Searching the MINT Database for Protein Interaction Information
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- Abstract
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- Literature Cited
Abstract
The Molecular Interactions Database (MINT) is a relational database designed to store information about protein interactions. Expert curators extract the relevant information from the scientific literature and deposit it in a computer readable form. Currently (April 2008), MINT contains information on almost 29,000 proteins and more than 100,000 interactions from more than 30 model organisms. This unit provides protocols for searching MINT over the Internet, using the MINT Viewer. Curr. Protoc. Bioinform. 22:8.5.1?8.5.13. © 2008 by John Wiley & Sons, Inc.
Keywords: MINT; protein?protein interaction; database
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- Introduction
- Basic Protocol 1: Searching MINT Over the Internet
- Alternate Protocol 1: MINT Viewer
- Basic Protocol 2: Submitting Interaction Data
- Guidelines for Understanding Results
- Commentary
- Literature Cited
- Figures
- Tables
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PDF or HTML at Wiley Online LibraryFigures
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Figure 8.5.1 MINT homepage. View Image -
Figure 8.5.2 Search page. SwissProt/Trembl accession numbers, gene and protein names, or keywords can be used to search the database. View Image -
Figure 8.5.3 Result of a search with the protein name Lck. Each protein ID can be clicked to obtain more detailed information about the selected protein. View Image -
Figure 8.5.4 Result of clicking on the gene name on the protein name search results page (Fig. ).The panel on the left displays information about the selected protein. Most of this information is automatically extracted from the SwissProt/Trembl database. The panel on the right lists all the interactions, among the ones stored in MINT, in which the selected protein participates. The MINT VIEWER icon permits graphical display of the interactions listed in the interaction table. View Image -
Figure 8.5.5 Result of clicking on the interaction number in the right panel of the previous page (Fig. ). A new table is presented that contains detailed information about the experimental evidences supporting the interaction. View Image -
Figure 8.5.6 Graphic representation of the Lck interaction network obtained by clicking the MINT Viewer icon. View Image -
Figure 8.5.7 Detailed information supporting the interaction between Lck and MAPK1. This was obtained by clicking on the circle sitting on the connecting edge in the previous figure (see Fig. and text). View Image -
Figure 8.5.8 Extension of the Lck interaction network, obtained by clicking on the (+) symbol representing the Cbl protein (see Fig. and text). View Image -
Figure 8.5.9 The Lck interaction network with interactions having a confidence score lower than a set threshold deleted from the viewer (see Fig. and text). View Image -
Figure 8.5.10 Manuscript information page. Excel spreadsheet page downloaded from http://imex.sourceforge.net/doc/imex‐curationManual.doc and used to provide contact and bibliographical information when submitting protein interaction data to the curators of MINT. View Image -
Figure 8.5.11 Interaction submission form. Excel spreadsheet page downloaded from http://imex.sourceforge.net/doc/imex‐curationManual.doc and used to submit protein interaction information to the curators of MINT. View Image
Videos
Literature Cited
| Chatr‐aryamontri, A., Ceol, A., Licata, L., and Cesareni, G. 2008. Protein interactions: Integration leads to belief. TiBS. In press. | |
| Chatr‐aryamontri, A., Ceol, A., Palazzi, L.M., Nardelli, G., Schneider, M.V., Castagnoli, L., and Cesareni, G. 2007. MINT: The Molecular INTeraction database. Nucleic Acids Res. 35:D572‐D574. | |
| Guldener, U., Munsterkotter, M., Oesterheld, M., Pagel, P., Ruepp, A., Mewes, H.W., and Stumpflen, V. 2006. MPact: The MIPS protein interaction resource on yeast. Nucleic Acids Res. 34:D436‐D441. | |
| Kerrien, S., Alam‐Faruque, Y., Aranda, B., Bancarz, I., Bridge, A., Derow, C., Dimmer, E., Feuermann, M., Friedrichsen, A., Huntley, R., Kohler, C., Khadake, J., Leroy, C., Liban, A., Lieftink, C., Montecchi‐Palazzi, L., Orchard, S., Risse, J., Robbe, K., Roechert, B., Thorneycroft, D., Zhang, Y., Apweiler, R., and Hermjakob, H. 2007. IntAct—Open source resource for molecular interaction data. Nucleic Acids Res. 35:D561‐D565. | |
| Mishra, G.R., Suresh, M., Kumaran, K., Kannabiran, N., Suresh, S., Bala, P., Shivakumar, K., Anuradha, N., Reddy, R., Raghavan, T.M., Menon, S., Hanumanthu, G., Gupta, M., Upendran, S., Gupta, S., Mahesh, M., Jacob, B., Mathew, P., Chatterjee, P., Arun, K.S., Sharma, S., Chandrika, K.N., Deshpande, N., Palvankar, K., Raghavnath, R., Krishnakanth, R., Karathia, H., Rekha, B., Nayak, R., Vishnupriya, G., Kumar, H.G., Nagini, M., Kumar, G.S., Jose, R., Deepthi, P., Mohan, S.S., Gandhi, T.K., Harsha, H.C., Deshpande, K.S., Sarker, M., Prasad, T.S., and Pandey, A. 2006. Human protein reference database—2006 update. Nucleic Acids Res. 34:D411‐D414. | |
| Salwinski, L., Miller, C.S., Smith, A.J., Pettit, F.K., Bowie, J.U., and Eisenberg, D. 2004. The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 32:D449‐D451. | |
| Stark, C., Breitkreutz, B.J., Reguly, T., Boucher, L., Breitkreutz, A., and Tyers, M. 2006. BioGRID: A general repository for interaction datasets. Nucleic Acids Res. 34:D535‐D539. | |
| Internet Resources | |
| http://mint.bio.uniroma2.it/mint | |
| The Molecular Interactions Database (MINT), Database of Interacting Proteins (DIP), and IntAct Web sites. These are founders and active members of the IMEx consortium, which shares curation efforts and exchanges completed records on molecular interaction data. | |
| http://dip.doe‐mbi.ucla.edu | |
| The MIPS, BioGRID, and HPRD Web sites for other well established protein interaction databases currently accessible on the Web. | |
| http://www.ebi.ac.uk/intact | |
| http://mips.gsf.de | |
| http://www.thebiogrid.org | |
| http://www.hprd.org |
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