Question: Guildeline Required For Gene Ontology, after Differntial expression analysis
0
gravatar for hirahameed222
6 weeks ago by
hirahameed2220 wrote:

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

rna-seq next-gen R gene • 240 views
ADD COMMENTlink modified 6 weeks ago by jared.andrews072.3k • written 6 weeks ago by hirahameed2220
2
gravatar for Vijay Lakhujani
6 weeks ago by
Vijay Lakhujani4.1k
India
Vijay Lakhujani4.1k wrote:

check out topGO

ADD COMMENTlink written 6 weeks ago by Vijay Lakhujani4.1k

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.

ADD REPLYlink written 6 weeks ago by hirahameed2220
1

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

ADD REPLYlink written 6 weeks ago by Kevin Blighe42k
2
gravatar for Luiz
6 weeks ago by
Luiz30
Brazil / São Paulo / UNIFESP
Luiz30 wrote:

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

ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by Luiz30

can you please explain for wheat RNA-seq data Can i use this ?

ADD REPLYlink written 6 weeks ago by hirahameed2220
1

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.

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by Luiz30
1
gravatar for Giovanni.madrigal12
6 weeks ago by
Giovanni.madrigal1280 wrote:

Although you may need to may an account (which is free), omictools can be used to search for numerous bioinformatic programs that are designed for whatever task you have in mind.

ADD COMMENTlink written 6 weeks ago by Giovanni.madrigal1280
1
gravatar for i.sudbery
6 weeks ago by
i.sudbery4.5k
Sheffield, UK
i.sudbery4.5k wrote:

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.

ADD COMMENTlink written 6 weeks ago by i.sudbery4.5k
1
gravatar for jared.andrews07
6 weeks ago by
jared.andrews072.3k
St. Louis, MO
jared.andrews072.3k wrote:

enrichR is extremely easy to use. clusterProfiler is a more advanced solution that takes a little bit more time to get acquainted with.

ADD COMMENTlink written 6 weeks ago by jared.andrews072.3k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2003 users visited in the last hour