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. 2009 Jan;37(Database issue):D767-72.
doi: 10.1093/nar/gkn892. Epub 2008 Nov 6.

Human Protein Reference Database--2009 update

T S Keshava Prasad  1 , Renu Goel, Kumaran Kandasamy, Shivakumar Keerthikumar, Sameer Kumar, Suresh Mathivanan, Deepthi Telikicherla, Rajesh Raju, Beema Shafreen, Abhilash Venugopal, Lavanya Balakrishnan, Arivusudar Marimuthu, Sutopa Banerjee, Devi S Somanathan, Aimy Sebastian, Sandhya Rani, Somak Ray, C J Harrys Kishore, Sashi Kanth, Mukhtar Ahmed, Manoj K Kashyap, Riaz Mohmood, Y L Ramachandra, V Krishna, B Abdul Rahiman, Sujatha Mohan, Prathibha Ranganathan, Subhashri Ramabadran, Raghothama Chaerkady, Akhilesh Pandey
Affiliations

Human Protein Reference Database--2009 update

T S Keshava Prasad et al. Nucleic Acids Res. 2009 Jan.

Abstract

Human Protein Reference Database (HPRD--http://www.hprd.org/), initially described in 2003, is a database of curated proteomic information pertaining to human proteins. We have recently added a number of new features in HPRD. These include PhosphoMotif Finder, which allows users to find the presence of over 320 experimentally verified phosphorylation motifs in proteins of interest. Another new feature is a protein distributed annotation system--Human Proteinpedia (http://www.humanproteinpedia.org/)--through which laboratories can submit their data, which is mapped onto protein entries in HPRD. Over 75 laboratories involved in proteomics research have already participated in this effort by submitting data for over 15,000 human proteins. The submitted data includes mass spectrometry and protein microarray-derived data, among other data types. Finally, HPRD is also linked to a compendium of human signaling pathways developed by our group, NetPath (http://www.netpath.org/), which currently contains annotations for several cancer and immune signaling pathways. Since the last update, more than 5500 new protein sequences have been added, making HPRD a comprehensive resource for studying the human proteome.

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Figures

Figure 1.
Figure 1.
Display of PhosphoMotif Finder integrated into HPRD. Screen shot shows molecule page of MASTL, a hypothetical protein implicated in autosomal dominant thrombocytopenia. ‘PhosphoMotif Finder’ tab in the HPRD page leads to the utility page where the sequence of the MASTL is displayed. Users can select either serine/threonine or tyrosine motifs and submit the query by clicking ‘Find Motifs’ button. Result page displays mapped experimentally derived motifs present in sequence along with the information on position, actual sequence, experimentally derived consensus phosphorylation motifs and link to the PubMed abstracts where these motifs have been described. MASTL sequence is shown to contain 30 potential tyrosine phosphorylation sites as seen in this figure.
Figure 2.
Figure 2.
Linking to human signaling pathways from HPRD. ‘Pathways’ button in the HPRD page of JAK2 is hyperlinked to its NetPath page. It shows the list of signaling pathways in which the protein is involved along with the description of its interactors in each pathway. Each interaction or catalysis event is linked to the PubMed abstract of the original article. The pathway name is linked to the specific signaling pathway annotated in NetPath.
Figure 3.
Figure 3.
Display of PTM data in HPRD submitted through Human Proteinpedia. Adducin1 molecule page in HPRD shows five novel phosphorylation sites submitted through Human Proteinpedia. Phosphorylation sites are hyperlinked to Human Proteinpedia page with information on the investigator, laboratory and meta-annotation of mass spectrometry experiment. Corresponding MS/MS spectrum for a peptide is also displayed using spectrum viewer developed by PRIDE.
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