Table 1 List of 254 genes used at least once in the 30 leave-one-out cross-validation loops

From: Molecular mechanisms of action and prediction of response to oxaliplatin in colorectal cancer cells

Accession

Name

Correlationa

Count in LOOCVb

Biological process (GO)c

AA455003

General transcription factor IIH, polypeptide 1, 62 kDa

−0.77

30

DNA repair

R98008

Progestin and adipoQ receptor family member III

−0.70

30

Biological process unknown

AA417012

Zinc-finger protein 336

−0.67

30

Regulation of transcription, DNA-dependent

AA412691

Nuclear transcription factor Y, alpha

−0.67

30

Regulation of transcription, DNA-dependent

AA030029

Protein kinase C, alpha

−0.65

30

Regulation of cell cycle

R06567

Clone 23907 mRNA sequence

−0.64

30

Biological process unknown

AA521025

G protein pathway suppressor 1

−0.62

30

JNK cascade

AA405769

Phosphoenolpyruvate carboxykinase 1 (soluble)

−0.62

30

Gluconeogenesis

AA608576

Microtubule-associated protein, RP/EB family, member 2

−0.62

30

Cell proliferation

AA083385

BTB (POZ) domain containing 1

−0.62

30

Biological process unknown

W32660

RAP2A, member of RAS oncogene family

−0.61

30

Signal transduction

R46662

RAP2A, member of RAS oncogene family

−0.61

30

Signal transduction

H14343

Cell division cycle 25B

−0.60

30

M phase of mitotic cell cycle

AA480071

Transcription factor 7 (T-cell specific, HMG-box)

−0.60

29

Wnt receptor signaling pathway

AA456014

Hypothetical protein FLJ20580

−0.60

30

Biological process unknown

H09906

2′,3′-cyclic nucleotide 3′ phosphodiesterase

−0.60

30

Synaptic transmission

N51260

KIAA0240

−0.60

29

Biological process unknown

H56069

Glutamate–cysteine ligase, catalytic subunit

−0.59

30

Cysteine metabolism

AA489104

Thyroid hormone receptor interactor 3

−0.59

29

Regulation of transcription, DNA-dependent

T77959

Tripeptidyl peptidase II

−0.59

29

Proteolysis and peptidolysis

AA479196

General transcription factor IIF, polypeptide 2, 30 kDa

−0.59

30

Transcription initiation from Pol II promoter

AA430656

Docking protein 4

−0.58

29

Biological process unknown

H30688

Spectrin, beta, nonerythrocytic 2

−0.58

29

Vesicle-mediated transport

R10570

Hypothetical protein KIAA1434

−0.58

28

Biological process unknown

R54358

Ligase IV, DNA, ATP-dependent

−0.57

27

DNA repair

H08548

ATP citrate lyase

−0.57

27

Coenzyme A biosynthesis

AA418811

Fibrillin 1 (Marfan syndrome)

−0.57

26

Skeletal development

AA410591

Met proto-oncogene (hepatocyte growth factor receptor)

−0.57

28

Cell proliferation

W86653

FK506-binding protein 5

−0.56

27

Protein folding

H11501

Hypothetical protein BC017169

−0.56

27

Transport

AA521490

Limkain b1

−0.56

27

Biological process unknown

AA447691

Pitrilysin metalloproteinase 1

−0.56

27

Activation of MAP/ERK kinase kinase

R42187

ESTs

−0.56

27

Biological process unknown

H89996

CCCTC-binding factor (zinc-finger protein)

−0.56

27

Negative regulation of cell cycle

AA148536

Nucleoporin 98 kDa

−0.56

25

Intracellular protein transport

R01323

Microfibrillar-associated protein 1

−0.56

25

Biological process unknown

AA425401

Serine/threonine kinase 24 (STE20 homolog, yeast)

−0.55

25

Signal transduction

T49159

Serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2

−0.55

24

Antiapoptosis

AA001918

ESTs

−0.55

24

Biological process unknown

N70759

KIAA0996 protein

−0.55

24

Biological process unknown

AA232979

Zinc-finger RNA binding protein

−0.55

19

Biological process unknown

AA521232

ras-related C3 botulinum toxin substrate 2

−0.55

20

Small GTPase mediated signal transduction

AA426311

Mesenchyme homeo box 1

−0.55

21

Development

AA074666

ESTs

−0.54

15

Biological process unknown

AA479888

Rabaptin, RAB GTPase binding effector protein 1

−0.54

14

Endocytosis

AA701929

Bystin-like

−0.54

15

Cell adhesion

AA479771

KIAA0076

−0.54

19

Biological process unknown

R76314

ras homolog gene family, member G (rho G)

−0.54

15

Positive regulation of cell proliferation

AA004484

F-box only protein 9

−0.54

17

Protein modification

AA458840

Cell death-regulatory protein GRIM19

−0.54

9

Apoptosis

AA036974

Amine oxidase, copper containing 3

−0.54

9

Amine metabolism

R28280

Solute carrier family 7, member 1

−0.54

10

Amino acid metabolism

AA045192

Retinoblastoma 1 (including osteosarcoma)

−0.53

8

Negative regulation of cell cycle

H99215

Discs, large homolog 3 (neuroendocrine-dlg, Drosophila)

−0.53

10

Negative regulation of cell proliferation

T71757

Heme oxygenase (decycling) 1

−0.53

6

Heme oxidation

AA453175

Bridging integrator 1

−0.53

7

Negative regulation of cell cycle

R12275

Hypothetical protein FLJ21827

−0.53

6

Biological process unknown

AA478524

M-phase phosphoprotein 6

−0.53

7

M phase of mitotic cell cycle

AA434342

Proline arginine-rich end leucine-rich repeat protein

−0.53

6

Skeletal development

AA459266

Postmeiotic segregation increased 2-like 6

−0.53

5

Mismatch repair

H49592

Guanine nucleotide binding protein (G protein), alpha activating activity polypeptide

−0.53

7

G-protein coupled receptor protein signaling pathway

R99749

B-cell CLL/lymphoma 6 (zinc-finger protein 51)

−0.53

7

Cell growth and/or maintenance

AA621031

KIAA0056 protein

−0.53

7

Biological process unknown

AA232647

Zinc-finger protein 161

−0.52

5

Regulation of transcription from Pol II promoter

AA485214

Nucleobindin 2

−0.52

5

Biological process unknown

AA458973

Polymerase (DNA-directed), delta interacting protein 3

−0.52

3

Biological process unknown

AA608730

HBS1-like (S. cerevisiae)

−0.52

3

Protein biosynthesis

H98688

ESTs

−0.52

4

Biological process unknown

AA425908

ADP-ribosylation factor interacting protein 2 (arfaptin 2)

−0.52

3

Small GTPase mediated signal transduction

AA424937

Protein kinase C, alpha

−0.52

4

Regulation of cell cycle

AA017042

HIV-1 Tat interactive protein, 60 kDa

−0.52

3

Regulation of transcription, DNA-dependent

AA284338

Chromobox homolog 5 (HP1 alpha homolog, Drosophila)

−0.51

2

Chromatin assembly

AA040170

Chemokine (C-C motif) ligand 7

−0.51

3

Antimicrobial humoral response

AA425089

Clock homolog (mouse)

−0.51

4

Circadian rhythm

N58136

Similar to KIAA0393 protein

−0.51

2

Biological process unknown

R24543

Neuroepithelial cell transforming gene 1

−0.51

2

Regulation of cell growth

R15708

Insulin-like 4 (placenta)

−0.51

2

Cell proliferation

W47073

Solute carrier family 20 (phosphate transporter), member 1

−0.51

3

Phosphate transport

AA703187

Solute carrier family 33 (acetyl-CoA transporter), member 1

−0.51

4

Transport

W79444

UBX domain containing 2

−0.51

2

Biological process unknown

R35292

Growth arrest-specific 2 like 1

−0.51

3

Cell cycle arrest

AA406027

CD5 antigen (p56-62)

−0.51

2

Cell proliferation

W06875

Hypothetical protein MGC14816

−0.51

2

Biological process unknown

R14855

F-box only protein 34

−0.50

2

Biological process unknown

R01451

Hypothetical protein KIAA1259

−0.50

1

Biological process unknown

AA449154

Skeletal muscle and kidney enriched inositol phosphatase

−0.50

2

Actin cytoskeleton organization and biogenesis

H48420

Prothymosin alpha

−0.50

1

Biological process unknown

AA455043

Holocarboxylase synthetase

−0.50

2

Protein modification

AA232647

Zinc-finger protein 161

−0.50

2

Regulation of transcription from Pol II promoter

R11490

Translocated promoter region (to activated MET oncogene)

−0.50

2

Transport

T58146

HLA complex P5

−0.50

2

Defense response

H54366

KIAA0034 gene, complete cds

−0.50

2

Biological process unknown

AA406269

Nuclear factor I/X (CCAAT-binding transcription factor)

−0.50

2

DNA replication

R02346

Small nuclear ribonucleoprotein 70 kDa polypeptide (RNP antigen)

−0.50

1

RNA splicing

H64850

Clone 23612 mRNA sequence

−0.50

1

Biological process unknown

N74574

Hypothetical protein MGC9084

−0.49

3

Biological process unknown

N26645

Neurofibromin 1 (neurofibromatosis, von Recklinghausen disease, Watson disease)

−0.49

2

RAS protein signal transduction

R26434

Protein phosphatase 1, catalytic subunit, beta isoform

−0.49

1

Biological process unknown

AA025850

Myosin VA (heavy polypeptide 12, myoxin)

−0.49

1

Transport

H59208

ESTs

−0.49

1

Biological process unknown

AA490721

Splicing factor, arginine/serine-rich 9

−0.49

2

mRNA splice site selection

R10604

Spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2)

−0.49

1

mRNA splicing

R95732

DNA (cytosine-5-)-methyltransferase 2

−0.49

1

DNA methylation

AA149096

Hemopoietic cell kinase

−0.49

2

Biological process unknown

AA489714

Chromosome 9 open reading frame 60

−0.49

1

Biological process unknown

AA045587

TAF12 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 20 kDa

−0.49

2

Regulation of transcription, DNA-dependent

AA485443

Ring finger protein 41

−0.48

1

Biological process unknown

AA085676

ADP-ribosylation factor guanine nucleotide factor 6

−0.48

1

Biological process unknown

W58032

Frizzled-related protein

−0.48

1

Wnt receptor signaling pathway

N71653

Aspartoacylase (aminoacylase 2, Canavan disease)

−0.48

2

Aspartate catabolism

AA004324

Hypothetical protein BC007706

−0.48

1

Biological process unknown

AA441935

Achaete-scute complex-like 1 (Drosophila)

−0.48

1

Cell differentiation

R22050

Topoisomerase (DNA) II beta (180kD)

−0.48

1

DNA topological change

W31074

Fatty-acid-Coenzyme A ligase, long-chain 3

−0.48

3

Fatty acid metabolism

T72581

Matrix metalloproteinase 9

−0.48

3

Collagen catabolism

AA453105

Histone 1, H2ac

−0.48

1

Nucleosome assembly

AA988746

WD repeat and SOCS box containing protein 2

−0.48

1

Intracellular signaling cascade

AA495766

Chromosome condensation 1-like

−0.48

1

Biological process unknown

AA489699

COP9 constitutive photomorphogenic homolog subunit 8 (Arabidopsis)

−0.48

1

Biological process unknown

T65902

Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)

−0.48

1

mRNA splice site selection

AA446908

Kinesin family member 3C

−0.47

1

Biological process unknown

AA047812

Origin recognition complex, subunit 2-like (yeast)

−0.47

1

DNA replication

AA452566

Peroxisomal membrane protein 3, 35 kDa (Zellweger syndrome)

−0.47

1

Peroxisome organization and biogenesis

R91948

Pantothenate kinase 3

−0.47

1

Coenzyme A biosynthesis

T52894

Myosin light chain 1 slow a

−0.47

1

Muscle development

AA001749

Microtubule-associated protein, RP/EB family, member 1

−0.47

1

Cell proliferation

AA430035

Reticulon 3

−0.47

1

Biological process unknown

N79179

Pyruvate dehydrogenase complex, lipoyl-containing component X; E3-binding protein

−0.47

1

Biological process unknown

R13911

T54 protein

−0.47

1

Biological process unknown

AA447579

Hypothetical protein FLJ11101

−0.47

1

Biological process unknown

AA454639

F-box only protein 9

−0.47

1

Protein modification

AA476460

Protein tyrosine phosphatase, receptor-type, Z polypeptide 1

−0.46

2

One-carbon compound metabolism

AA147642

cDNA: FLJ21949 fis, clone HEP04922

−0.46

1

Biological process unknown

AA479954

Similar to RNA polymerase B transcription factor 3

−0.46

1

Biological process unknown

N80382

Phosphodiesterase 6D, cGMP-specific, rod, delta

−0.46

1

Visual perception

R88246

Adrenergic, beta, receptor kinase 1

−0.45

1

Signal transduction

AA150895

Hypothetical protein MGC26690

−0.45

1

Biological process unknown

AA680407

Similar to ubiquitin binding protein

−0.45

1

Biological process unknown

AA063398

Chromosome 15 open reading frame 15

−0.45

1

Protein biosynthesis

AA459572

Protein phosphatase 1, regulatory subunit 7

−0.45

1

Biological process unknown

AA401429

Dynein light chain 2

−0.45

2

Microtubule-based process

AA434130

Thioredoxin reductase 2

−0.44

1

Response to oxygen radicals

AA453593

BB1=malignant cell expression-enhanced gene/tumor progression-enhanced gene

−0.44

1

Protein arginylation

T77891

ESTs

−0.44

1

Biological process unknown

N48137

Glycophorin E

−0.44

1

Biological process unknown

N30147

CDNA FLJ34899 fis, clone NT2NE2018594.

−0.43

1

Biological process unknown

AA011185

Hypothetical protein FLJ14431

−0.43

1

Metabolism

N58558

Serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4

−0.43

1

Acute-phase response

AA055221

Apoptosis, caspase activation inhibitor

−0.43

1

Apoptosis

AA280677

Zinc-finger protein 258

−0.43

1

Development

AA026709

Dedicator of cytokinesis 6

−0.43

1

Biological process unknown

AA487070

Similar to CGI-55 protein (LOC152502), mRNA

−0.43

1

Biological process unknown

AA284282

Hypothetical protein FLJ30277

−0.43

1

Biological process unknown

T57859

Natural killer cell group 7 sequence

−0.42

1

Biological process unknown

AA448001

TBP-like 1

−0.42

1

Regulation of transcription

N92085

ESTs

−0.41

1

Biological process unknown

AA423867

Multimerin

−0.41

1

Blood coagulation

AA443302

ras homolog gene family, member E

−0.38

1

Small GTPase mediated signal transduction

H52361

ESTs

−0.37

1

Biological process unknown

AA482198

Mannose phosphate isomerase

−0.36

1

Carbohydrate metabolism

H66030

Centrosomal protein 1

−0.36

1

Biological process unknown

AA458472

Major histocompatibility complex, class II, DQ beta 1

−0.36

1

Immune response

AA447696

Yippee protein

−0.35

1

Biological process unknown

AA419164

Retinoic acid receptor, beta

−0.34

1

Cell growth and/or maintenance

AA453849

ATP synthase, H+ transporting, mitochondrial F0 complex, subunit b, isoform 1

−0.32

1

ATP synthesis coupled proton transport

T96688

PBX/knotted 1 hoemobox 1

−0.32

1

Biological process unknown

R41732

Mitogen-activated protein kinase 8 interacting protein 1

0.28

1

Vesicle-mediated transport

AA419622

Hypothetical protein FLJ10134

0.31

1

Biological process unknown

AA128017

Clone DNA100312 VSSW1971 (UNQ1971) mRNA

0.33

1

Biological process unknown

R23810

Full-length insert cDNA YI09H09

0.33

1

Biological process unknown

T90871

EST

0.35

1

Biological process unknown

AA005228

ESTs

0.39

1

Biological process unknown

AA004811

ESTs

0.39

1

Biological process unknown

R54797

ESTs, Weakly similar to reverse transcriptase homolog

0.39

1

Biological process unknown

T95930

ESTs

0.40

1

Biological process unknown

AA058713

ESTs

0.41

1

Biological process unknown

T84865

ESTs

0.41

1

Biological process unknown

N46943

GGA binding partner

0.41

1

Biological process unknown

AA677403

Glycoprotein hormones, alpha polypeptide

0.42

1

Cell–cell signaling

AA872379

SMT3 suppressor of mif two 3 homolog 1 (yeast)

0.42

1

Biological process unknown

T96870

ESTs

0.42

1

Biological process unknown

AA610111

Hypothetical protein FLJ21868

0.43

1

Biological process unknown

AA400121

A-kinase anchoring protein 28

0.44

1

Biological process unknown

H72319

ESTs

0.44

1

Biological process unknown

H23124

Olfactomedin related ER localized protein

0.44

1

Biological process unknown

AA447515

MAX dimerization protein 4

0.44

1

Negative regulation of cell proliferation

N62914

EST

0.44

1

Biological process unknown

T53298

Insulin-like growth factor binding protein 7

0.45

1

Negative regulation of cell proliferation

AA421488

CDNA FLJ26472 fis, clone KDN04506

0.46

1

Biological process unknown

H93837

Apolipoprotein B (including Ag(x) antigen)

0.46

1

Lipid transport

N78306

ESTs

0.46

1

Biological process unknown

N32502

ESTs

0.46

1

Biological process unknown

AA488672

Kruppel-like factor 7 (ubiquitous)

0.47

1

Regulation of transcription from Pol II promoter

AA053815

Hypothetical protein FLJ11767

0.47

1

Biological process unknown

R02716

Hypothetical protein FLJ14639

0.47

1

Biological process unknown

AA701545

Ribonuclease, RNase A family, k6

0.47

1

RNA catabolism

R93069

ESTs

0.47

1

Biological process unknown

T54121

Cyclin E1

0.48

2

Regulation of cell cycle

H57309

Snail homolog 2 (Drosophila)

0.48

1

Development

T56948

Pumilio homolog 1 (Drosophila)

0.48

1

Biological process unknown

N93191

Voltage-dependent calcium channel gamma subunit-like protein

0.48

1

Biological process unknown

W33154

Formin binding protein 1

0.49

1

Biological process unknown

T95113

Viperin

0.49

1

Biological process unknown

AA679177

Butyrate-induced transcript 1

0.49

2

Activation of JUNK

W89074

ESTs

0.49

1

Biological process unknown

R97540

Down syndrome critical region gene 3

0.49

2

Intracellular protein transport

W60581

Brain expressed, X-linked 1

0.49

2

Biological process unknown

AA037352

Paired box gene 1

0.50

2

Biological process unknown

T53389

Fc fragment of IgG binding protein

0.50

1

Biological process unknown

N53480

Clone IMAGE:4794941, mRNA

0.50

3

Biological process unknown

AA410604

CDC16 cell division cycle 16 homolog (S. cerevisiae)

0.50

1

Cell cycle

N22827

Ferredoxin 1

0.50

1

Steroid metabolism

R95893

EST

0.50

1

Biological process unknown

AA872397

Lectin, galactoside-binding, soluble, 2 (galectin 2)

0.50

2

Heterophilic cell adhesion

H72588

ESTs

0.51

2

Biological process unknown

N92048

ESTs

0.51

1

Biological process unknown

N54793

ESTs

0.51

3

Biological process unknown

AA136699

ESTs

0.51

1

Biological process unknown

AA131466

Leukemia inhibitory factor receptor

0.51

4

Cell surface receptor linked signal transduction

N33331

Peroxisome proliferative activated receptor, delta

0.52

3

Lipid metabolism

AA668527

Mucosal vascular addressin cell adhesion molecule 1

0.52

5

Cell adhesion

AA677706

Lactotransferrin

0.52

3

Iron ion transport

AA459390

Hypothetical protein FLJ22169

0.53

6

Biological process unknown

W02624

Kelch repeat and BTB (POZ) domain containing 2

0.53

6

Biological process unknown

AA984940

Ribonuclease, RNase A family, 2 (liver, eosinophil-derived neurotoxin)

0.53

11

RNA catabolism

AA464180

X-linked protein

0.53

9

Biological process unknown

R89765

Full-length insert cDNA clone YP91F02

0.54

11

Biological process unknown

AA102068

F-box and leucine-rich repeat protein 8

0.54

13

Biological process unknown

AA431429

ESTs, Weakly similar to A-kinase anchor protein DAKAP550 [D. melanogaster]

0.54

20

Biological process unknown

AA009671

ESTs

0.54

21

Biological process unknown

AA458965

Natural killer cell transcript 4

0.55

19

Cell adhesion

H51438

ESTs

0.55

24

Biological process unknown

AA447593

Dynein, axonemal, light intermediate polypeptide 1

0.55

26

Cell motility

T98717

ESTs

0.56

26

Biological process unknown

AA485358

Seven transmembrane domain protein

0.56

25

Biological process unknown

AA022935

Formin-like 2

0.56

27

Regulation of transcription, DNA-dependent

H87770

Full-length insert cDNA YI27F12

0.56

25

Biological process unknown

AA024866

Hypothetical protein FLJ32731

0.56

28

Biological process unknown

AA055992

Hypothetical protein MGC17791

0.57

28

Biological process unknown

R92446

Cytokine receptor-like molecule 9

0.57

28

Biological process unknown

AA443971

ESTs

0.57

29

Biological process unknown

N79813

CDNA FLJ45930 fis, clone PLACE7000707

0.59

28

Biological process unknown

W80688

Zinc finger, CW-type with coiled-coil domain 1

0.59

29

Biological process unknown

N72185

ESTs

0.60

30

Biological process unknown

AA136666

CDNA: FLJ22750 fis, clone KAIA0478

0.60

30

Biological process unknown

AA133167

KIAA1644 protein

0.60

30

Biological process unknown

T84703

ESTs

0.61

30

Biological process unknown

AA029997

Collagen, type IV, alpha 5 (Alport syndrome)

0.62

30

Biological process unknown

AA953975

Nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, epsilon

0.62

30

I-kappaB kinase/NF-kappaB cascade

W88801

Trans-prenyltransferase

0.63

30

Isoprenoid biosynthesis

N70632

Alcohol dehydrogenase, iron containing, 1

0.65

30

Metabolism

AA701081

Leucine-rich repeat transmembrane neuronal 2 protein

0.65

30

Biological process unknown

W93482

LOC374841 (LOC374841), mRNA

0.67

30

Biological process unknown

R20886

Stanniocalcin 2

0.68

30

Cell–cell signaling

  1. aCorrelation coefficient between expression levels in 30 colorectal cancer cell lines (Ln) and the corresponding proportion of apoptotic cells after 72 h exposure to 10 μ M oxaliplatin (Ln). The correlation of all 9216 genes can be found in our website: www.augenlichtlab.com.
  2. bNumber of times used in the leave-one-out cross-validation process.
  3. cBiological process from Gene Ontology.