| Full text | |
| Author(s): Show less - |
Russo, Pedro S. T.
[1]
;
Ferreira, Gustavo R.
[1]
;
Cardozo, Lucas E.
[1]
;
Buerger, Matheus C.
[1]
;
Arias-Carrasco, Raul
[2]
;
Maruyama, Sandra R.
[3]
;
Hirata, Thiago D. C.
[1]
;
Lima, Diogenes S.
[1]
;
Passos, Fernando M.
[1]
;
Fukutani, Kiyoshi F.
[3]
;
Lever, Melissa
[1]
;
Silva, Joao S.
[3]
;
Maracaja-Coutinho, Vinicius
[2]
;
Nakaya, Helder I.
[1]
Total Authors: 14
|
| Affiliation: | [1] Univ Sao Paulo, Sch Pharmaceut Sci, Dept Clin & Toxicol Anal, BR-05508900 Sao Paulo, SP - Brazil
[2] Univ Chile, Adv Ctr Chron Dis ACCDiS, Fac Ciencias Quim & Farmaceut, Santiago - Chile
[3] Univ Sao Paulo, Dept Biochem Immunol & Cell Biol, Ribeirao Preto, SP - Brazil
Total Affiliations: 3
|
| Document type: | Journal article |
| Source: | BMC Bioinformatics; v. 19, FEB 20 2018. |
| Web of Science Citations: | 15 |
| Abstract | |
Background: The analysis of modular gene co-expression networks is a well-established method commonly used for discovering the systems-level functionality of genes. In addition, these studies provide a basis for the discovery of clinically relevant molecular pathways underlying different diseases and conditions.\& para;\& para;Results: In this paper, we present a fast and easy-to-use Bioconductor package named CEMiTool that unifies the discovery and the analysis of co-expression modules. Using the same real datasets, we demonstrate that CEMiTool outperforms existing tools, and provides unique results in a user-friendly html report with high quality graphs. Among its features, our tool evaluates whether modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group, as well as it integrates transcriptomic data with interactome information, identifying the potential hubs on each network. We successfully applied CEMiTool to over 1000 transcriptome datasets, and to a new RNA-seq dataset of patients infected with Leishmania, revealing novel insights of the disease's physiopathology.\& para;\& para;Conclusion: The CEMiTool R package provides users with an easy-to-use method to automatically implement gene co-expression network analyses, obtain key information about the discovered gene modules using additional downstream analyses and retrieve publication-ready results via a high-quality interactive report. (AU) | |
| FAPESP's process: | 15/25825-8 - Analysis of metabolic regulatory networks in inflammation |
| Grantee: | Melissa Lever |
| Support Opportunities: | Scholarships in Brazil - Post-Doctoral |
| 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: | 12/19278-6 - Systems biology of long non-coding RNAs |
| Grantee: | Helder Takashi Imoto Nakaya |
| Support Opportunities: | Research Grants - Young Investigators Grants |
| FAPESP's process: | 14/19323-7 - Long noncoding RNAs as potential biomarkers of arthritis |
| Grantee: | Gustavo Rodrigues Ferreira |
| Support Opportunities: | Scholarships in Brazil - Scientific Initiation |
| FAPESP's process: | 14/24162-2 - Analyses of the regulatory transcriptional mechanisms mediated by miRNAs in metabolic syndrome |
| Grantee: | Thiago Dominguez Crespo Hirata |
| Support Opportunities: | Scholarships in Brazil - Doctorate (Direct) |
| 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: | 15/20897-0 - ConsensusGraph: Assessing the Stability of Gene Networks |
| Grantee: | Pedro de Sá Tavares Russo |
| Support Opportunities: | Scholarships in Brazil - Master |