Infinium Methylation450K manifest column headings

03/31/21


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.