Question: Functional Annotation Of Pathways
2
gravatar for Pi
9.1 years ago by
Pi510
Pi510 wrote:

Greetings

I have a list of genes and I wish to know the pathways they are in or if any pathways are statistically enriched. I have seen various questions about this on this website but please don't close this question as a duplicate as I hope my question has a slightly different slant.

Is there a tool for reconciling the different descriptions/names of pathways in the common resourses such as wikipathways, reactome, Kegg. For example if you perform functional annotation clustering in DAVID using example dataset 2 you will get these results. Is there an obvious way (without painstaking manual analysis) to tell which are the same pathways but named differently in different data sources

Thank you for your time

edit: in this question I have seen mention of the fact that PathVisio, which is not only the editor applet of WikiPathways is standalone pathway tool, to also search the converted KEGG pathways. Does this mean KEGG pathways have been converted into WikiPathways as this seems a good first step into reconciling disparate pathway resources. I will look into this now but didn't see it until after i posted the question. Hopefully the question will yield other helpful responses too.

pathway annotation • 3.3k views
ADD COMMENTlink modified 4.4 years ago by Biostar ♦♦ 20 • written 9.1 years ago by Pi510
2
gravatar for Russh
9.1 years ago by
Russh1.2k
U. Liverpool
Russh1.2k wrote:

A naive approach would start - if you had the pathwayName => {geneset} mappings from each of the above tools, you could determine which pathways are enriched in the members of other pathways (using the same method you would for determining whether your genelist is enriched in the members of a given pathway; typically Fisher-based). This is all nice and easy for KEGG and GO, where the pathway member lists are easily accessible. Some pathway databases are less transparent. [?]. Having found pairs of pathways that are mutually enriched you have a good grasp on your question.

R

ADD COMMENTlink written 9.1 years ago by Russh1.2k
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