KEGG analysis
1
0
Entering edit mode
Daniel Brewer ★ 1.9k
@daniel-brewer-1791
Last seen 9.6 years ago
Hello, I have two gene lists and I want to find out whether there are genes in list one that occur in well known networks (KEGG?) where genes in list 2 also appear. For example, List 1: RAS, SPINK1 List 2: ERBB2 Both RAS and ERBB2 occur in ERBB signalling pathway defined by KEGG. SPINK1 does not appear in any common network (I think). Has anyone got any ideas what the best way to do this is? Many thanks Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis MUCRC 15 Cotswold Road Sutton, Surrey SM2 5NG United Kingdom Tel: +44 (0) 20 8722 4109 ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the a...{{dropped:2}}
Network Cancer Network Cancer • 896 views
ADD COMMENT
0
Entering edit mode
Daniel Brewer ★ 1.9k
@daniel-brewer-1791
Last seen 9.6 years ago
Just to answer my own question. It seems that with a combination of the annotation libraries "org.Hs.eg" and "KEGG", and a bit of scripting you can do this sort of thing. Dan Daniel Brewer wrote: > Hello, > > I have two gene lists and I want to find out whether there are genes in > list one that occur in well known networks (KEGG?) where genes in list 2 > also appear. > > For example, > > List 1: RAS, SPINK1 > List 2: ERBB2 > > Both RAS and ERBB2 occur in ERBB signalling pathway defined by KEGG. > SPINK1 does not appear in any common network (I think). > > Has anyone got any ideas what the best way to do this is? > > Many thanks > > Dan > > -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis Email: daniel.brewer at icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the a...{{dropped:2}}
ADD COMMENT
0
Entering edit mode
The tools in the gseaBase package are also pretty helpful for these kinds of problems. Florian On 06.04.2009, at 08:07, Daniel Brewer wrote: > Just to answer my own question. It seems that with a combination of > the > annotation libraries "org.Hs.eg" and "KEGG", and a bit of scripting > you > can do this sort of thing. > > Dan > > Daniel Brewer wrote: >> Hello, >> >> I have two gene lists and I want to find out whether there are >> genes in >> list one that occur in well known networks (KEGG?) where genes in >> list 2 >> also appear. >> >> For example, >> >> List 1: RAS, SPINK1 >> List 2: ERBB2 >> >> Both RAS and ERBB2 occur in ERBB signalling pathway defined by KEGG. >> SPINK1 does not appear in any common network (I think). >> >> Has anyone got any ideas what the best way to do this is? >> >> Many thanks >> >> Dan >> >> > > -- > ************************************************************** > Daniel Brewer, Ph.D. > > Institute of Cancer Research > Molecular Carcinogenesis > Email: daniel.brewer at icr.ac.uk > ************************************************************** > > The Institute of Cancer Research: Royal Cancer Hospital, a > charitable Company Limited by Guarantee, Registered in England under > Company No. 534147 with its Registered Office at 123 Old Brompton > Road, London SW7 3RP. > > This e-mail message is confidential and for use by the a...{{dropped: > 2}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLY

Login before adding your answer.

Traffic: 963 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6