Infinium Methylation450K manifest column headings
Detailed descriptions of the Infinium HumanMethylation450K manifest file column headings are listed.
IlmnID: Unique identifier from the Illumina CG database. (The probe ID).
Name: The IlmnID.
Infinium_Design_Type: Infinium I (2 probes/locus) or Infinium II (1 probe/locus).
Next_Base: For Infinium I probes, the nucleotide immediately following the CpG. Blank for Infinium II.
Color_Channel: For Infinium I probes, the color channel of the “Next_Base” signal.
Forward_Sequence: Plus (+) strand (HapMap) sequence (5'-3') flanking the CG.
Genome_Build: Genome Build referenced by the manifest.
CHR: Chromosome containing the CpG (Build 37).
MAPINFO: Chromosomal coordinates of the CpG (Build 37).
SourceSeq: The original, genomic sequence used for probe design before bisulfite conversion.
Chromosome_36: Chromosome containing the CpG (Build 36).
Coordinate_36: Chromosomal coordinates of the CpG (Build 36).
Strand: The Forward (F) or Reverse (R) designation of the Design Strand.
*Note: in methylation manifest files, the Forward Strand = the genomic Plus (+) Strand and the Reverse Strand = the genomic Minus (-) Strand. In this context, Forward and Reverse ARE NOT EQUIVALENT to the Forward and Reverse Strand designations originating from dbSNP or as given in Infinium Genotyping manifests.
Probe_SNPs: rsid(s) of SNP(s) located 10-50 bases from the target CpG.
Probe_SNPs_10: rsid(s) of SNP(s) located ≤ 10 bases from the target CpG.
Random_Loci: CpG loci chosen randomly by consortium members during the design process are marked “True”.
Methyl27_Loci: CpG’s carried over from the HumanMethylation27 array (95% carryover) are marked “True”.
UCSC_RefGene_Name: Target gene name(s), from the UCSC database. *Note: multiple listings of the same gene name indicate splice variants.
UCSC_RefGene_Accession: The UCSC accession number(s) of the target transcript(s). Accession numbers are given in the same order as the target gene transcripts.
UCSC_RefGene_Group: Gene region feature category describing the CpG position, from UCSC. Features listed in the same order as the target gene transcripts.
TSS200 = 0-200 bases upstream of the transcriptional start site (TSS). TSS1500 = 200-1500 bases upstream of the TSS. 5'UTR = Within the 5' untranslated region, between the TSS and the ATG start site. Body = Between the ATG and stop codon; irrespective of the presence of introns, exons, TSS, or promoters. 3'UTR = Between the stop codon and poly A signal.
UCSC_CpG_Islands_Name: Chromosomal coordinates of the CpG Island from UCSC.
Relation_to_UCSC_CpG_Island: The location of the CpG relative to the CpG island.
Shore = 0-2 kb from island. Shelf = 2-4 kb from island. N = upstream (5’) of CpG island. S = downstream (3’) of CpG island.
Phantom: Classifications from the FANTOM (Functional Annotation of the Mammalian Genome) consortium as a low- or high-CpG density region associated with FANTOM 4 promoters.
DMR: Differentially methylated regions (experimentally determined).
DMR = Differentially Methylated Region. CDMR = Cancer-specific Differentially Methylated Region. RDMR = Reprogramming-specific Differentially Methylated Region.
Enhancer: Predicted enhancer elements (determined by the ENCODE Consortium using informatics) are marked “True”.
HMM_Island:Hidden Markov Model Islands. Chromosomal map coordinates of computationally predicted CpG islands.
Regulatory_Feature_Name: Chromosomal map coordinates of the regulatory feature (determined by the ENCODE Consortium using informatics).
Regulatory_Feature_Group: Description of the regulatory feature referenced in “Regulatory_Feature_Name” as provided by the Methylation Consortium.
Gene_Associated Gene_Associated_Cell_type_specific NonGene_Associated Promoter_Associated Promoter_Associated_Cell_type_specific Unclassified Unclassified_Cell_type_specific
DHS: DNase I Hypersensitivity Site (experimentally determined by the ENCODE project).
Information in the methylation manifest references Genome Build 37 (HG19) unless otherwise stated.
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