I have a batch of maize RNA-seq datasets on RNAs that were collected from different maize lines . I have generated several differential expression lists by using Tophat/Cufflink RNA-seq pipeline. Currently I am trying to identify the gene categories, pathways or networks that are enriched in one line in compared with the rest of lines.
Does anyone has good experience performing GO, pathway/network enrichment analysis on Maize RNA-seq datasets? Any recommendation on tools, websites, resource or methods will be greatly appreciated.
Hi, you can use any one of these
http://www-labgtp.na.icar.cnr.it/Transcriptator/
http://www.nematodes.org/bioinformatics/annot8r/
or BLAST2GO.
Regards
I prefer topGO. Super easy to use.
http://bioconductor.org/packages/release/bioc/html/topGO.html
Maize probably has not super-abundant annotation in terms of GO and pathways.
You can try to translate your significant maize genes from RNA-seq into their Arabidopsis ortholog genes (chances are you have such table already) and use the Arabidopsis toolboxes/databases (eg from KEGG). Of course it cannot be guaranteed that AT is a good model - it has simply the richest annotations...
Hi You can use Annocript program for GO annotation and pathway analysis.
I would recommend you to start with the official GO website. They have the most up-to-date database. You can also use some third party online tools but their databases can be very outdated.
I could not find any GO information for maize, so you probably have to use the GO of Arabidopsis. Define orthologs between your genes and Arabidopsis and perform the test using Arabidopsis orthologs list.
Alternatively, you can try Blast2GO which can automatically annotate your genes and perform the GO enrichment test.
See the links below.
http://geneontology.org/page/go-enrichment-analysis
https://www.blast2go.com/
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