Validation tools in bioinformatics

Question

[tonmoya.22]

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

[dsull]

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.

Answer 1

[GenoMax]

"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.

Answer 2

[Kristoffer Vitting-Seerup]

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