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Question: GO terms: Annotation for HumanMethylation450
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gravatar for Fabrice Tourre
5.2 years ago by
Fabrice Tourre970 wrote:
Dear list, In the annotation file of Infinium HumanMethylation450 BeadChip, http://support.illumina.com/documents/MyIllumina/b78d361a-def5-4adb- ab38-e8990625f053/HumanMethylation450_15017482_v.1.2.csv for each probe set, they do not have annotation for GO terms, pathways. As they have done in the annotation file: HG- U133_Plus_2.na32.annot.csv. Is there some bioconductor package to annotated the Infinium HumanMethylation450 probes? Given a probe, feed back the GO terms and pathways. Thank you very much in advance.
ADD COMMENTlink modified 3 months ago by m0 • written 5.2 years ago by Fabrice Tourre970
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gravatar for Tim Triche
5.2 years ago by
Tim Triche4.2k
United States
Tim Triche4.2k wrote:
Oddly enough, the paper from UCSD with Illumina's folks on it (*) used the IlluminaHumanMethylation450k.db package (which I am currently rebuilding to have a startup message about toggleProbes()) to annotate both CpG islands and GO terms. (*) http://idekerlab.ucsd.edu/publications/Documents/Hannum_MolCell_2012.p df On Fri, Mar 29, 2013 at 8:49 AM, Fabrice Tourre <fabrice.ciup@gmail.com>wrote: > Dear list, > > In the annotation file of Infinium HumanMethylation450 BeadChip, > > http://support.illumina.com/documents/MyIllumina/b78d361a-def5-4adb- ab38-e8990625f053/HumanMethylation450_15017482_v.1.2.csv > > for each probe set, they do not have annotation for GO terms, pathways. > > As they have done in the annotation file: HG- U133_Plus_2.na32.annot.csv. > > Is there some bioconductor package to annotated the Infinium > HumanMethylation450 probes? Given a probe, feed back the GO terms and > pathways. > > Thank you very much in advance. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]
ADD COMMENTlink written 5.2 years ago by Tim Triche4.2k
Tim, Thank you very much for your reply. I have a list of probe list. Do you a example script for me to get the GO terms, instead of GO ID? The Documentation is not very clear for this. http://www.bioconductor.org/packages/2.11/data/annotation/html/Illumin aHumanMethylation450k.db.html On Fri, Mar 29, 2013 at 12:29 PM, Tim Triche, Jr. <tim.triche at="" gmail.com=""> wrote: > Oddly enough, the paper from UCSD with Illumina's folks on it (*) used the > IlluminaHumanMethylation450k.db package (which I am currently rebuilding to > have a startup message about toggleProbes()) to annotate both CpG islands > and GO terms. > > (*) > http://idekerlab.ucsd.edu/publications/Documents/Hannum_MolCell_2012 .pdf > > > On Fri, Mar 29, 2013 at 8:49 AM, Fabrice Tourre <fabrice.ciup at="" gmail.com=""> > wrote: >> >> Dear list, >> >> In the annotation file of Infinium HumanMethylation450 BeadChip, >> >> http://support.illumina.com/documents/MyIllumina/b78d361a-def5 -4adb-ab38-e8990625f053/HumanMethylation450_15017482_v.1.2.csv >> >> for each probe set, they do not have annotation for GO terms, pathways. >> >> As they have done in the annotation file: HG- U133_Plus_2.na32.annot.csv. >> >> Is there some bioconductor package to annotated the Infinium >> HumanMethylation450 probes? Given a probe, feed back the GO terms and >> pathways. >> >> Thank you very much in advance. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > -- > A model is a lie that helps you see the truth. > > Howard Skipper
ADD REPLYlink written 5.2 years ago by Fabrice Tourre970
0
gravatar for m
3 months ago by
m0
m0 wrote:

Is there any update on this? I used http://great.stanford.edu/public/html/ but would like to put more weight on relative TSS distance and direction of methylation change.

ADD COMMENTlink written 3 months ago by m0
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