TSUNAMI:Translational Bioinformatics Tool Suite for Network Analysis and Mining

作     者：Zhi Huang Zhi Han Tongxin Wang Wei Shao Shunian Xiang Paul Salama Maher Rizkalla Kun Huang Jie Zhang Zhi Huang;Zhi Han;Tongxin Wang;Wei Shao;Shunian Xiang;Paul Salama;Maher Rizkalla;Kun Huang;Jie Zhang

作者机构：School of Electrical and Computer EngineeringPurdue UniversityWest LafayetteIN 47907USA Department of Electrical and Computer EngineeringIndiana University-Purdue University IndianapolisIndianapolisIN 46202USA Department of MedicineIndiana University School of MedicineIndianapolisIN 46202USA Department of Computer ScienceIndiana UniversityBloomingtonIN 47405USA Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisIN 46202USA Department of Biostatistics and Health Data ScienceIndiana University School of MedicineIndianapolisIN 46202USA 

出 版 物：《Genomics, Proteomics & Bioinformatics》 (基因组蛋白质组与生物信息学报（英文版）)

年 卷 期：2021年第19卷第6期

页      面：1023-1031页

核心收录：

学科分类：0831[工学-生物医学工程（可授工学、理学、医学学位）] 0711[理学-系统科学] 07[理学] 08[工学] 

基　　金：supported by the American Cancer Society Inernal Reseatch Grant (to JZ) the National Cancer Institure Informatics Technology for Ccance Research U01 grant (Grant No. CA188547 to JZ and KH) the Indiana University Precision Health Initiative (to JZ and KH) the support from Indiana University Information Technologies and Advanced Biomedical IT Core 

主　　题：Network mining Gene co-expression network Transcriptomic data analysis lmQCM Web server Survival analysis 

摘      要：Gene co-expression network(GCN)mining identifies gene modules with highly correlated expression profiles across samples/*** enables researchers to discover latent gene/molecule interactions,identify novel gene functions,and extract molecular features from certain disease/condition groups,thus helping to identify disease ***,there lacks an easy-to-use tool package for users to mine GCN modules that are relatively small in size with tightly connected genes that can be convenient for downstream gene set enrichment analysis,as well as modules that may share common *** address this need,we developed an online GCN mining tool package:TSUNAMI(Tools SUite for Network Analysis and MIning).TSUNAMI incorporates our state-of-the-art lmQCM algorithm to mine GCN modules for both public and user-input data(microarray,RNA-seq,or any other numerical omics data),and then performs downstream gene set enrichment analysis for the identified *** has several features and advantages:1)a user-friendly interface and real-time co-expression network mining through a web server;2)direct access and search of NCBI Gene Expression Omnibus(GEO)and The Cancer Genome Atlas(TCGA)databases,as well as user-input gene ex-pression matrices for GCN module mining;3)multiple co-expression analysis tools to choose from,all of which are highly flexible in regards to parameter selection options;4)identified GCN modules are summarized to eigengenes,which are convenient for users to check their correlation with other clinical traits;5)integrated downstream Enrichr enrichment analysis and links to other gene set enrichment tools;and 6)visualization of gene loci by Circos plot in any step of the *** web service is freely accessible through URL:https://***/.Source code is available at https://***/huangzhii/TSUNAMI/.