title: DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections.
abstract: The DiseaseConnect (http://disease-connect.org) is a web server for analysis and visualization of a comprehensive knowledge on mechanism-based disease connectivity. The traditional disease classification system groups diseases with similar clinical symptoms and phenotypic traits. Thus, diseases with entirely different pathologies could be grouped together, leading to a similar treatment design. Such problems could be avoided if diseases were classified based on their molecular mechanisms. Connecting diseases with similar pathological mechanisms could inspire novel strategies on the effective repositioning of existing drugs and therapies. Although there have been several studies attempting to generate disease connectivity networks, they have not yet utilized the enormous and rapidly growing public repositories of disease-related omics data and literature, two primary resources capable of providing insights into disease connections at an unprecedented level of detail. Our DiseaseConnect, the first public web server, integrates comprehensive omics and literature data, including a large amount of gene expression data, Genome-Wide Association Studies catalog, and text-mined knowledge, to discover disease-disease connectivity via common molecular mechanisms. Moreover, the clinical comorbidity data and a comprehensive compilation of known drug-disease relationships are additionally utilized for advancing the understanding of the disease landscape and for facilitating the mechanism-based development of new drug treatments.
authors.affiliation: Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan Agricultural Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan xjzhou@usc.edu.
authors.forename: Chun-Chi
authors.initials: CC
authors.lastname: Liu
authors.affiliation: Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan.
authors.forename: Yu-Ting
authors.initials: YT
authors.lastname: Tseng
authors.affiliation: Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Wenyuan
authors.initials: W
authors.lastname: Li
authors.affiliation: Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan.
authors.forename: Chia-Yu
authors.initials: CY
authors.lastname: Wu
authors.affiliation: Computation Institute, Institute for Genomics and Systems Biology University of Chicago, Chicago, IL 60637, USA.
authors.forename: Ilya
authors.initials: I
authors.lastname: Mayzus
authors.affiliation: Computation Institute, Institute for Genomics and Systems Biology University of Chicago, Chicago, IL 60637, USA.
authors.forename: Andrey
authors.initials: A
authors.lastname: Rzhetsky
authors.affiliation: Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Fengzhu
authors.initials: F
authors.lastname: Sun
authors.affiliation: Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Waterman
authors.affiliation: Agricultural Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan Institute of Molecular Biology, National Chung Hsing University, Taichung 402, Taiwan Institute of Biomedical Sciences, National Chung Hsing University, Taichung 402, Taiwan.
authors.forename: Jeremy J W
authors.initials: JJ
authors.lastname: Chen
authors.affiliation: Jane Anne Nohl Division of Hematology and Center for the Study of Blood Diseases, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA.
authors.forename: Preet M
authors.initials: PM
authors.lastname: Chaudhary
authors.affiliation: Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Joseph
authors.initials: J
authors.lastname: Loscalzo
authors.affiliation: Will Rogers Institute Pulmonary Research Center, University of Southern California, Los Angeles, CA 90033, USA Department of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Edward
authors.initials: E
authors.lastname: Crandall
authors.affiliation: Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA xjzhou@usc.edu.
authors.forename: Xianghong Jasmine
authors.initials: XJ
authors.lastname: Zhou
mesh_terms: D015897:Comorbidity; D004194:Disease / Q000235:genetics*; D004358:Drug Therapy; D015870:Gene Expression; D006801:Humans; D020407:Internet; D035683:MicroRNAs / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D012984:Software
chemical_list: D035683:MicroRNAs