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Platform GPL15380 Query DataSets for GPL15380
Status Public on Mar 29, 2012
Title Illumina Sentrix Array Matrix (SAM) - GoldenGate Methylation Cancer Panel I
Technology type oligonucleotide beads
Distribution custom-commercial
Organism Homo sapiens
Manufacturer Illumina
Manufacture protocol http://www.illumina.com
Catalog number GM-17-211
 
Description High-Throughput DNA Methylation Profiling with Illumina GoldenGate® Technology
Experimentally validated Oligo pool for Methylation Assay (OMA) for 1,505 CpG sites selected in promoter regions and/or first exon of over 800 genes. Sufficient for the analysis of 96 samples.
 
Submission date Mar 27, 2012
Last update date Mar 29, 2012
Contact name Nahid Turan
E-mail(s) nturan@temple.edu
Phone 215-707-7302
Organization name Temple University School of Medicine
Department Fels Institute
Street address 3307 North Broad Street, AHB
City Philadelphia
State/province PA
ZIP/Postal code 19140
Country USA
 
Samples (92) GSM902951, GSM902952, GSM902953, GSM902954, GSM902955, GSM902956 
Series (2)
GSE36831 DNA methylation and gene expression differences at growth related genes correlate with birth weight.
GSE36852 Epigenome analysis of newborn placenta and cord blood samples

Data table header descriptions
ID CpG PROBE_ID
GID GID
GB_ACC GenBank Accession number
ACCESSION ACCESSION number
SYMBOL Gene SYMBOL
CUSTOMER_ANNOTATION CUSTOMER_ANNOTATION
GENE_ID GENE_ID
CHROMOSOME CHROMOSOME
REFSEQ REFSEQ
CPG_COORDINATE CPG_COORDINATE
DIST_TO_TSS DIST_TO_TSS
CPG_ISLAND CPG_ISLAND
SEQUENCE INPUT_SEQUENCE
SYNONYM SYNONYM
ANNOTATION ANNOTATION
PRODUCT PRODUCT
CG_NO CG_NO
CUSTOMER_ANNOTATION CUSTOMER_ANNOTATION
TSS_COORDINATE TSS_COORDINATE
GENE_STRAND GENE_STRAND
SYMBOL SYMBOL
TargetID TargetID
ProbeID ProbeID

Data table
ID GID GB_ACC ACCESSION SYMBOL CUSTOMER_ANNOTATION GENE_ID CHROMOSOME REFSEQ CPG_COORDINATE DIST_TO_TSS CPG_ISLAND SEQUENCE SYNONYM ANNOTATION PRODUCT CG_NO CUSTOMER_ANNOTATION TSS_COORDINATE GENE_STRAND SYMBOL TargetID ProbeID
cg00009321 GI:51317362 NM_002473.3 NM_002473.3 MYH9 MYH9 GeneID:4627 22 36.1 35113838 -89 TRUE CGGGAACAGGCGCTGCTTCTCC[CG]AGAGGACTTTCTCGAGCGCTCGGGC MHA; FTNS; DFNA17; NMMHCA; NMHC-II-A cellular myosin heavy chain; type A; nonmuscle myosin heavy chain II-A; non-muscle myosin heavy polypeptide 9; go_component: myosin; go_component: intracellular; go_function: ATP binding; go_function: actin binding; go_function: motor activity; go_function: calmodulin binding; go_function: nucleotide binding; go_process: signal transduction; go_process: regulation of cell shape; go_process: sensory perception of sound myosin; heavy polypeptide 9; non-muscle cg00009321 MYH9 35113927 - MYH9 cg00009321 925
cg00014705 GI:10863922 NM_021127.1 NM_021127.1 PMAIP1 PMAIP1 GeneID:5366 18 36.1 55718307 -90 TRUE CTGCAGGACTGTTCGTGTTCAGCTCG[CG]TCCTGCAGCTGTCCGAGGTGCTCCAG APR; NOXA adult T cell leukemia-derived PMA-responsive; go_function: protein binding; go_function: protein binding phorbol-12-myristate-13-acetate-induced protein 1 cg00014705 PMAIP1 55718217 + PMAIP1 cg00014705 2717
cg00039439 GI:33469921 NM_182776.1 NM_182776.1 MCM7 MCM7 GeneID:4176 7 36.1 99537269 -94 TRUE CGTCTTCTTGTCTACTCTCCAGAA[CG]GCCATGATTTCCCAATTCTTCATT MCM2; CDC47; P85MCM; P1CDC47; PNAS-146; CDABP0042; P1.1-MCM3 isoform 2 is encoded by transcript variant 2; minichromosome maintenance deficient (S. cerevisiae) 7; DNA replication licensing factor MCM7; homolog of S. cerevisiae Cdc47; go_component: nucleus; go_component: chromatin; go_function: ATP binding; go_function: DNA binding; go_function: nucleotide binding; go_function: protein binding; go_function: protein binding; go_function: DNA-dependent ATPase activity; go_function: nucleoside-triphosphatase activity; go_process: cell cycle; go_process: transcription; go_process: DNA replication; go_process: DNA replication initiation; go_process: regulation of transcription; DNA-dependent minichromosome maintenance protein 7 isoform 2 cg00039439 MCM7 99537363 - MCM7 cg00039439 4334
cg00045781 GI:89025413 XM_168578.6 XM_168578.6 MUC3B MUC3B GeneID:57876 7 36.1 100382469 96 FALSE AGTTACCCCCAGTGGTGTCATTGT[CG]GGCTCTGAGCTCCACCTCATTTGGACTC Derived by automated computational analysis using gene prediction method: GNOMON. mucin 3B cg00045781 MUC3B 100382565 + MUC3B cg00045781 4166
cg00058480 GI:24497502 NM_021784.3 NM_021784.3 FOXA2 FOXA2 GeneID:3170 20 36.1 22513921 -181 TRUE AAAAACTACGTACACACCTTTAACT[CG]CCCGCTGCTGCTCCTGCGAGGCCCC HNF3B; TCF3B; MGC19807 hepatocyte nuclear factor 3; beta; hepatic nuclear factor-3-beta; go_component: nucleus; go_function: transcription factor activity; go_process: transcription; go_process: regulation of transcription; DNA-dependent forkhead box A2 cg00058480 FOXA2 22514102 - FOXA2 cg00058480 101
cg00058786 GI:16936521 NM_003394.2 NM_003394.2 WNT10B WNT10B GeneID:7480 12 36.1 47651732 -78 TRUE GGAGTGATCGAGAGAGCTAGCAAGCCGG[CG]AGCAAAGGACTGGGGGCT WNT-12 WNT-10B protein; go_component: extracellular region; go_function: signal transducer activity; go_process: development; go_process: signal transduction; go_process: frizzled-2 signaling pathway wingless-type MMTV integration site family; member 10B precursor cg00058786 WNT10B 47651810 - WNT10B cg00058786 2160
cg00067721 GI:23110933 NM_002786.2 NM_002786.2 PSMA1 PSMA1 GeneID:5682 11 36.1 14621665 -74 TRUE CGTCCTTCTCTTTCAGTCC[CG]GTGGGTCTTCGGACTGCCGCCGCC NU; HC2; PROS30; MGC1667; MGC14542; MGC14575; MGC14751; MGC21459; MGC22853; MGC23915 isoform 2 is encoded by transcript variant 2; proteasome subunit; alpha-type; 1; proteasome subunit nu; macropain subunit nu; protein P30-33K; proteasome component C2; multicatalytic endopeptidase complex subunit C2; proteasome nu chain; 30 kDa prosomal protein; go_component: polysome; go_component: proteasome core complex (sensu Eukaryota); go_function: RNA binding; go_function: threonine endopeptidase activity; go_process: ubiquitin-dependent protein catabolism proteasome alpha 1 subunit isoform 2 cg00067721 PSMA1 14621739 - PSMA1 cg00067721 5252
cg00077055 GI:24307882 NM_001986.1 NM_001986.1 ETV4 ETV4 GeneID:2118 17 36.1 38979027 254 TRUE AGTGAGTGTGGTGTGCATTGGAGG[CG]AGGCGGGGAATCACAGACACTC E1AF; PEA3; E1A-F; PEAS3 polyomavirus enhancer activator-3; ets variant gene 4 (E1A enhancer-binding protein; E1AF); go_component: nucleus; go_function: sequence-specific DNA binding; go_function: transcription factor activity; go_function: transcriptional activator activity; go_process: transcription; go_process: regulation of transcription; DNA-dependent ets variant gene 4 (E1A enhancer binding protein; E1AF) cg00077055 ETV4 38978773 - ETV4 cg00077055 2024
cg00096407 GI:14110406 NM_031372.1 NM_031372.1 HNRPDL HNRPDL GeneID:9987 4 36.1 83570041 -406 TRUE CTTGGGAGCCTTTGTCTCTGGCGTC[CG]GTCCAGCCCACTCCTACCAAA HNRNP; JKTBP; JKTBP2; laAUF1 A+U-rich element RNA binding factor; go_component: heterogeneous nuclear ribonucleoprotein complex; go_function: nucleotide binding; go_function: poly(A) binding; go_function: nucleic acid binding; go_function: double-stranded DNA binding; go_function: single-stranded DNA binding; go_process: RNA processing heterogeneous nuclear ribonucleoprotein D-like cg00096407 HNRPDL 83570447 - HNRPDL cg00096407 721
cg00115213 Chr15b 15 36.1 21358321 TRUE TCTGCGGCCCTTGCAGCTGCCGG[CG]CAGGCGCTGCACCCAGCGCTGCTCC human putative regulatory element and DMR cg00115213 Chr15b cg00115213 4279
cg00122038 GI:49574524 NM_002178.2 NM_002178.2 IGFBP6 IGFBP6 GeneID:3489 12 36.1 51777375 328 TRUE CGGGTCCCTGCATGCCCCT[CG]TCGTCCTACACATACACACTAAGTGGATT IBP6 IGF binding protein 6; go_component: extracellular space; go_function: insulin-like growth factor binding; go_process: signal transduction; go_process: regulation of cell growth; go_process: negative regulation of cell proliferation insulin-like growth factor binding protein 6 cg00122038 IGFBP6 51777703 + IGFBP6 cg00122038 5293
cg00137554 GI:71143136 NM_005342.2 NM_005342.2 HMGB3 HMGB3 GeneID:3149 X 36.1 149901896 525 TRUE GATAGGCAGCGAGATCCGAGGACTAAATCC[CG]AGGTCTTGGCGAGCAAGCAGCTG HMG4; HMG2A; MGC90319 high-mobility group (nonhistone chromosomal) protein 4; non-histone chromosomal protein; go_component: nucleus; go_component: chromatin; go_function: DNA binding; go_function: DNA bending activity; go_process: development; go_process: regulation of transcription; DNA-dependent high-mobility group box 3 cg00137554 HMGB3 149902421 + HMGB3 cg00137554 442
cg00147976 GI:54873621 NM_005016.3 NM_005016.3 PCBP2 PCBP2 GeneID:5094 12 36.1 52132496 -333 TRUE TTCCACTTTTGTCTTCTTCTTAGC[CG]GCTCGGGTCCTAGTCACGAGCCGC HNRPE2; hnRNP-E2; MGC110998 isoform a is encoded by transcript variant 1; alpha-CP2; poly(rC)-binding protein 2; heterogenous nuclear ribonucleoprotein E2; go_component: nucleus; go_component: cytoplasm; go_component: ribonucleoprotein complex; go_function: DNA binding; go_function: RNA binding; go_function: catalytic activity; go_function: nucleic acid binding; go_process: mRNA metabolism poly(rC)-binding protein 2 isoform a cg00147976 PCBP2 52132163 + PCBP2 cg00147976 976
cg00164898 GI:47519715 NM_138993.2 NM_138993.2 MAPK11 MAPK11 GeneID:5600 22 36.1 49051254 348 TRUE TCCCCAACGAGGGAGAACCGTCAAAAG[CG]AAGAAGCCAGGGGTAAACCATGG P38B; SAPK2; p38-2; PRKM11; SAPK2B; p38Beta; P38BETA2 stress-activated protein kinase-2; stress-activated protein kinase-2b; mitogen-activated protein kinase p38 beta; mitogen-activated protein kinase p38-2; go_component: cellular component unknown; go_function: ATP binding; go_function: nucleotide binding; go_function: transferase activity; go_function: MP kinase activity; go_function: MAP kinase activity; go_function: protein serine/threonine kinase activity; go_process: response to stress; go_process: signal transduction; go_process: protein kinase cascade; go_process: protein amino acid phosphorylation; go_process: antimicrobial humoral response (sensu Vertebrata) mitogen-activated protein kinase 11 cg00164898 MAPK11 49050906 - MAPK11 cg00164898 1324
cg00181037 GI:60302916 NM_000621.2 NM_000621.2 HTR2A HTR2A GeneID:3356 13 36.1 46367901 -275 FALSE GAAAGGTTGGTTCGATTTTCAGAGT[CG]ACTGTCCAGTTAAATGCATCAGAAGTG HTR2; 5-HT2A 5-HT2 receptor; go_component: membrane; go_component: integral to plasma membrane; go_function: receptor activity; go_function: serotonin receptor activity; go_function: rhodopsin-like receptor activity; go_process: signal transduction; go_process: synaptic transmission; go_process: serotonin receptor signaling pathway 5-hydroxytryptamine (serotonin) receptor 2A cg00181037 HTR2A 46368176 - HTR2A cg00181037 74
cg00187125 GI:30039709 NM_178161.1 NM_178161.1 PTF1A PTF1A GeneID:256297 10 36.1 23520981 485 TRUE GGGACGCAGGTGCCCCTGGAGC[CG]CACGCGGGGCAGGTACAGAATCCAGT PTF1-p48 bHLH transcription factor p48; class II bHLH protein PTF1A; go_component: nucleus; go_function: transcription regulator activity; go_process: regulation of transcription pancreas specific transcription factor; 1a cg00187125 PTF1A 23521466 + PTF1A cg00187125 5268
cg00264963 GI:10800414 NM_002487.2 NM_002487.2 NDN NDN GeneID:4692 15 36.1 21483775 232 TRUE GGCAGGAGAGAAGTGAGATGGATG[CG]TACTGGAGAAGGGGCCAGTTTA HsT16328 necdin (mouse) homolog; go_component: nucleus; go_function: DNA binding; go_process: transcription; go_process: regulation of cell growth; go_process: nervous system development; go_process: regulation of transcription; DNA-dependent; go_process: negative regulation of cell proliferation; go_process: regulation of progression through cell cycle necdin cg00264963 NDN 21483543 - NDN cg00264963 5118
cg00279981 GI:58331232 NM_012073.3 NM_012073.3 CCT5 CCT5 GeneID:22948 5 36.1 10303473 -191 TRUE TGCACCATGGCGTCCATGGGGACCCT[CG]CCTTCGATGAATATGGGCGCCC CCTE; KIAA0098; CCT-epsilon; TCP-1-epsilon T-complex protein 1; epsilon subunit; chaperonin containing TCP1; epsilon; go_function: ATP binding; go_function: nucleotide binding; go_function: unfolded protein binding; go_process: protein folding chaperonin containing TCP1; subunit 5 (epsilon) cg00279981 CCT5 10303282 + CCT5 cg00279981 5879
cg00307463 GI:19549332 NM_015983.2 NM_015983.2 UBE2D4 UBE2D4 GeneID:51619 7 36.1 43932332 240 TRUE CGCCCAGGATGTAGGAACAGGGAGCAGG[CG]AGCGTGTGGCACCTTGAGGG HBUCE1 ubiquitin-conjugating enzyme HBUCE1; go_function: ligase activity; go_function: protein binding; go_function: ubiquitin-protein ligase activity; go_process: ubiquitin cycle ubiquitin-conjugating enzyme E2D 4 (putative) cg00307463 UBE2D4 43932572 + UBE2D4 cg00307463 2180
cg00337492 GI:89050434 XM_375550.3 XM_375550.3 SHC2 SHC2 GeneID:25759 19 36.1 411168 376 TRUE CCCACCGCAGGCCAGCGTCTCGGGCCC[CG]TCTGTCATTCGTGAACAGCTGTCCG Derived by automated computational analysis using gene prediction method: GNOMON. SHC (Src homology 2 domain containing) transforming protein 2 cg00337492 SHC2 410792 - SHC2 cg00337492 3262

Total number of rows: 1536

Table truncated, full table size 933 Kbytes.




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