title: HIVed, a knowledgebase for differentially expressed human genes and proteins during HIV infection, replication and latency.
abstract: Measuring the altered gene expression level and identifying differentially expressed genes/proteins during HIV infection, replication and latency is fundamental for broadening our understanding of the mechanisms of HIV infection and T-cell dysfunction. Such studies are crucial for developing effective strategies for virus eradication from the body. Inspired by the availability and enrichment of gene expression data during HIV infection, replication and latency, in this study, we proposed a novel compendium termed HIVed (HIV expression database; http://hivlatency.erc.monash.edu/) that harbours comprehensive functional annotations of proteins, whose genes have been shown to be dysregulated during HIV infection, replication and latency using different experimental designs and measurements. We manually curated a variety of third-party databases for structural and functional annotations of the protein entries in HIVed. With the goal of benefiting HIV related research, we collected a number of biological annotations for all the entries in HIVed besides their expression profile, including basic protein information, Gene Ontology terms, secondary structure, HIV-1 interaction and pathway information. We hope this comprehensive protein-centric knowledgebase can bridge the gap between the understanding of differentially expressed genes and the functions of their protein products, facilitating the generation of novel hypotheses and treatment strategies to fight against the HIV pandemic.
authors.affiliation: Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia.|Department of Microbiology, Monash University, Melbourne, VIC 3800, Australia.|Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia.
authors.forename: Chen
authors.initials: C
authors.lastname: Li
authors.affiliation: Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia.|Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia.
authors.forename: Sri H
authors.initials: SH
authors.lastname: Ramarathinam
authors.affiliation: Monash Bioinformatics Platform, Monash University, Melbourne, VIC 3800, Australia.
authors.forename: Jerico
authors.initials: J
authors.lastname: Revote
authors.affiliation: Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC 3010, Australia.
authors.forename: Georges
authors.initials: G
authors.lastname: Khoury
authors.affiliation: Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia.|Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia.|Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia.
authors.forename: Jiangning
authors.initials: J
authors.lastname: Song
authors.affiliation: Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia.|Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia.
authors.forename: Anthony W
authors.initials: AW
authors.lastname: Purcell
mesh_terms: D062126:Databases, Chemical; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D015658:HIV Infections / Q000473:pathology* / Q000821:virology; D015497:HIV-1 / Q000502:physiology*; D006801:Humans; D058977:Molecular Sequence Annotation; D017735:Virus Latency; D014779:Virus Replication