Question: GO term enrichment
1
gravatar for F
2.9 years ago by
F3.0k
Iran
F3.0k wrote:

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???

gene • 1.3k views
ADD COMMENTlink modified 18 months ago by EagleEye5.1k • written 2.9 years ago by F3.0k
5
gravatar for Deepak Tanwar
2.9 years ago by
Deepak Tanwar3.8k
ETH Zürich, Switzerland
Deepak Tanwar3.8k wrote:

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.

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Deepak Tanwar3.8k
1

thank you Deepak

ADD REPLYlink written 2.9 years ago by F3.0k
3
gravatar for seidel
2.9 years ago by
seidel6.5k
United States
seidel6.5k wrote:

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.

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by seidel6.5k

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

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by F3.0k
0
gravatar for jin
18 months ago by
jin80
jin80 wrote:

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

ADD COMMENTlink modified 18 months ago • written 18 months ago by jin80
0
gravatar for EagleEye
18 months ago by
EagleEye5.1k
Sweden
EagleEye5.1k wrote:

Try

Gene Set Clustering based on Functional annotation (GeneSCF)

Wikipedia list

ADD COMMENTlink modified 18 months ago • written 18 months ago by EagleEye5.1k
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