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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