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4.11 PPI view -Protein-Protein Interaction viewer

The PPI view displays H-InvDB human protein-protein interaction (PPI) information. It is constructed by assigning interaction data to H-InvDB proteins which were originally predicted from transcriptional products generated by the H-Invitational project.

4.11.1 Access to the PPI view

1) Through H-InvDB
Users may access to the PPI view from "Protein-protein interaction (PPI)" in a Function section of the transcript view.

2) Direct access to the PPI view
Users may access to the top search page of the PPI view from the following URL.
http://h-invitational.jp/hinv/ppi/

4.11.2 Sections of the PPI view

HIP: H-Invitational Protein
HIP is an originally predicted protein from H-InvDB transcriptional product. All proteins in H-InvDB are assigned their own HIP IDs. If one residue in two protein sequences is different they have distinct HIP IDs.

Definition of identical proteins in the PPI view
The identical proteins in the PPI view are defined as clusters of proteins concatenated by single linkage clustering in which their sequence identities are over or same 98% and the alignment length coverage to each other are over or same 95%.

Data sources
We collected PPI data from the following six PPI databases.

 
BIND1 http://www.bind.ca/Action
DIP2 http://dip.doe-mbi.ucla.edu
MINT3 http://mint.bio.uniroma2.it/mint/Welcome.do
HPRD4 http://www.hprd.org
IntAct5 http://www.ebi.ac.uk/intact/index.jsp
GNP_Y2H http://genomenetwork.nig.ac.jp/public/sys/gnppub/Top.do

We removed redundancies of the PPI data among the databases with the sequence similarity (98% identity in 95% alignment length coverage to each other) and integrated them with the H-InvDB proteins. As the result, we got 32,198 human PPIs comprised of 9,268 proteins.

Data download
We will provide download files at the next release.

4.11.3 Page layout of the PPI view

Top search page
You can search for your proteins of interest by inputting their keywords, gene symbol, H-InvDB IDs (HIX: gene cluster ID, HIT: transcript ID, HIP: protein ID), or protein accession number (UniProt, RefSeq, GI, CCDS, PDB) into a search box then click a search button.


Fig 4.11.1 Top search page

Search results page
It displays hit proteins by your query. Please click Human PPIs botton to show PPI information.


Fig 4.11.2 Search results page

Sections of interacting protein data
It displays human PPI information. Your query protein (red title) is displayed above and a view of its interacting proteins (blue titles) is displayed below.


Fig 4.11.3 Human PPI information page

It shows the following information of a protein which interacts with the query protein.

  1. Title
    Protein ID: H-InvDB representative HIP ID
    Symbol: A symbol of the protein
    You can click Human PPIs botton icon then the PPI view displays human PPI information of the title protein. () includes the number of PPIs which the protein has.

  2. Definitions
    Annotation of the title protein.

  3. H-InvDB IDs
    H-InvDB provides series of data such as gene clusters, transcriptional products (transcripts) from the gene clusters, and proteins predicted from the transcripts.
    Gene cluster ID : HIX ID (H-InvDB gene cluster ID)
      If you want to check a location of genes in a chromosome, please click IDs to access to H-InvDB Locus view.
    Transcript ID : HIT ID (H-InvDB transcript ID)
      If you want to check the detailed transcript information, please click IDs to access to H-InvDB transcript view.
    Protein ID : HIP ID (H-InvDB protein ID)
      It shows identical protein HIP IDs of the representative HIP ID.
      Please see "HIP: H-Invitational Protein" section for the detailed HIP description.

  4. Protein Accession Numbers
    It shows the protein accession numbers of UniProt, RefSeq, and GI. These accession numbers are displayed if the HIP sequence has a perfect match (identity 100%, coverage 100%) to the protein accession numbers except PDB IDs (identity 98%, coverage 95%).

  5. Human PPI cross reference information
    Database cross reference information : Provides links to PPI databases (BIND, DIP, MINT, HPRD, IntAct, and GNP_Y2H) which we use as data sources.
    PubMed IDs (Number of reporting PPIs) : PubMed IDs of evidential publications for the PPI
      () includes the number of PPIs which the publication reports. It may be an indicator whether the PPI experiments had been performed as large scale or small scale.
      * This number of reporting PPIs of the publication may be different to the actual numbers because of the data compiling procedures.
    Experimental methods : Experimental methods to detect the PPI

Fig 4.11. Information of a protein which interacts with the query protein

References

  1. Alfarano C, et al. The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res. 2005 Jan 1;33
  2. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D. The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 2004 Jan 1;32
  3. Zanzoni A., Montecchi-Palazzi L., Quondam M., Ausiello G., Helmer-Citterich M. and Cesareni G. MINT: a Molecular INTeraction database. FEBS Letters. 2002, 513(1);135-140.
  4. Peri, S. et al. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Research. 2003, 13:2363-2371.
  5. IntAct - an open source molecular interaction database. H. Hermjakob, L. Montecchi-Palazzi, C. Lewington, S. Mudali, S. Kerrien, S. Orchard, M. Vingron, B. Roechert, P. Roepstorff, A. Valencia, H. Margalit, J. Armstrong, A. Bairoch, G. Cesareni, D. Sherman, R. Apweiler. Nucl. Acids. Res. 2004 32: D452-D455.