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Table 1 Enrichment tests for the list of 287 genes and 688 genes

From: A factor model to analyze heterogeneity in gene expression

LIST OF 287 GENES
GOID GO Term Size Count Pvalue HGNC ID
GO.0006470 protein amino acid dephosphorylation 56 5 0.015 ACP1, PTPN14, PTPRE, PTP4A3, PTPN6
GO.0006725 cellular aromatic compound metabolic process 38 4 0.017 PPME1, GART, MOCS1, ALDH6A1
GO.0007259 JAK STAT cascade 9 2 0.022 SOCS1, STAMBP
GO.0043543 protein amino acid acylation 9 2 0.022 NULL, ZDHHC17
GO.0044259 multicellular macromolecule metabolic process 10 2 0.027 ACE2, SERPINH1
GO.0008033 tRNA processing 26 3 0.0296 TSEN15, FARS2, NSUN2
GO.0033002 muscle cell proliferation 11 2 0.032 NOX1, BMP10
GO.0050730 regulation of peptidyl tyrosine phosphorylation 12 2 0.038 SOCS1, EGFR
Kegg ID Kegg pathway Size Count Pvalue HGNC ID
map04320 Dorso ventral axis formation 9 3 2.38E-03 EGFR, SPIRE1, ETS1
LIST OF 688 GENES
GOID GO Term Size Count Pvalue HGNC ID
GO.0006470 protein amino acid dephosphorylation 56 10 1.80E-03 ACP1, PPM1E, PTPN14, PTPRE, PTP4A3, PPM1G, PTPRU, PPP3CB, PPM1L, PTPRF
GO.0046483 heterocycle metabolic process 33 7 3.21E-03 AMBP, GART, P4HA2, HMOX2, AFMID, MTHFS, ALDH6A1
GO.0051186 cofactor metabolic process 64 10 4.97E-03 AMBP, TXNRD3, NOX1, HMOX2, AFMID, GGT7, MTHFS, MOCS1, HMGCS1, ACO2
GO.0016202 regulation of striated muscle development 15 4 0.011 MBNL3, LEF1, NRG1, BMP4
GO.0007259 JAK STAT cascade 9 3 0.014 SOCS1, HCLS1, STAMBP
GO.0040011 locomotion 111 13 0.017 PRKG1, EDNRB, ACE2, NOX1, EGFR, NRG1, BMP10, ARAP3, JPH3, VHL, VAX1, DAB1, LAMA2
GO.0001932 regulation of protein amino acid phosphorylation 26 5 0.019 PDGFA, SOCS1, HCLS1, EGFR, BMP4
GO.0048585 negative regulation of response to stimulus 10 3 0.020 AMBP, PPP3CB, FABP7
GO.0006534 cysteine metabolic process 4 2 0.021 CBS, CDO1
GO.0002274 myeloid leukocyte activation 11 3 0.026 IRF4, LCP2, NDRG1
GO.0006725 cellular aromatic compound metabolic process 38 6 0.026 PPME1, GART, AFMID, MTHFS, MOCS1, ALDH6A1
GO.0007185 transmembrane receptor tyrosine phosphatase signaling 5 2 0.033 PTPRE, PTPRF
GO.0007271 synaptic transmission cholinergic 5 2 0.033 CHRNA4, LAMA2
GO.0000097 sulfur amino acid biosynthetic process 5 2 0.033 CBS, CDO1
GO.0006700 C21 steroid hormone biosynthetic process 5 2 0.033 STAR, CYP17A1
GO.0006787 porphyrin catabolic process 5 2 0.033 AMBP, HMOX2
GO.0001764 neuron migration 12 3 0.033 PRKG1, VAX1, DAB1
GO.0030509 BMP signaling pathway 21 4 0.036 SOSTDC1, BMP10, MSX2, BMP4
GO.0045321 leukocyte activation 64 8 0.040 SWAP70, CHRNA4, FKBP1B, IRF4, LCP2, PPP3CB, NDRG1, SFRS17A
GO.0006790 sulfur metabolic process 32 5 0.043 CBS, CDO1, TXNRD3, GGT7, CHST1
GO.0018193 peptidyl amino acid modification 43 6 0.045 PDGFA, SOCS1, P4HA2, HCLS1, EGFR, MAP2
GO.0008211 glucocorticoid metabolic process 6 2 0.048 STAR, CYP17A1
GO.0006769 nicotinamide metabolic process 6 2 0.048 NOX1, AFMID
GO.0030111 regulation of Wnt receptor signaling pathway 14 3 0.050 SENP2, LEF1, SENP2
Kegg ID Kegg pathway Size Count Pvalue HGNC ID
map00630 Glyoxylate and dicarboxylate metabolism 9 4 1.87E-03 GLYCTK, HYI, AFMID, ACO2
map00140 C21 Steroid hormone metabolism 6 3 5.11E-03 DHCR7, HSD11B1, CYP17A1
map04320 Dorso ventral axis formation 9 3 0.018 EGFR, SPIRE1, ETS1
map04012f ErbB signaling pathway 35 6 0.026 PIK3R5, PLCG1, PAK3, EGFR, NRG1, PTK2
  1. Enrichment tests were performed using an R program (see Methods section) with GO BP terms and Kegg pathways. The tests were done on the list of 287 genes found using the classical approach and the list of 688 genes found by FAMT. For each enriched term, the identifier (ID), the biological term, the size of the whole list of genes related to the term (size), the number of genes in the sub-list related to the term (count), the pvalue of the test and the HGNC Hugo abbreviations of the related genes are given. Italic terms are those which are present in both lists.