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Table 3 List of most differentially methylated genes in non-small cell carcinoma

From: Genome-wide DNA methylation profiling of non-small cell lung carcinomas

  Gene Log2ratio Gene class/type/ biological function Gene name HGNC ID
Common in all tumors BARX1 4.8 transcription regulator BARX homeobox 1 HGNC:955
PAX9 4.3 transcription regulator paired box 9 HGNC:8623
OTX1 4.0 transcription regulator orthodenticle homeobox 1 HGNC:8521
NPR3 3.8 G-protein coupled receptor natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C) HGNC:7945
FGF12 3.7 growth factor fibroblast growth factor 12 HGNC:3668
ONECUT2 3.6 transcription regulator one cut homeobox 2 HGNC:8139
PRDM14 3.5 transcription regulator PR domain containing 14 HGNC:14001
RAX 3.5 transcription regulator retina and anterior neural fold homeobox HGNC:18662
SHOX2 3.3 transcription regulator short stature homeobox 2 HGNC:10854
DMRTA2 3.1 transcription regulator DMRT-like family A2 HGNC:13908
FER1L4 3.1 unknown fer-1-like 4 (Caenorhabditis. elegans) pseudogene HGNC:15801
SIX6 3.1 transcription regulator SIX homeobox 6 HGNC:10892
GATA3 3 transcription regulator GATA binding protein 3 HGNC:4172
SKOR1 3 transcription regulator SKI familytranscriptional corepressor 1 HGNC:21326
HOXA9 3 transcription regulator homeobox A9 HGNC:5109
SALL1 2.9 transcription regulator sal-like 1 (Drosophila) HGNC:10524
IRX2 2.7 transcription regulator iroquois homeobox 2 HGNC:14359
GRIK2 2.7 ion channel glutamate receptor, ionotropic, kainate 2 HGNC:4580
SATB2 2.6 transcription regulator SATB homeobox 2 HGNC:21637
MEIS1 2.5 transcription regulator Meis homeobox 1 HGNC:7000
VAX1 2.4 transcription regulator ventral anterior homeobox 1 HGNC:12660
TBX15 2.3 transcription regulator T-box 15 HGNC:11594
CNTD2 −2.4 unknown cyclin N-terminal domain containing 2 HGNC:25805
ZMYND10 −2.6 unknown zinc finger, MYND-type containing 10 HGNC:19412
MYC −2.9 transcription regulator v-myc myelocytomatosis viral oncogene homolog (avian) HGNC:7553
TSPAN9 −2.9 Plasma Membrane tetraspanin 9 HGNC:21640
NAV1 −3.1 unknown neuron navigator 1 HGNC:15989
CPEB3 −3.4 unknown cytoplasmic polyadenylation element binding protein 3 HGNC:21746
Unique for squamous cell carcinomas TRAPPC9 6.5 cell differentiation trafficking protein particle complex 9 HGNC:30832
ABHD2 6.3 hydrolase abhydrolase domain containing 2 HGNC:18717
CTNND1 6.2 transcrption regulator catenin (cadherin-associated protein), delta 1 HGNC:2515
HIST1H2BB 6.2 histone protein histone cluster 1, H2bb HGNC:4751
EMP1 5.8 protein binding epithelial membrane protein 1 HGNC:3333
TBL1XR1 5.6 transcription regulator transducin (beta)-like 1 X-linked receptor 1 HGNC:29529
NXPH1 5.6 protein binding neurexophilin 1 HGNC:20693
ZIC4 5.6 transcription regulator Zic family member 4 HGNC:20393
AOAH 5.4 hydrolase acyloxyacyl hydrolase (neutrophil) HGNC:548
ACTN4 5.4 transporter actinin, alpha 4 HGNC:166
C1orf21 5.2 unknown chromosome 1 open reading frame 21 HGNC:15494
PACSIN2 5.2 transporter protein kinase C and casein kinase substrate in neurons 2 HGNC:8571
PMM2 5.2 isomerase phosphomannomutase 2 HGNC:9115
DOT1L 5.1 histone methyltransferase DOT1-like, histone H3 methyltransferase (Sacchormyces. cerevisiae) HGNC:24948
WWP2 5 e3 ubiquitin-protein ligase WW domain containing E3 ubiquitin protein ligase 2 HGNC:16804
GTF3C1 5 transcription regulator generaltranscription factor IIIC, polypeptide 1, alpha 220 kDa HGNC:4664
MDN1 5 nuclear chaperone MDN1, midasin homolog (yeast) HGNC:18302
DIDO1 5 transcrption regulator death inducer-obliterator 1 HGNC:2680
HIST1H3C 5 histone protein histone cluster 1, H3c HGNC:4768
ANKRD13B 4.9 unknown ankyrin repeat domain 13B HGNC:26363
CALCB 4.9 hormone calcitonin-related polypeptide beta HGNC:1438
PTPRA 4.9 phosphatase protein tyrosine phosphatase, receptor type, A HGNC:9664
STAT5A 4.8 transcription regulator signal transducer and activator of transcription 5A HGNC:11366
LIMK1 4.8 cytoskeleton LIM domain kinase 1 HGNC:6613
SLC23A2 4.7 transporter solute carrier family 23 (nucleobase transporters), member 2 HGNC:10973
BARX1 4.5 transcription regulator BARX homeobox 1 HGNC:955
NHS 4.5 unknown Nance-Horan syndrome (congenital cataracts and dental anomalies) HGNC:7820
MTAP 4.5 glycosyltransferase methylthioadenosine phosphorylase HGNC:7413
FOXK1 4.5 transcription regulator forkhead box K1 HGNC:23480
PCMT1 4.4 O-methyltransferase activity protein-L-isoaspartate (D-aspartate) O-methyltransferase HGNC:8728
SETD1A 4.3 transcription regulator SET domain containing 1A HGNC:29010
CENPP 4.2 centromere protein centromere protein P HGNC:32933
KIAA1217 4.1 unknown KIAA1217 HGNC:25428
SLITRK1 4.1 enhances neuronal dendrite outgrowth SLIT and NTRK-like family, member 1 HGNC:20297
RORB 4 transcription regulator RAR-related orphan receptor B HGNC:10259
DLGAP1 4 postsynaptic scaffold in neuronal cells discs, large (Drosophila) homolog-associated protein 1 HGNC:2905
C3orf21 4 unknown chromosome 3 open reading frame 21 HGNC:26639
ST6GALNAC1 4 protein glycosylation ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1 HGNC:23614
ZIC3 3.9 transcription regulator Zic family member 3 (odd-paired homolog, Drosophila) HGNC:12874
LYPLA1 3.8 hydrolase lysophospholipase I HGNC:6737
REST 3.8 transcription regulator RE1-silencingtranscription factor HGNC:9966
TMEM132D -2 unknown transmembrane protein 132D HGNC:29411
MAP1LC3B2 -2.1 microtubule microtubule-associated protein 1 light chain 3 beta 2 HGNC:34390
CBY3 -2.2 unknown chibby homolog 3 (Drosophila) HGNC:33278
RASIP1 -2.3 signal transduction Ras interacting protein 1 HGNC:24716
PRKG1 -2.3 kinase protein kinase, cGMP-dependent, type I HGNC:9414
WDR72 -2.4 unknown WD repeat domain 72 HGNC:26790
KCNQ2 -2.7 ion channel potassium voltage-gated channel, KQT-like subfamily, member 2 HGNC:6296
BAIAP3 -2.8 G-protein coupled receptor BAI1-associated protein 3 HGNC:948
MAP3K10 -30 kinase mitogen-activated protein kinase kinase kinase 10 HGNC:6849
Unique for Adenocarcinomas MSC 4.4 transcription regulator musculin HGNC:7321
FAM78B 4.1 unknown family with sequence similarity 78, member B HGNC:13495
HOXA1 3.6 transcription regulator homeobox A1 HGNC:5099
SEPT9 3.3 enzyme septin 9 HGNC:7323
GAS1 3.3 Cell cycle/growth growth arrest-specific 1 HGNC:4165
PTPRN2 3.1 phosphatase protein tyrosine phosphatase, receptor type, N polypeptide 2 HGNC:9677
RSPO2 2.7 Wnt receptor signaling pathway R-spondin 2 homolog (Xenopus laevis) HGNC:28583
POU3F3 2.6 transcription regulator POU class 3 homeobox 3 HGNC:9216
TRPA1 2.5 transporter transient receptor potential cation channel, subfamily A, member 1 HGNC:497
SYT6 2.3 transporter synaptotagmin VI HGNC:18638
SLC6A2 2.3 transporter solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2 HGNC:11048
LHX1 2.1 transcription regulator LIM homeobox 1 HGNC:6593
RAPGEF5 2.1 small GTPase mediated signal transduction Rap guanine nucleotide exchange factor (GEF) 5 HGNC:16862
GDF10 2.1 growth factor growth differentiation factor 10 HGNC:4215
C3orf45 1.6 unknown chromosome 3 open reading frame 45 HGNC:26781
SLIT2 1.6 differentiation/apoptosis slit homolog 2 (Drosophila) HGNC:11086
ZNF423 −1.6 transcription regulator zinc finger protein 423 HGNC:16762
RHOF −1.8 actin filament organization ras homolog gene family, member F (in filopodia) HGNC:15703
  1. Genes were selected based on the average of log2 ratios from the samples in each group. Hypermethylated genes common in all tumors and unique for the ADC groups were selected based on log2 ratio > 2.5; hypomethylation included all genes from those groups. For SCC we selected the first 50 genes with the highest log2 ratios in hypermethylation, and log2 ratio < −2.0 for hypomethylated genes. Gene classes and their correspondent biological functions were retrieved from Gene Ontology ( and Protein Knowledgebase UniProtKb (