I have a list of genes and wish to know the pathways in which the expression of these genes is upregulated or downregulated. How do I do this?
Without respect to you expression values (...because we don't know, how those expression values were calculated...) a good choice for your list of genes could be http://david.abcc.ncifcrf.gov/home.jsp or http://bioinfo.vanderbilt.edu/webgestalt/.
If you will use those sources, keep in mind your reference dataset! ...default reference set is the whole genome!
Furthermore, if you gene list is just a small list. Try http://biogps.org/#goto=welcome and add your pathway modules of interest (STRING, KEGG, etc).
I second my colleagues: Your question is not very clear.
As far as I understand your question, a good start would be to use the KEGG database or download flat files of interest on their FTP server: http://www.genome.jp/kegg/download/
Depending on your programming skills you can either write your own parser, or use available tools, like KeggArray if you are working with arrays.
Hope it helps
I developed a script that takes a directory with several gene list inside (Entrez Ids) and a universe set, a pvalue cutoff and an FDR cutoff and looks for enrichment in KEGG pathways, could be also GO ( I am using GOStats bioconductor package )
The script is just right here, if you find it useful please leave a comment
Cheers
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Joel, I think that you will have several answers to this question and can find many by looking at past postings to this site. However, you have selected the "SNP" tag - why? Do you have association or eQTL data? I ask because that implies you have phenotypes and those may influence the pathway information you'll want or where you'd look for those data.
Also, you should probably add some detail with regard to the conditions under which the genes are up- or down-regulated.
You have a list of genes for which you know their expression or you have a list of genes and you want to know their expression status in pathways that contain them?
Agree with Sean, this is ambiguous - do you know the expression levels of the list of genes or not?
@Sean: Imagine if this guy has a list of genes and no expression information, is it still possible to identify the pathways in which these genes are being upregulated or downregulated? I am very interested in knowing this part of the question.....
I just read a paper in PNAS on TP53 (p53), NR0B2 (SHP), CYP7A1 and CYP8B1 with regard to reprogramming of metabolism during cancer. NR0B2 negatively regulates the CYPs and TP53 stimulates expression and protein activity of NR0B2. Thus, you could put these 4 genes into a pathway and know the resulting up-/down-regulation without measuring mRNAs. However, those data are for liver and don't tell you about the other genes in the bile acid/cholesterol pathway, of which the4se 2 CYPs are members.