title: MitProNet: A knowledgebase and analysis platform of proteome, interactome and diseases for mammalian mitochondria.
abstract: Mitochondrion plays a central role in diverse biological processes in most eukaryotes, and its dysfunctions are critically involved in a large number of diseases and the aging process. A systematic identification of mitochondrial proteomes and characterization of functional linkages among mitochondrial proteins are fundamental in understanding the mechanisms underlying biological functions and human diseases associated with mitochondria. Here we present a database MitProNet which provides a comprehensive knowledgebase for mitochondrial proteome, interactome and human diseases. First an inventory of mammalian mitochondrial proteins was compiled by widely collecting proteomic datasets, and the proteins were classified by machine learning to achieve a high-confidence list of mitochondrial proteins. The current version of MitProNet covers 1124 high-confidence proteins, and the remainders were further classified as middle- or low-confidence. An organelle-specific network of functional linkages among mitochondrial proteins was then generated by integrating genomic features encoded by a wide range of datasets including genomic context, gene expression profiles, protein-protein interactions, functional similarity and metabolic pathways. The functional-linkage network should be a valuable resource for the study of biological functions of mitochondrial proteins and human mitochondrial diseases. Furthermore, we utilized the network to predict candidate genes for mitochondrial diseases using prioritization algorithms. All proteins, functional linkages and disease candidate genes in MitProNet were annotated according to the information collected from their original sources including GO, GEO, OMIM, KEGG, MIPS, HPRD and so on. MitProNet features a user-friendly graphic visualization interface to present functional analysis of linkage networks. As an up-to-date database and analysis platform, MitProNet should be particularly helpful in comprehensive studies of complicated biological mechanisms underlying mitochondrial functions and human mitochondrial diseases. MitProNet is freely accessible at http://bio.scu.edu.cn:8085/MitProNet.
authors.affiliation: College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People's Republic of China.
authors.forename: Jiabin
authors.initials: J
authors.lastname: Wang
authors.affiliation: College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People's Republic of China.
authors.forename: Jian
authors.initials: J
authors.lastname: Yang
authors.affiliation: College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People's Republic of China.
authors.forename: Song
authors.initials: S
authors.lastname: Mao
authors.affiliation: College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People's Republic of China.
authors.forename: Xiaoqiang
authors.initials: X
authors.lastname: Chai
authors.affiliation: College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People's Republic of China.
authors.forename: Yuling
authors.initials: Y
authors.lastname: Hu
authors.affiliation: College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People's Republic of China.
authors.forename: Xugang
authors.initials: X
authors.lastname: Hou
authors.affiliation: College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People's Republic of China.
authors.forename: Yiheng
authors.initials: Y
authors.lastname: Tang
authors.affiliation: College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People's Republic of China.
authors.forename: Cheng
authors.initials: C
authors.lastname: Bi
authors.affiliation: College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People's Republic of China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Li
mesh_terms: D000818:Animals; D066264:Datasets as Topic; D050259:Genes, Mitochondrial; D030342:Genetic Diseases, Inborn / Q000235:genetics*; D006801:Humans; D008322:Mammals / Q000378:metabolism; D055442:Metabolome; D024101:Mitochondrial Proteins / Q000235:genetics* / Q000378:metabolism; D020543:Proteome; D012984:Software
chemical_list: D024101:Mitochondrial Proteins; D020543:Proteome