Relation between "MAPINFO" and "UCSC_CpG_Islands_Name" in Illumina manifest file

Question

[Tanvir Ahamed]

In Illumina manifest file what is the relation between MAPINFO and UCSC_CpG_Islands_Name ?

In the illumina description file it says, MAPINFO: Chromosomal coordinates of the CpG (Build 37) UCSC_CpG_Islands_Name: Chromosomal coordinates of the CpG Island from UCSC

In 450k or 850k Illumina manifest file, all probe has "MAPINFO" but not "UCSC_CpG_Islands_Name", why ?

[Tanvir Ahamed]

What i have understand :

MAPINFO : Nucleotide position on the chromosome where this CpG is located.

UCSC_CpG_Islands_Name: A window (Up and downstream) of CpG location. but still not clear about this. If so, how the window length has determined ?

Example :

IlmnID      Chr   MAPINFO     UCSC_CpG_Islands_Name
-----------------------------------------------------
cg18478105  20    61847650    chr20:61846843-61848103
cg23875663  20    17299350    chr20:17296125-17296531

Read more :

Researchgate

Wikipedia

If any one has better explanation, please share.

Answer 1

[Charles Warden]

For the 450k array, MAPINFO is the hg19 position coordinate.

If the CpG site is in a CpG island, it will have that extra annotations. However, all probes do not lie within CpG islands.

[Tanvir Ahamed]

Thanks for your reply . Can you please explain in brief with an example ?

[Charles Warden]

You can take a look at the probe design information using these files:

https://support.illumina.com/array/array_kits/infinium_humanmethylation450_beadchip_kit/downloads.html

IlmnID  CHR MAPINFO UCSC_RefGene_Name   UCSC_RefGene_Group UCSC_CpG_Islands_Name    Relation_to_UCSC_CpG_Island

cg00035864  Y   8553009 TTTY18  TSS1500     
cg00050873  Y   9363356 TSPY4;FAM197Y2  Body;TSS1500    chrY:9363680-9363943    N_Shore

cg00050873 is located in the north shore of the CpG island chrY:9363680-9363943 near the TSPY4 and FAM197Y2 genes.

cg00035864 is located near the transcription start site for TTTY18, but it is not contained with in a UCSC CpG Island

[jiang.hk.xm]

Is the cg00050873 in TSPY4 and FAM197Y2 ? or the the CpG island chrY:9363680-9363943 near the TSPY4 and FAM197Y2 genes?

[Charles Warden]

If you are asking how the CpG islands are defined, you can look here for more information about that track:

https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=480394203_ljGtilAdSsfG1MTL83AnAFHafKxE&c=chr17&g=cpgIslandSuper

[ahsan.raza.rana]

I want to have methylation information(mouse probe ids)CpGmarker CoefficientTraining CoefficientTrainingShrunk varByCpG minByCpG maxByCpG medianByCpG medianByCpGYoung medianByCpGOld Gene_ID GenomeBuild Chr MapInfo SourceVersion TSS_Coordinate Gene_Strand Symbol Synonym Accession GID Annotation Product Marginal Age Relationship for 450KIllumina.but I am not finding it any where.Can any one tell me how to calculate the above mentioned fields for mouse.

[psq]

Hello, sorry to post to an old thread but I'm not having any luck mapping MAPINFO to hg19 in the 450k download file from Illumina(HumanMethylation450_15017482_v.1-2.csv). I tried other external ID mappings and only got some matches against GI Number but only 18k of 200k of those mapped which is too low to be reliable. Is there some indirect mapping that is involved here?

Thanks,