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Table 4 Genes on pathway, relevance accounts, and estimated parameters

From: Survival associated pathway identification with group L p penalized global AUC maximization

w i GeneID Gene Name
ECM-receptor interaction (relevance counts: 200)
0.2239 CD36 cd36 antigen (collagen type i receptor, thrombospondin receptor)
0.0409 FNDC1 fibronectin type iii domain containing 1
0.0746 SV2C synaptic vesicle glycoprotein 2c
0.0804 SDC1 syndecan 1
-0.1255 FN1 fibronectin 1
0.0211 LAMC1 laminin, gamma 1 (formerly lamb2)
-0.0854 GP5 glycoprotein v (platelet)
-0.1130 CD47 cd47 antigen (rh-related antigen, integrin-associated signal transducer)
-0.1296 THBS2 thrombospondin 2
-0.0547 COL1A2 collagen, type i, alpha 2
-0.1024 COL5A2 collagen, type v, alpha 2
0.0861 LAMB4 laminin, beta 4
-0.0315 COL1A1 collagen, type i, alpha 1
0.0395 AGRN agrin RG
Focal adhesion (relevance counts 145)
0.0054 PAK3 p21 (cdkn1a)-activated kinase 3
0.0446 PIK3R3 phosphoinositide-3-kinase, regulatory subunit 3 (p55, gamma)
0.0044 PDPK1 3-phosphoinositide dependent protein kinase-1
-0.0045 BAD bcl2-antagonist of cell death
0.0087 PARVA parvin, alpha
-0.0144 FN1 fibronectin 1
0.0041 LAMC1 laminin, gamma 1 (formerly lamb2)
-0.0202 PARVG parvin, gamma
-0.0158 THBS2 thrombospondin 2
0.0134 PPP1R12A protein phosphatase 1, regulatory (inhibitor) subunit 12a
-0.0044 SOS1 son of sevenless homolog 1 (drosophila)
-0.0084 COL1A2 collagen, type i, alpha 2
-0.0122 COL5A2 collagen, type v, alpha 2
0.0091 LAMB4 laminin, beta 4 RG Homo sapiens
-0.0068 RAF1 v-raf-1 murine leukemia viral oncogene homolog 1
-0.0038 ACTN1 actinin, alpha 1
-0.0034 COL1A1 collagen, type i, alpha 1
-0.0067 GSK3B glycogen synthase kinase 3 beta
-0.0065 MAPK8 mitogen-activated protein kinase 8
-0.0030 MYL7 myosin, light polypeptide 7, regulatory
Neuroactive ligand-receptor interaction (relevance counts: 200)
0.0894 P2RY6 pyrimidinergic receptor p2y, g-protein coupled, 6
-0.2753 PTAFR platelet-activating factor receptor
0.1648 GLRA3 glycine receptor, alpha 3
0.0857 FPRL1 formyl peptide receptor-like 1
-0.1783 EDNRA endothelin receptor type a
0.3233 HRH4 histamine receptor h4
0.2106 GRM2 glutamate receptor, metabotropic 2
-0.1112 GRIN1 glutamate receptor, ionotropic, n-methyl d-aspartate 1
-0.0220 PTHR1 parathyroid hormone receptor 1
0.0971 OPRM1 opioid receptor, mu 1
-0.4303 CTSG cathepsin g
-0.0404 P2RY8 purinergic receptor p2y, g-protein coupled, 8
-0.0783 BDKRB1 bradykinin receptor b1
0.3247 FSHR follicle stimulating hormone receptor
-0.1430 ADRA1B adrenergic, alpha-1b-, receptor
0.1464 C3AR1 complement component 3a receptor 1
0.1120 P2RX2 purinergic receptor p2x, ligand-gated ion channel, 2
0.0311 AVPR1B arginine vasopressin receptor 1b
0.2646 FPR1 formyl peptide receptor 1
0.2003 GABRA5 gamma-aminobutyric acid (gaba) a receptor, alpha 5
-0.0278 PRLR prolactin receptor
-0.1070 ADORA1 adenosine a1 receptor
0.2652 HTR7 5-hydroxytryptamine (serotonin) receptor 7 (adenylate cyclase-coupled)
-0.0194 GABRA4 gamma-aminobutyric acid (gaba) a receptor, alpha 4
0.0145 GHRHR growth hormone releasing hormone receptor
-0.3163 MAS1 mas1 oncogene
-0.0760 PTGER3 prostaglandin e receptor 3 (subtype ep3)
0.2196 PARD3 par-3 partitioning defective 3 homolog (c. elegans)
Ubiquitin mediated proteolysis (relevance counts: 200)
0.0186 UBE2B ubiquitin-conjugating enzyme e2b (rad6 homolog)
-0.0677 CUL4A cullin 4a
0.0051 PML promyelocytic leukemia
-0.1023 UBE3B ubiquitin protein ligase e3b
-0.1581 UBE3C ubiquitin protein ligase e3c
0.1390 BTRC beta-transducin repeat containing
-0.0669 HERC3 hect domain and rld 3
0.00009 RBX1 ring-box 1
0.0011 CUL5 cullin 5
0.0267 ANAPC4 anaphase promoting complex subunit 4
-0.0253 UBE2L3 ubiquitin-conjugating enzyme e2l 3
0.0096 KEAP1 kelch-like ech-associated protein 1
-0.0267 UBE2E1 ubiquitin-conjugating enzyme e2e 1 (ubc4/5 homolog, yeast)
0.0116 CBL cas-br-m (murine) ecotropic retroviral transforming sequence
0.0328 BIRC6 baculoviral iap repeat-containing 6 (apollon)
Porphyrin and chlorophyll metabolism (relevance counts: 185)
0.0330 BLVRA biliverdin reductase a
-0.0103 FTH1 ferritin, heavy polypeptide 1
0.0227 ALAD aminolevulinate, delta-, dehydratase
0.1983 HMOX1 heme oxygenase (decycling) 1
0.0070 UROS uroporphyrinogen iii synthase (congenital erythropoietic porphyria)
-0.1596 GUSB glucuronidase, beta
0.0077 UGT2B15 udp glucuronosyltransferase 2 family, polypeptide b15
Calcium signaling pathway (relevance counts: 200)
-0.0025 BST1 bone marrow stromal cell antigen 1
0.0003 BDKRB1 bradykinin receptor b1
-0.0016 PTAFR platelet-activating factor receptor
-0.0002 ADRA1B adrenergic, alpha-1b-, receptor
-0.0007 PPP3CC protein phosphatase 3 (formerly 2b), catalytic subunit, gamma isoform
-0.0001 ADCY7 adenylate cyclase 7
0.0008 GNA11 guanine nucleotide binding protein (g protein), alpha 11 (gq class)
-0.0013 AVPR1B arginine vasopressin receptor 1b
0.0014 P2RX2 purinergic receptor p2x, ligand-gated ion channel, 2
-0.0013 CACNA1E calcium channel, voltage-dependent, alpha 1e subunit
0.0004 EDNRA endothelin receptor type a
0.00009 SLC8A1 solute carrier family 8 (sodium/calcium exchanger), member 1
0.0006 CACNA1B calcium channel, voltage-dependent, l type, alpha 1b subunit
-0.0013 PLCD1 phospholipase c, delta 1
-0.0029 HTR7 5-hydroxytryptamine (serotonin) receptor 7 (adenylate cyclase-coupled)
0.0014 GRIN1 glutamate receptor, ionotropic, n-methyl d-aspartate 1
0.0028 CAMK2A calcium/calmodulin-dependent protein kinase (cam kinase) ii alpha
-0.0024 CACNA1I calcium channel, voltage-dependent, alpha 1i subunit
-0.0002 TNNC1 troponin c type 1 (slow)
0.0009 PTGER3 prostaglandin e receptor 3 (subtype ep3)
0.0012 CACNA1F calcium channel, voltage-dependent, alpha 1f subunit
Fatty acid metabolism (relevance counts: 192)
0.0043 ACSL3 acyl-coa synthetase long-chain family member 3
0.0675 ALDH2 aldehyde dehydrogenase 2 family (mitochondrial)
-0.0491 ACAT2 acetyl-coenzyme a acetyltransferase 2 (acetoacetyl coenzyme a thiolase)
0.0120 ALDH1B1 aldehyde dehydrogenase 1 family, member b1
0.0597 CYP4A11 cytochrome p450, family 4, subfamily a, polypeptide 11
-0.1447 ACADSB acyl-coenzyme a dehydrogenase, short/branched chain
0.0736 CPT1A carnitine palmitoyltransferase 1a (liver)
0.1075 CPT1B carnitine palmitoyltransferase 1b (muscle)
-0.0366 ACADVL acyl-coenzyme a dehydrogenase, very long chain
0.2168 ADH4 alcohol dehydrogenase 4 (class ii), pi polypeptide
MAPK signaling pathway (relevance counts: 200)
-0.1570 PLA2G10 phospholipase a2, group x
-0.2415 MAPKAPK5 mitogen-activated protein kinase-activated protein kinase 5
-0.1636 IL1B interleukin 1, beta
-0.0651 ZAK sterile alpha motif and leucine zipper containing kinase azk
0.0572 PPP3CC protein phosphatase 3 (formerly 2b), catalytic subunit, gamma isoform
-0.0674 MAP3K2 mitogen-activated protein kinase kinase kinase 2
-0.1729 JUND jun d proto-oncogene
-0.1718 SOS1 son of sevenless homolog 1 (drosophila)
0.1082 FGF14 fibroblast growth factor 14
0.3102 PTPN5 protein tyrosine phosphatase, non-receptor type 5
-0.3903 CACNB1 calcium channel, voltage-dependent, beta 1 subunit
0.2678 MAP3K7 mitogen-activated protein kinase kinase kinase 7
0.3176 CACNG8 calcium channel, voltage-dependent, gamma subunit 8
0.0893 FGF19 fibroblast growth factor 19
-0.0853 RRAS2 related ras viral (r-ras) oncogene homolog 2
0.0215 NLK nemo-like kinase
0.0452 MAP4K4 mitogen-activated protein kinase kinase kinase kinase 4
0.1639 CACNA1E calcium channel, voltage-dependent, alpha 1e subunit
-0.0290 ARRB1 arrestin, beta 1
-0.1169 STK4 serine/threonine kinase 4
0.1008 CACNA1B calcium channel, voltage-dependent, l type, alpha 1b subunit
0.0839 MOS v-mos moloney murine sarcoma viral oncogene homolog
-0.1244 MEF2C mads box transcription enhancer factor 2, polypeptide c
0.1572 RAF1 v-raf-1 murine leukemia viral oncogene homolog 1
0.1757 MAPK8IP1 mitogen-activated protein kinase 8 interacting protein 1
0.2908 IKBKB inhibitor of kappa light polypeptide gene enhancer in b-cells, kinase beta
-0.3452 CACNA1I calcium channel, voltage-dependent, alpha 1i subunit
-0.2473 MAPK8 mitogen-activated protein kinase 8
-0.2339 CACNA1F calcium channel, voltage-dependent, alpha 1f subunit
0.0979 CD14 cd14 antigen
-0.1047 MRAS muscle ras oncogene homolog