 0.0001253 3854 GTEx DepMap Descartes 0.00 0.01
FECH 0.0000232 4237 GTEx DepMap Descartes 0.29 2.01
ALAS2 -0.0000698 4716 GTEx DepMap Descartes 0.00 0.00
GYPC -0.0000836 4824 GTEx DepMap Descartes 0.00 0.00
RHD -0.0000987 4933 GTEx DepMap Descartes 0.00 0.02
RGS6 -0.0001376 5263 GTEx DepMap Descartes 0.00 0.00
SLC25A37 -0.0002003 5779 GTEx DepMap Descartes 2.09 23.70
CPOX -0.0002835 6360 GTEx DepMap Descartes 0.24 4.62
TMCC2 -0.0003057 6491 GTEx DepMap Descartes 0.05 0.56
SPTB -0.0005048 7591 GTEx DepMap Descartes 0.02 0.08
TFR2 -0.0005958 8055 GTEx DepMap Descartes 0.05 0.75
ABCB10 -0.0006657 8343 GTEx DepMap Descartes 0.19 2.47
SLC25A21 -0.0007297 8636 GTEx DepMap Descartes 0.00 0.00
TRAK2 -0.0008199 9057 GTEx DepMap Descartes 0.50 4.18
ANK1 -0.0009560 9565 GTEx DepMap Descartes 0.00 0.00
RAPGEF2 -0.0009738 9627 GTEx DepMap Descartes 0.39 2.52
XPO7 -0.0010069 9748 GTEx DepMap Descartes 0.55 5.82
DENND4A -0.0010570 9897 GTEx DepMap Descartes 0.20 1.22
GCLC -0.0011727 10265 GTEx DepMap Descartes 0.32 4.39
SOX6 -0.0015039 11093 GTEx DepMap Descartes 0.02 0.08
SPECC1 -0.0021020 11898 GTEx DepMap Descartes 0.07 0.45
EPB41 -0.0031985 12380 GTEx DepMap Descartes 0.89 7.21
NA NA NA NA NA NA NA NA


Descartes myeloid markers
Top 50 marker genes of myeloid cells in the Decartes fetal adrenal single cell map (https://atlas.brotmanbaty.org/bbi/human-gene-expression-during-development/cell/myeloid/in/adrenal)
Wilcoxon ranksum test P-value for gene set overrepresentation: 4.67e-02
Mean rank of genes in gene set: 5290.37
Median rank of genes in gene set: 5276.5
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
CTSD 0.0072166 215 GTEx DepMap Descartes 4.95 122.88
CTSB 0.0048645 450 GTEx DepMap Descartes 3.59 51.09
RGL1 0.0046617 481 GTEx DepMap Descartes 1.60 17.17
CST3 0.0028802 903 GTEx DepMap Descartes 12.03 183.26
PTPRE 0.0023573 1127 GTEx DepMap Descartes 1.26 11.81
CTSS 0.0023438 1135 GTEx DepMap Descartes 0.11 1.53
CTSC 0.0010895 2005 GTEx DepMap Descartes 4.54 36.23
CD14 0.0004739 2920 GTEx DepMap Descartes 0.02 0.71
MERTK 0.0003302 3255 GTEx DepMap Descartes 0.07 1.08
LGMN 0.0003116 3302 GTEx DepMap Descartes 0.59 14.16
CSF1R 0.0002616 3430 GTEx DepMap Descartes 0.00 0.04
SLCO2B1 0.0001888 3651 GTEx DepMap Descartes 0.01 0.05
CD163L1 -0.0000447 4537 GTEx DepMap Descartes 1.30 14.21
HCK -0.0000646 4674 GTEx DepMap Descartes 0.00 0.00
SPP1 -0.0000994 4940 GTEx DepMap Descartes 0.03 0.56
MS4A4A -0.0001123 5040 GTEx DepMap Descartes 0.00 0.00
FGD2 -0.0001192 5105 GTEx DepMap Descartes 0.00 0.00
CD163 -0.0001272 5175 GTEx DepMap Descartes 0.00 0.00
ADAP2 -0.0001299 5203 GTEx DepMap Descartes 0.00 0.04
TGFBI -0.0001462 5350 GTEx DepMap Descartes 0.65 7.41
ABCA1 -0.0001700 5538 GTEx DepMap Descartes 0.08 0.45
CD74 -0.0001790 5599 GTEx DepMap Descartes 0.00 0.04
CYBB -0.0001850 5661 GTEx DepMap Descartes 0.00 0.00
FGL2 -0.0001891 5703 GTEx DepMap Descartes 0.00 0.00
ATP8B4 -0.0002249 5966 GTEx DepMap Descartes 0.00 0.00
SFMBT2 -0.0003057 6492 GTEx DepMap Descartes 0.18 1.23
SLC9A9 -0.0003254 6620 GTEx DepMap Descartes 0.00 0.07
MSR1 -0.0003454 6726 GTEx DepMap Descartes 0.00 0.00
AXL -0.0003686 6861 GTEx DepMap Descartes 0.62 6.09
HRH1 -0.0004176 7133 GTEx DepMap Descartes 0.05 0.49


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: 7.90e-01
Mean rank of genes in gene set: 6714.11
Median rank of genes in gene set: 7004.5
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
PTN 0.0081589 161 GTEx DepMap Descartes 17.85 601.20
VIM 0.0038763 640 GTEx DepMap Descartes 87.24 1757.36
SFRP1 0.0037791 654 GTEx DepMap Descartes 16.34 195.40
VCAN 0.0024894 1069 GTEx DepMap Descartes 4.46 19.70
EDNRB 0.0022403 1187 GTEx DepMap Descartes 0.08 0.98
LAMC1 0.0021989 1206 GTEx DepMap Descartes 2.07 13.58
GAS7 0.0021572 1229 GTEx DepMap Descartes 0.17 1.11
KCTD12 0.0010919 2003 GTEx DepMap Descartes 1.25 10.69
SOX5 0.0006086 2660 GTEx DepMap Descartes 0.31 2.51
LRRTM4 0.0005688 2726 GTEx DepMap Descartes 0.03 0.47
COL25A1 0.0004323 3009 GTEx DepMap Descartes 0.07 0.51
PMP22 0.0003516 3196 GTEx DepMap Descartes 1.56 44.29
EGFLAM 0.0000257 4232 GTEx DepMap Descartes 0.06 0.77
STARD13 -0.0000024 4345 GTEx DepMap Descartes 0.15 1.39
OLFML2A -0.0000642 4665 GTEx DepMap Descartes 0.02 0.18
ERBB3 -0.0000913 4883 GTEx DepMap Descartes 0.01 0.09
IL1RAPL2 -0.0001011 4952 GTEx DepMap Descartes 0.00 0.00
MPZ -0.0001211 5125 GTEx DepMap Descartes 0.01 0.41
PLP1 -0.0001247 5156 GTEx DepMap Descartes 0.00 0.06
XKR4 -0.0002148 5903 GTEx DepMap Descartes 0.00 0.00
COL18A1 -0.0003061 6496 GTEx DepMap Descartes 0.69 5.19
NRXN3 -0.0003438 6711 GTEx DepMap Descartes 0.01 0.03
IL1RAPL1 -0.0004507 7298 GTEx DepMap Descartes 0.04 0.57
GFRA3 -0.0004667 7394 GTEx DepMap Descartes 0.00 0.00
LAMB1 -0.0005692 7918 GTEx DepMap Descartes 1.92 18.16
SCN7A -0.0006477 8275 GTEx DepMap Descartes 0.01 0.10
PLCE1 -0.0006659 8344 GTEx DepMap Descartes 0.38 1.73
MDGA2 -0.0007233 8603 GTEx DepMap Descartes 0.00 0.00
HMGA2 -0.0007869 8909 GTEx DepMap Descartes 1.04 6.64
PAG1 -0.0008871 9308 GTEx DepMap Descartes 0.12 0.58


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: 6.37e-01
Mean rank of genes in gene set: 6463.76
Median rank of genes in gene set: 6449
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
FERMT3 0.0137798 29 GTEx DepMap Descartes 1.56 34.99
LIMS1 0.0074615 199 GTEx DepMap Descartes 7.01 83.87
TGFB1 0.0062761 298 GTEx DepMap Descartes 2.87 52.46
TMSB4X 0.0061834 303 GTEx DepMap Descartes 89.56 2655.10
P2RX1 0.0023257 1147 GTEx DepMap Descartes 0.01 0.14
PDE3A 0.0017484 1463 GTEx DepMap Descartes 0.38 2.69
TPM4 0.0017069 1484 GTEx DepMap Descartes 11.61 124.91
ITGB3 0.0010077 2100 GTEx DepMap Descartes 0.03 0.23
FLNA 0.0008891 2246 GTEx DepMap Descartes 4.29 24.97
THBS1 0.0007116 2509 GTEx DepMap Descartes 1.50 9.79
RAB27B 0.0004854 2892 GTEx DepMap Descartes 0.40 3.08
PLEK 0.0001421 3798 GTEx DepMap Descartes 0.00 0.00
PSTPIP2 0.0000886 3984 GTEx DepMap Descartes 0.10 1.81
ZYX 0.0000398 4177 GTEx DepMap Descartes 2.12 46.33
GSN 0.0000176 4268 GTEx DepMap Descartes 0.40 3.38
SLC2A3 -0.0000260 4442 GTEx DepMap Descartes 0.13 1.58
MMRN1 -0.0001072 5001 GTEx DepMap Descartes 0.00 0.00
CD84 -0.0001484 5369 GTEx DepMap Descartes 0.00 0.00
VCL -0.0001646 5497 GTEx DepMap Descartes 1.83 12.08
ITGA2B -0.0001943 5735 GTEx DepMap Descartes 0.01 0.21
TUBB1 -0.0002054 5830 GTEx DepMap Descartes 0.00 0.00
GP1BA -0.0002239 5961 GTEx DepMap Descartes 0.00 0.00
FLI1 -0.0002983 6449 GTEx DepMap Descartes 0.02 0.17
MCTP1 -0.0003869 6968 GTEx DepMap Descartes 0.06 0.63
ACTB -0.0004145 7113 GTEx DepMap Descartes 57.35 1265.28
SPN -0.0004224 7152 GTEx DepMap Descartes 0.00 0.00
DOK6 -0.0004441 7249 GTEx DepMap Descartes 0.37 2.14
RAP1B -0.0004610 7367 GTEx DepMap Descartes 4.68 18.14
TRPC6 -0.0007285 8627 GTEx DepMap Descartes 0.00 0.00
UBASH3B -0.0007523 8732 GTEx DepMap Descartes 0.05 0.33


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: 5.21e-01
Mean rank of genes in gene set: 6303.81
Median rank of genes in gene set: 6518
Rank on gene expression program of top 30 genes in gene set:

Genes Weight Rank GTEx DepMap Descartes Mean.Counts Mean.TPM
PTPRC 0.0166774 10 GTEx DepMap Descartes 4.20 43.46
B2M 0.0108168 70 GTEx DepMap Descartes 44.73 970.70
TMSB10 0.0104722 74 GTEx DepMap Descartes 201.82 21711.40
SP100 0.0078802 179 GTEx DepMap Descartes 1.52 15.14
ARHGDIB 0.0073805 204 GTEx DepMap Descartes 1.78 73.29
MSN 0.0050903 426 GTEx DepMap Descartes 3.72 51.15
GNG2 0.0043246 550 GTEx DepMap Descartes 3.37 49.36
CD44 0.0040316 610 GTEx DepMap Descartes 2.11 20.76
CCND3 0.0018353 1396 GTEx DepMap Descartes 1.08 23.14
IKZF1 0.0012119 1878 GTEx DepMap Descartes 0.06 0.59
WIPF1 0.0008156 2345 GTEx DepMap Descartes 0.83 9.98
ARID5B 0.0007680 2415 GTEx DepMap Descartes 1.29 9.39
PLEKHA2 0.0004585 2952 GTEx DepMap Descartes 0.26 2.56
NCALD 0.0004231 3032 GTEx DepMap Descartes 0.42 5.60
ITPKB 0.0001891 3650 GTEx DepMap Descartes 0.21 1.98
CCL5 -0.0000837 4825 GTEx DepMap Descartes 0.00 0.03
PRKCH -0.0001109 5030 GTEx DepMap Descartes 0.04 0.60
ARHGAP15 -0.0001471 5358 GTEx DepMap Descartes 0.00 0.00
MCTP2 -0.0002198 5936 GTEx DepMap Descartes 0.01 0.10
SKAP1 -0.0002469 6119 GTEx DepMap Descartes 0.00 0.00
SCML4 -0.0002816 6348 GTEx DepMap Descartes 0.00 0.00
SAMD3 -0.0003404 6688 GTEx DepMap Descartes 0.00 0.00
RCSD1 -0.0003762 6903 GTEx DepMap Descartes 0.00 0.01
ETS1 -0.0006047 8088 GTEx DepMap Descartes 0.34 3.35
LCP1 -0.0008354 9116 GTEx DepMap Descartes 0.01 0.09
PDE3B -0.0008619 9215 GTEx DepMap Descartes 0.28 2.42
PITPNC1 -0.0009057 9373 GTEx DepMap Descartes 0.42 3.23
BACH2 -0.0009264 9458 GTEx DepMap Descartes 0.03 0.15
TOX -0.0009746 9630 GTEx DepMap Descartes 0.36 4.32
SORL1 -0.0009992 9719 GTEx DepMap Descartes 0.06 0.27


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.


T cells: Tcm/Naive helper T cells (model markers)
CD4+ helper T lymphocytes mainly localized in secondary lymphoid tissues and sustaining the responses by proliferating and producing new effectors:
Wilcoxon ranksum test P-value for gene set overrepresentation: 8.34e-04
Mean rank of genes in gene set: 581.25
Rank on gene expression program of genes in gene set:
Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
TMSB10 0.0104722 74 GTEx DepMap Descartes 201.82 21711.40
CTSL 0.0057966 344 GTEx DepMap Descartes 3.28 NA
FCGRT 0.0040914 598 GTEx DepMap Descartes 2.37 45.22
LTB 0.0020056 1309 GTEx DepMap Descartes 0.02 0.72


Macrophages: Macrophages (model markers)
specialised mononuclear phagocytic cells which recognise:
Wilcoxon ranksum test P-value for gene set overrepresentation: 3.47e-03
Mean rank of genes in gene set: 1385
Rank on gene expression program of genes in gene set:

Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
FTH1 0.0189562 3 GTEx DepMap Descartes 222.31 9126.40
APOE 0.0124783 40 GTEx DepMap Descartes 11.85 580.18
CD5L 0.0010190 2088 GTEx DepMap Descartes 0.00 0.06
APOC1 0.0002708 3409 GTEx DepMap Descartes 0.33 25.28


Mono-mac: Mono-mac (model markers)
mononuclear phagocytes including monocytes and macrophages that are involved in the regulation of innate and adaptive immunity:
Wilcoxon ranksum test P-value for gene set overrepresentation: 5.72e-03
Mean rank of genes in gene set: 1694.75
Rank on gene expression program of genes in gene set:

Genes Weight Rank GTEx DepMap Decartes Mean.Counts Mean.TPM
FTH1 0.0189562 3 GTEx DepMap Descartes 222.31 9126.40
SAT1 0.0035782 707 GTEx DepMap Descartes 1.36 59.74
S100A2 0.0018433 1387 GTEx DepMap Descartes 1.61 77.62
KLRB1 -0.0000656 4682 GTEx DepMap Descartes 0.00 0.00