Human protein reference database—2006 update

Human Protein Reference Database (HPRD) () was developed to serve as a comprehensive collection of protein features, post-translational modifications (PTMs) and protein–protein interactions. Since the original report, this database has increased to >20 000 proteins entries and has become the largest database for literature-derived protein–protein interactions (>30 000) and PTMs (>8000) for human proteins. We have also introduced several new features in HPRD including: (i) protein isoforms, (ii) enhanced search options, (iii) linking of pathway annotations and (iv) integration of a novel browser, GenProt Viewer (), developed by us that allows integration of genomic and proteomic information. With the continued support and active participation by the biomedical community, we expect HPRD to become a unique source of curated information for the human proteome and spur biomedical discoveries based on integration of genomic, transcriptomic and proteomic data.

[1]  Zhenjun Hu,et al.  Visant: an Integrative Framework for Networks in Systems Biology , 2008 .

[2]  Richard J. Edwards,et al.  CompariMotif: quick and easy comparisons of sequence motifs , 2008, Bioinform..

[3]  Y. L. Ramachandra,et al.  Human Proteinpedia enables sharing of human protein data , 2008, Nature Biotechnology.

[4]  Kengo Kinoshita,et al.  COXPRESdb: a database of coexpressed gene networks in mammals , 2007, Nucleic Acids Res..

[5]  Seth I. Berger,et al.  Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases , 2007, BMC Bioinformatics.

[6]  Richard J. Edwards,et al.  SLiMFinder: A Probabilistic Method for Identifying Over-Represented, Convergently Evolved, Short Linear Motifs in Proteins , 2007, PloS one.

[7]  Timur Shtatland,et al.  PepBank - a database of peptides based on sequence text mining and public peptide data sources , 2007, BMC Bioinformatics.

[8]  Tamara Munzner,et al.  Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation , 2007, Bioinform..

[9]  S. Mathivanan,et al.  A curated compendium of phosphorylation motifs , 2007, Nature Biotechnology.

[10]  James E. Allen,et al.  T1DBase: integration and presentation of complex data for type 1 diabetes research , 2006, Nucleic Acids Res..

[11]  Erich E. Wanker,et al.  UniHI: an entry gate to the human protein interactome , 2006, Nucleic Acids Res..

[12]  David J. Reiss,et al.  BioNetBuilder: automatic integration of biological networks , 2006, Bioinform..

[13]  Jeffrey W. Smith,et al.  CutDB: a proteolytic event database , 2006, Nucleic Acids Res..

[14]  Christian von Mering,et al.  STRING 7—recent developments in the integration and prediction of protein interactions , 2006, Nucleic Acids Res..

[15]  Tatiana Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[16]  Tatiana A. Tatusova,et al.  Entrez Gene: gene-centered information at NCBI , 2004, Nucleic Acids Res..

[17]  Kumaran Kandasamy,et al.  An evaluation of human protein-protein interaction data in the public domain , 2006, BMC Bioinformatics.

[18]  K. N. Chandrika,et al.  Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets , 2006, Nature Genetics.

[19]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Lennart Martens,et al.  PRIDE: The proteomics identifications database , 2005, Proteomics.

[21]  Nichole L. King,et al.  Human Plasma PeptideAtlas , 2005, Proteomics.

[22]  Mark Daly,et al.  Haploview: analysis and visualization of LD and haplotype maps , 2005, Bioinform..

[23]  Anthony K. L. Leung,et al.  Nucleolar proteome dynamics , 2005, Nature.

[24]  Tatiana A. Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[25]  Zemin Zhang,et al.  Signal peptide prediction based on analysis of experimentally verified cleavage sites , 2004, Protein science : a publication of the Protein Society.

[26]  Steven P Gygi,et al.  Large-scale characterization of HeLa cell nuclear phosphoproteins. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[27]  C. Sander,et al.  The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data , 2004, Nature Biotechnology.

[28]  Hisashi Koga,et al.  HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE , 2004, Nucleic Acids Res..

[29]  Dipanwita Roy Chowdhury,et al.  Human protein reference database as a discovery resource for proteomics , 2004, Nucleic Acids Res..

[30]  Akhilesh Pandey,et al.  BioBuilder as a database development and functional annotation platform for proteins , 2004, BMC Bioinformatics.

[31]  Hanno Steen,et al.  Development of human protein reference database as an initial platform for approaching systems biology in humans. , 2003, Genome research.

[32]  Maria Jesus Martin,et al.  The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 , 2003, Nucleic Acids Res..

[33]  Steven C. Lawlor,et al.  GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways , 2002, Nature Genetics.

[34]  M. Mann,et al.  Directed Proteomic Analysis of the Human Nucleolus , 2002, Current Biology.

[35]  Alan F. Scott,et al.  Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders , 2004, Nucleic Acids Res..

[36]  M. Vidal,et al.  Protein interaction maps for model organisms , 2001, Nature Reviews Molecular Cell Biology.