The source code that supports the findings of this study (Deep Multiomics Profiling of Brain Tumors Identifies Signaling Networks Downstream of Cancer Driver Genes) includes two major parts: JUMPp and JUMPq.
Function of JUMPp is to pre-process mass spectrometer generated raw data for protein identification and quantificaiton JUMPp composes of 4 segments:
i. JUMPps: Protein database search; ii. JUMPpf: Putative Match filtering using a target-decoy strategy. iii. JUMPpl: Phosphosite site localization score calculation for phosphoproteome analysis. iv. JUMPpg: protein/peptide quantification for TMT labelling
Function of JUMPn is for network analyses of post-processed proteomics-centered multi-omics data. JUMPn composes of 5 segments:
i. JUMPnc: Proteome co-expression clustering analysis using weighted correlation network analysis(WGCNA) published by: Peter Langfelder and Steve Horvath,WGCNA: an R package for weighted correlation network analysis.BMC Bioinformatics.2008. R package was downlaoded: https://cran.r-project.org/web/packages/WGCNA/index.html ii.JUMPnp: Pathway enrichment of each co-expression clusters using Fisher's exact test iii. JUMPnk: Kinase activity reference using IKAP, published by Mischnik M et al, IKAP: A heuristic framework for inference of kinase activities from Phosphoproteomics data. Bioinformatics.2016.Downloaded at https://omictools.com/ikap-tool iv. JUMPnt: transcriptional factor activity reference based on target gene expression v. JUMPna: Pathway activity calculation
JUMP software suite that produced by Peng lab were developed by: Xusheng Wang, Ji-Hoon Cho, Yuxin Li, Timothy Shaw, Hong Wang and Junmin Peng