GO term enrichment

Question

[zizigolu]

hello friends,

i have a list of GO terms, for example GO:0005975, how i can fine that which of these GO terms is related with cirus fruit senescence please???

Answer 1

[Deepak Tanwar]

Try DAVID for the start, than you should read the manuals of some Bioconductor packages.

• topGO
• GOexpress
• Tools To Find Gene Ontology Term Enrichment
• Go Annotation By Bioconductor
• David Pathway Analysis
• GO Analysis
• GO analysis with R code

Read properly and perform the commands for the dataset provided by the packages. Don't simply try to copy paste, to do analysis yourself. Understand the commands properly, what's going on and then try to implement the codes accordingly.

[zizigolu]

thank you Deepak

Answer 2

[seidel]

For such a general question I would start with http://geneontology.org/ where you can begin a search based on "fruit senescence" (is there such a thing as cirus fruit?, did you mean citrus fruit?), as fruit senescence is more general and you're more likely to find results than requiring a particular type of fruit - unless deep knowledge already exists in that domain. However, this site will simply leave you over at http://amigo.geneontology.org/ where you can explore the relationships among terms and everything else. If you want a programmatic way of doing things - do what Deepak said.

[zizigolu]

thank you in your mentioned website there are only arabidopsis...

Answer 3

[jin]

You can try PlantRegMap, which integrated GO annotation for 132 plant species and perform enrichment analysis.

Answer 4

[EagleEye]

Try

Gene Set Clustering based on Functional annotation (GeneSCF)

Wikipedia list