Questions tagged [go]

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Retrieve gene symbols of genes from GO term with Python

Is there a way to retrieve the gene symbols belonging to a GO term with Python ? For example, the GO:0006096 (glycolytic process) contains 96 genes: ...
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1answer
25 views

Number of edges in Graphical Analysis using Jupyter with Go Programming language

I'm trying to learn graphical analysis in a biological setting. The online course suggested using the Go Programming language, so I'm new to it and help to understand why the number of edges that I ...
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1answer
160 views

Choosing Fisher's Exact or Binomial test for overrepresentation in PANTHER

The PANTHER website offers a tool to obtain the GO-based overrepresentation of a gene list (the analyzed list) versus a reference gene list. After entering both these lists, the tool asks to choose ...
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1answer
40 views

After KEGG and GO analysis, how to make tables+phylogenetic trees

hope everyone is ok. I used Trinity to do a de novo transcriptome assembly, then blastp/blastx and then used Blast2GO software to do KEGG and GO analysis. So i got some txt files with header : for GO ...
4
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1answer
172 views

GOseq analysis with evidence code filter

When using GOseq analysis on RNA-seq data, I often find many 'false positives'. What I mean with that is that some genes in certain categories are not really involved in the process, but are only ...
7
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2answers
390 views

Correct for gene length or read counts in GO enrichment analysis

It is a well reported fact that GO analysis of RNAseq results is affected by a number of biases, including length bias and expression level bias. The bioconductor ...
5
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2answers
718 views

How to run enrichment analysis of protein functional annotation?

I have a lot of protein clusters. I want to perform an enrichment analysis of their functional annotations, against reference datasets or list of genes I select. More precisely: a method yields ...