Computational protocol: MicroRNA Regulation and Tissue-Specific Protein Interaction Network

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Protocol publication

[…] We used the protein tissue expression data in HPRD of Release 9 . Totally 10 human tissues were finally selected because of large quantity of experimentally validated proteins. They included brain, heart, kidney, liver, lung, skeletal muscle, pancreas, placenta, spleen and testis. Notably, the ubiquitously expressed proteins were also included in the protein list of each tissue. The Cytoscape plug-in BisoGenet was used to retrieve human experimentally validated protein interactions from 6 datasets (BIOGRID, INTACT, MINT, DIP, BIND and HPRD). After removing self-loops, isolated nodes and small network components, NetworkAnalyzer calculated the degree value of each node representing protein which was then categorized following the classification scheme used by Lu et al. . In addition, proteins represented as nodes were also sorted into four subunits according to their tissue expression specificity. In particular, proteins that expressed in all of the 10 tissues were defined as commonly expressed proteins, and proteins that expressed in only in less number of tissues (n≤3) were defined as tissue-specific proteins. […]

Pipeline specifications

Software tools BisoGenet, NetworkAnalyzer
Application Protein interaction analysis
Organisms Homo sapiens