webCEMiTool: Co-expression Modular Analysis Made Easy

Author(s)

Cardozo, Lucas E. ^[1] ; Russo, Pedro S. T. ^[1] ; Gomes-Correia, Bruno ^[2] ; Araujo-Pereira, Mariana ^[1] ; Sepulveda-Hermosilla, Gonzalo ^[3] ; Maracaja-Coutinho, Vinicius ^[2] ; Nakaya, I, Helder

Affiliation

^[1] I, Univ Sao Paulo, Sch Pharmaceut Sci, Dept Clin & Toxicol Anal, Sao Paulo - Brazil

^[2] Univ Chile, Fac Ciencias Quim & Farmaceut, Adv Ctr Chron Dis ACCDiS, Santiago - Chile

^[3] Univ Mayor, Fac Ciencias, Ctr Genom & Bioinformat, Santiago - Chile

• Document type: Journal article
• Source: FRONTIERS IN GENETICS; v. 10, MAR 6 2019.
• Web of Science Citations: 1

Abstract

Co-expression analysis has been widely used to elucidate the functional architecture of genes under different biological processes. Such analysis, however, requires substantial knowledge about programming languages and/or bioinformatics skills. We present webCEMiTool,(1) a unique online tool that performs comprehensive modular analyses in a fully automated manner. The webCEMiTool not only identifies co-expression gene modules but also performs several functional analyses on them. In addition, webCEMiTool integrates transcriptomic data with interactome information (i.e., protein-protein interactions) and identifies potential hubs on each network. The tool generates user-friendly html reports that allow users to search for specific genes in each module, as well as check if a module contains genes overrepresented in specific pathways or altered in a specific sample phenotype. We used webCEMiTool to perform a modular analysis of single-cell RNA-seq data of human cells infected with either Zika virus or dengue virus. (AU)

• FAPESP's process: 13/08216-2 - CRID - Center for Research in Inflammatory Diseases
• Grantee: Fernando de Queiroz Cunha
• Support Opportunities: Research Grants - Research, Innovation and Dissemination Centers - RIDC
• FAPESP's process: 17/05762-7 - ConsensusGraph: identifying consensus gene networks
• Grantee: Pedro de Sá Tavares Russo
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• FAPESP's process: 18/10748-6 - Analysis of long non-coding RNAs in transcriptome of mammals infected with zika virus
• Grantee: Mariana Araújo Pereira
• Support Opportunities: Scholarships in Brazil - Master
• FAPESP's process: 12/19278-6 - Systems biology of long non-coding RNAs
• Grantee: Helder Takashi Imoto Nakaya
• Support Opportunities: Research Grants - Young Investigators Grants