NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Platform GPL16304 Query DataSets for GPL16304
Status Public on Mar 04, 2013
Title Illumina HumanMethylation450 BeadChip [UBC enhanced annotation v1.0]
Technology type oligonucleotide beads
Distribution custom-commercial
Organism Homo sapiens
Manufacturer Illumina, Inc.
Manufacture protocol See manufacturer's website
 
 
Submission date Nov 20, 2012
Last update date Mar 04, 2013
Contact name Magda Price
Organization name University of British Columbia
Street address Rm 2071. 950 W 28th ave
City Vancouver
ZIP/Postal code v5z4h4
Country Canada
 
Samples (4653) GSM1039475, GSM1039476, GSM1039477, GSM1039478, GSM1039479, GSM1039480 
Series (50)
GSE42409 Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array
GSE46364 DNA methylome signature in rheumatoid arthritis
GSE50022 Illumina Infinium 450K array data for Diffuse Intrinsic Pontine Glioma
Relations
Alternative to GPL13534

Data table header descriptions
ID Illumina target ID (IlmnID)
MAPINFO-1 Illumina mapinfo location minus 1 bp
MAPINFO+1 Illumina mapinfo location plus 1 bp
Probe_start Starting location of probe
Probe_end End location of probe
Target CpG SNP Reports rs numbers for SNPs documented in the C or G of the target (dbSNP 131)
n_target CpG SNP Reports the number of SNPs documented in the C or G of the target (dbSNP 131)
SNPprobe Reports rs numbers for SNPs documented in the interval for which the Illumina probe is desinged to hybridize (dbSNP 131). This column excludes Target CpG SNPs.
n_SNPprobe Reports the number of SNPs documented in the interval for which the Illumina probe is desinged to hybridize (dbSNP 131). This column excludes Target CpG SNPs.
HIL_CpG_class Reports the HIL CpG class based on the probe location. Any probe that falls in a region with HC enrichment (see HIL_CpG_Island_Name) has been classified as an HC probe. Probes that fall in a region of IC enrichment and that island overlaps somewhere with a region of HC enrichment, have been called ICshore probes.
HIL_CpG_Island_Name Reports the name of the HIL CpG Island to which the probe maps. *NOTE islands named HCshore in this column are regions with HC enrichment that overlap with some region(s) of IC enrichment, whereas islands named ICshore are regions with IC enrichment that overlap with some region(s) of HC enrichment. In the HIL_CpG_class column, any probe that falls in a region with HC enrichment (including HCs that overlap with ICs i.e. HCshores) has been classified as an HC probe. Probes that fall in a region of IC enrichment and that island overlaps somewhere with a region of HC enrichment, have been called ICshore probes.
n_bp_repetitive Reports the number of probe bp that fall in a repetitive element (RepeatMasker) based on the interval the Illumina probe is desinged to hybridize.
AlleleA_Hits Reports the number of locations to which AlleleA hybridizes in silico.
AlleleB_Hits Reports the number of locations to which AlleleB hybridizes in silico.
XY_Hits Reports YES if the in silico cross hybridization of AlleleA or AlleleB is to the X or Y chromosome.
Autosomal_Hits Reports YES if the in silico cross hybridization of AlleleA or AlleleB is to an autosomal chromosome.
Closest_TSS Genomic location of the closest TSS
Closest_TSS_1 Genomic location of the closest TSS + 1 bp
Distance_closest_TSS Distance to closest TSS
Closest_TSS_gene_name Gene name of closest TSS based on UCSC knownGene table. *NOTE: An estimated 4% of probes are the same distance from more than one TSS. In this case, we have annotated the gene name of the first gene to appear in the UCSC knownGene table.
Closest_TSS_Transcript Transcript name of closest TSS based on UCSC knownGene table. *NOTE: An estimated 4% of probes are the same distance from more than one TSS. In this case, we have annotated the gene name of the first transcript to appear in the UCSC knownGene table.
SPOT_ID

Data table
ID MAPINFO-1 MAPINFO+1 Probe_start Probe_end Target CpG SNP n_target CpG SNP SNPprobe n_SNPprobe HIL_CpG_class HIL_CpG_Island_Name n_bp_repetitive AlleleA_Hits AlleleB_Hits XY_Hits Autosomal_Hits Closest_TSS Closest_TSS_1 Distance_closest_TSS Closest_TSS_gene_name Closest_TSS_Transcript SPOT_ID
cg00000029 53468111 53468113 53468112 53468162 HC chr16_HCshore:53467967-53469412;. 0 1 0 XY_NO A_NO 53468350 53468351 -238 RBL2 NM_005611 cg00000029
cg00000108 37459205 37459207 37459206 37459256 rs9857774 1 LC .;. 48 1 0 XY_NO A_NO 37458757 37458758 449 C3orf35 CCDS46792 cg00000108
cg00000109 171916036 171916038 171916037 171916087 rs9864492 1 LC .;. 50 1 0 XY_NO A_NO 171851260 171851261 64777 FNDC3B AY358367 cg00000109
cg00000165 91194673 91194675 91194624 91194674 rs76771611 1 ICshore .;chr1_ICshore:91194238-91195462 0 1 0 XY_NO A_NO 91182793 91182794 -11880 BARHL2 NM_020063 cg00000165
cg00000236 42263293 42263295 42263244 42263294 IC .;chr8_IC:42263109-42263318 0 1 0 XY_NO A_NO 42251727 42251728 11567 VDAC3 CCDS47850 cg00000236
cg00000289 69341138 69341140 69341139 69341189 LC .;. 0 1 0 XY_NO A_NO 69352291 69352292 11153 ACTN1 AK295175 cg00000289
cg00000292 28890099 28890101 28890100 28890150 rs62037371 1 IC .;chr16_IC:28889913-28890373 0 1 0 XY_NO A_NO 28889808 28889809 292 ATP2A1 NM_004320 cg00000292
cg00000321 41167801 41167803 41167752 41167802 ICshore .;chr8_ICshore:41165660-41169277 0 1 0 XY_NO A_NO 41166989 41166990 -812 SFRP1 NM_003012 cg00000321
cg00000363 230560792 230560794 230560793 230560843 ICshore .;chr1_ICshore:230560253-230563060 0 1 0 XY_NO A_NO 230513390 230513391 -47402 PGBD5 NM_024554 cg00000363
cg00000622 23034446 23034448 23034446 23034496 HC HCshore:23033748-23036029;ICshore:23033858-23036198 0 1 1 XY_NO A_NO 23034426 23034427 -20 NIPA2 NM_001008892 cg00000622
cg00000658 139997923 139997925 139997874 139997924 rs75884245,rs80125774 2 HC chr9_HCshore:139997626-139998178;chr9_ICshore:139995853-139998493 0 1 0 XY_NO A_NO 139997799 139997800 125 MAN1B1 AK128257 cg00000658
cg00000714 54695677 54695679 54695678 54695728 ICshore .;chr19_ICshore:54692575-54695762 0 1 0 XY_NO A_NO 54695103 54695104 575 TSEN34 NM_001077446 cg00000714
cg00000721 25282778 25282780 25282729 25282779 LC .;. 0 1 0 XY_NO A_NO 25279655 25279656 3124 LRRC16A NM_001173977 cg00000721
cg00000734 128902376 128902378 128902377 128902427 HC chr3_HCshore:128901778-128903319;chr3_ICshore:128901700-128903339 0 1 0 XY_NO A_NO 128902809 128902810 433 CNBP AK298154 cg00000734
cg00000769 124086476 124086478 124086476 124086526 HC chr12_HCshore:124085763-124087075;chr12_ICshore:124085639-124087234 0 1 1 XY_NO A_NO 124086671 124086672 -194 DDX55 NM_020936 cg00000769
cg00000807 23913413 23913415 23913414 23913464 IC .;chr2_IC:23913292-23914845 0 1 0 XY_NO A_NO 23911654 23911655 1760 KLHL29 AB067508 cg00000807
cg00000884 154609856 154609858 154609807 154609857 LC .;. 49 1 0 XY_NO A_NO 154609053 154609054 804 TLR2 AF051152 cg00000884
cg00000905 59785305 59785307 59785256 59785306 LC .;. 0 1 0 XY_NO A_NO 59730371 59730372 54935 FAM81A NM_152450 cg00000905
cg00000924 2720462 2720464 2720463 2720513 rs78369463 1 HC chr11_HCshore:2720123-2721845;chr11_ICshore:2720031-2722567 0 1 0 XY_NO A_NO 2721227 2721228 765 KCNQ1OT1 NR_002728 cg00000924
cg00000948 49890608 49890610 49890609 49890659 IC .;chr8_IC:49890018-49891221 0 1 0 XY_NO A_NO 49833998 49833999 -56610 SNAI2 NM_003068 cg00000948

Total number of rows: 485512

Table truncated, full table size 75139 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp

Supplementary file Size Download File type/resource
GPL16304_Gene_features_Metadata.txt.gz 726 b (ftp)(http) TXT
GPL16304_Gene_features_PlatformTable.txt.gz 11.1 Mb (ftp)(http) TXT

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap