protein pathway analysis software or tools

Question

[yueli7]

Hello,

Anyone know any software that can analysis protein pathway?

Just like:

GProX, a User-Friendly Platform for Bioinformatics Analysis and Visualization of Quantitative Proteomics Data

GSOA, Inferring pathway dysregulation in cancers from multiple types of omic data

Anyone know any software or tools that similar to that?

Thanks in advance!

Best,

Yue

Answer 1

[natasha.sernova]

See this article:

A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants

Elisa Cirillo,1,* Laurence D. Parnell,2 and Chris T. Evelo1

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5681904/

Below is a fragment of the article abstract:

"Pathway analysis is a powerful method for data analysis in genomics, most often applied to gene expression analysis. It is also promising for single-nucleotide polymorphism (SNP) data analysis, such as genome-wide association study data, because it allows the interpretation of variants with respect to the biological processes in which the affected genes and proteins are involved. Such analyses support an interactive evaluation of the possible effects of variations on function, regulation or interaction of gene products. Current pathway analysis software often does not support data visualization of variants in pathways as an alternate method to interpret genetic association results, and specific statistical methods for pathway analysis of SNP data are not combined with these visualization features. In this review, we first describe the visualization options of the tools that were identified by a literature review, in order to provide insight for improvements in this developing field."

The article is specific, if you need something different - look at the right panel of your own question page,

you will find a lot of related useful posts.

Another way to find some general information: it turned out that WIKI-page has a nice collection of db-links:

(KEGG, REACTOME, etc):

https://en.m.wikipedia.org/wiki/Biological_pathway

[yueli7]

Hello, natasha.sernova,

Thank you so much for your great help!

Thank you again!

Best,

Yue