TissueNexus: a database of human tissue functional gene networks built with a large compendium of curated RNA-seq data

Author:

Lin Cui-Xiang12,Li Hong-Dong12,Deng Chao12,Guan Yuanfang3ORCID,Wang Jianxin12ORCID

Affiliation:

1. School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P.R. China

2. Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, Hunan 410083, P.R. China

3. Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA

Abstract

Abstract Mapping gene interactions within tissues/cell types plays a crucial role in understanding the genetic basis of human physiology and disease. Tissue functional gene networks (FGNs) are essential models for mapping complex gene interactions. We present TissueNexus, a database of 49 human tissue/cell line FGNs constructed by integrating heterogeneous genomic data. We adopted an advanced machine learning approach for data integration because Bayesian classifiers, which is the main approach used for constructing existing tissue gene networks, cannot capture the interaction and nonlinearity of genomic features well. A total of 1,341 RNA-seq datasets containing 52,087 samples were integrated for all of these networks. Because the tissue label for RNA-seq data may be annotated with different names or be missing, we performed intensive hand-curation to improve quality. We further developed a user-friendly database for network search, visualization, and functional analysis. We illustrate the application of TissueNexus in prioritizing disease genes. The database is publicly available at https://www.diseaselinks.com/TissueNexus/.

Funder

National Natural Science Foundation of China

111 Project

Hunan Provincial Science and Technology Program

Publisher

Oxford University Press (OUP)

Subject

Genetics

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