Hepatitis C Virus Protein Interaction Database
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1. What is HCVpro?

HCVpro is a freely accessible online knowledgebase comprising of Hepatitis C Virus (HCV) and human protein interactions.

2. Why was HCVpro created?

Currently HCV protein interactions data are found in literature and other publicly available databases but there is no single database solely focused on HCV protein interactions. HCVpro was thus created to offer "a one stop" knowledgebase on HCV protein interactions. Data integrated in HCVpro may enhance understanding of HCV life cycle, molecular function of its proteins, pathways and infection, and thereby augment efforts towards discovery of drugs, drug targets and diagnostic biomarkers.

3. What are the data sources in HCVpro?

HCVpro comprises of both manually verified literature- and database-curated interactions. Protein interactions databases employed for the curations were: BIND, VirusMINT and VirHostNet. Additionally, functional annotation data were obtained from publicly available annotation resources and published literature.

4. What is unique about HCVpro, which cannot be found in other databases?

HCVpro provides enriched comprehensive and integrated data on HCV and human protein interactions, functional annotations, hepatocellular carcinoma (HCC) related gene expression, drug development, pathways, and cross referenced links to other essential biological databases.

5. What type of interaction data can be obtained from HCVpro?

HCVpro provides two types of interactions:
  1. HCV viral-viral protein interactions
  2. HCV viral-human protein interactions

6. How can I query HCVpro?

The enhanced user query interface enables users to perform searches via the HCVpro by browsing the following sub query menus:
  • Protein Select
  • - HCV proteins: e.g. E2
    - Human proteins: e.g. CD81
    - Human Chromosome number: e.g. 10
  • Evidence
  • - Experiment type: e.g. coimmunoprecipitation
    - PubMed ID: e.g. 10846074
  • Identifier Search
  • - HCVpro ID: e.g. hcv0128
    - BIND ID: e.g. 183964
    - MINT ID: e.g. MINT-14803
  • String Search
  • - Gene Name: e.g. Vimentin
    - Gene ID: e.g. 7431
    - Gene symbol: e.g. VIM

7. Are there any future updates or modification in the pipeline?

Yes, we would like to integrate Blast queries to enhance querying capabilities of HCVpro. Data on microRNA and siRNA would be integrated to augment efforts towards drug discovery. A complete HCV interactome would be provided in the background to enable users retrieve protein interaction sub-network and topological statistical features. Additionally, we will include features for computing druggability of protein interactions and also enable ligand and protein target screening online.

8. Can researchers submit interactions to HCVpro?

Yes, upon enquiries researchers may submit novel interactions either before or after publications in MIMIx compatible format. Data on interaction details such as domains, motif and residues involved in the interaction would be incorporated in the next update. Authors who have previously published HCV protein interactions would be called upon to submit interaction details or the developers involved in the HCVpro project will computationally infer as an alternative.

The basic format for submission of interactions has been adapted from VirHostNet and is found below:

Protein A id Protein B id PSI-MI 2.5 method id PubMed id

Users may use the following links to convert interaction detection methods to PSI-MI 2.5:

http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/protein/psi-mi.obo

or at

http://www.ebi.ac.uk/ontology-lookup/

Click the links below for more details on PSI-MI data format:
http://www.ncbi.nlm.nih.gov/pubmed/20078892
http://www.ncbi.nlm.nih.gov/pubmed/18936051
Click the links below for more details on MIMIx data formats:
http://www.ncbi.nlm.nih.gov/pubmed/17687370

9. Can I download interaction data from HCVpro?

Yes, users may download the full HCVpro interaction data in a tab delimited format via the Download menu item.

10. Is there a user manual on HCVpro?

Yes, users can access the manual via the Manual menu item.

11. To whom can I report a bug or discrepancy?

Please report all queries via the Contact menu item.


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