Tool: Bioconductor PoTRA: Pathways of Topological Rank Analysis
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8 months ago by
plink_985750
United States
plink_985750 wrote:

Bioconductor PoTRA: Pathways of Topological Rank Analysis

The PoTRA analysis is based on topological ranks of genes in biological pathways. PoTRA can be used to detect pathways involved in disease (Li, Liu & Dinu, 2018). We use PageRank to measure the relative topological ranks of genes in each biological pathway, then select hub genes for each pathway, and use Fishers Exact test to determine if the number of hub genes in each pathway is altered from normal to cancer (Li, Liu & Dinu, 2018). Alternatively, if the distribution of topological ranks of gene in a pathway is altered between normal and cancer, this pathway might also be involved in cancer (Li, Liu & Dinu, 2018). Hence, we use the Kolmogorov–Smirnov test to detect pathways that have an altered distribution of topological ranks of genes between two phenotypes (Li, Liu & Dinu, 2018). PoTRA can be used with the KEGG, Biocarta, Reactome, NCI, SMPDB and PharmGKB databases from the devel graphite library.

Home: https://www.bioconductor.org/packages/release/bioc/html/PoTRA.html
Vignette: https://www.bioconductor.org/packages/release/bioc/vignettes/PoTRA/inst/doc/PoTRA.html

ADD COMMENTlink modified 7 months ago • written 8 months ago by plink_985750

Hi Everyone,

Don't forget to try PoTRA for mRNA pathway analysis. It's very easy to use. Please post questions and I will help you if you need it.

Thanks.

ADD REPLYlink written 7 months ago by plink_985750

Hi Everyone,

Please try out the PoTRA algorithm and post suggestions here about what features would would like to have added to it. Its a really great, easy program for generating ranked KEGG pathways with mRNA data.

Thanks.

Home: https://www.bioconductor.org/packages/release/bioc/html/PoTRA.html
Vignette: https://www.bioconductor.org/packages/release/bioc/vignettes/PoTRA/inst/doc/PoTRA.htmls.

ADD REPLYlink modified 7 months ago • written 7 months ago by plink_985750
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