Hello!
I have done differential expression analysis for my RNA-seq data set by following the HISAT, Stringtie and Ballgown protocol. The next thing i want to do is some basic gene ontology. Can anyone please suggest me some Tools, protocol to follow for desired work.
Have you any guidelines ?
Thank you in advance
•
written
by
hirahameed222 •
check out topGO
Can you please share any tutorial or guide me how to do this for basic Ontology process. I am new to deal with RNA-seq data and i am doing this work for the first time and it will be easy to learn if i follow some protocol.
A simple one, here: A: GO analysis using topGO
Also, please read the topGO vignette: http://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf
You have more complex solutions in R by topGO package as recommended by bioExplorer. I would suggest DOSE and others by Guangchuang Yu available on bioconductor repository. A simple solution can be the use of WebGestalt http://webgestalt.org or network analyst with gene ontology enrichment in network menu networkanalyst.ca/faces/home.xhtml
can you please explain for wheat RNA-seq data Can i use this ?
Basically any data that you have an gene ID (entrez, RefSeq, Ensembl, Symbol..) and a value of expression.
For example, WebGestalt requires only your gene list. While network analyst can be used with your gene list only and your gene list + values of expression (positive or negative, such as log2 fold change). The packages of Guangchuang Yu can be used in R based on entrez ID to construct a table of GO:ID and build the plot. I would try to made this enrichment with online tools (webgestalt, network analyst, string) before reproduce in R.
If you are analysing RNA-seq data then you need to take account of the bias introduced by gene length and expression level. See my answer to this question A: What's your preferred pathway enrichment analysis tool after DEG analysis and wh for suggestions.
enrichR is extremely easy to use. clusterProfiler is a more advanced solution that takes a little bit more time to get acquainted with.
Log in to answer this question.
