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
| Â | 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 |