This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Validation tools in bioinformatics

I would like to have a list of validation tools used in bioinformatics. Such as tools used for validation of differential gene expression etc.

rna-seq gene sequence sequencing rna-seq
• 1,931 views • link
updated by Kristoffer Vitting-Seerup Kristoffer Vitting-Seerup • written by tonmoya.22 • tonmoya.22

If, by validation, you mean characterizing your differentially expressed genes, you can use GSEA, gene ontology term enrichment, pathway analysis, etc.

If I am validating my differential gene expression data for tumor versus normal, I might use one of those tools to see if the expected cancer pathways are represented among my differentially expressed genes.

If I'm analyzing a high-throughput genome-wide loss-of-function genetic screen, I might use one of those tools to validate whether known essential genes are represented among my hits.

It's basically using known annotated gene sets / pathways to serve as a positive control for analyzing your experiments.

• 0 views • link
written by dsull dsull

2 answers

"validation of differential expression"?

One would generally have to do that by doing additional experiments (e.g. qPCR etc). It would be out of the bioinformatics realm at that point.

• 0 views • link
written by GenoMax GenoMax

I think the most common ways of doing "bioinformatic validations" is the analyse another similar dataset and see if you find the same.

• 0 views • link
written by Kristoffer Vitting-Seerup Kristoffer Vitting-Seerup

Log in to answer this question.

More posts like this