Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach
Systematic identification of binding partners for modular domains such as Src homology 2 (SH2) is important for understanding the biological function of the corresponding SH2 proteins. We have developed a worldwide web-accessible computer program dubbed SMALI for scoring matrix-assisted ligand ident...
Gespeichert in:
Veröffentlicht in: | Nucleic acids research 2008-06, Vol.36 (10), p.3263-3273 |
---|---|
Hauptverfasser: | , , , , , |
Format: | Artikel |
Sprache: | eng |
Schlagworte: | |
Online-Zugang: | Volltext |
Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
container_end_page | 3273 |
---|---|
container_issue | 10 |
container_start_page | 3263 |
container_title | Nucleic acids research |
container_volume | 36 |
creator | Li, Lei Wu, Chenggang Huang, Haiming Zhang, Kaizhong Gan, Jacob Li, Shawn S.-C |
description | Systematic identification of binding partners for modular domains such as Src homology 2 (SH2) is important for understanding the biological function of the corresponding SH2 proteins. We have developed a worldwide web-accessible computer program dubbed SMALI for scoring matrix-assisted ligand identification for SH2 domains and other signaling modules. The current version of SMALI harbors 76 unique scoring matrices for SH2 domains derived from screening oriented peptide array libraries. These scoring matrices are used to search a protein database for short peptides preferred by an SH2 domain. An experimentally determined cut-off value is used to normalize an SMALI score, therefore allowing for direct comparison in peptide-binding potential for different SH2 domains. SMALI employs distinct scoring matrices from Scansite, a popular motif-scanning program. Moreover, SMALI contains built-in filters for phosphoproteins, Gene Ontology (GO) correlation and colocalization of subject and query proteins. Compared to Scansite, SMALI exhibited improved accuracy in identifying binding peptides for SH2 domains. Applying SMALI to a group of SH2 domains identified hundreds of interactions that overlap significantly with known networks mediated by the corresponding SH2 proteins, suggesting SMALI is a useful tool for facile identification of signaling networks mediated by modular domains that recognize short linear peptide motifs. |
doi_str_mv | 10.1093/nar/gkn161 |
format | Article |
fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_2425477</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><oup_id>10.1093/nar/gkn161</oup_id><sourcerecordid>71652321</sourcerecordid><originalsourceid>FETCH-LOGICAL-c526t-26c6bcd4b54d2cb79768a1f5396feca1dee96ee569f78ab9b3bb4bdfd6a22d963</originalsourceid><addsrcrecordid>eNqF0V1r1TAYB_AiijtOb_wAWgS9EOry3uZmIEM3YehgDsWb8DRJe7L1JDVpdfv25tjDfLnQi9CU_vj3Sf5F8RijVxhJeuAhHvRXHgt8p1hhKkjFpCB3ixWiiFcYsWaveJDSJUKYYc7uF3u4YYQ1CK-KcBatcXpywZehK8d1SHlNNzEk522ZXO9hcL4vvZ2-h3iVyjltX6FMOsTtbgNTdNcVpOTSZE05uB68KZ2xfnKd0_AzG8YxBtDrh8W9DoZkH-2e-8XF2zcfj06q0w_H745en1aaEzFVRGjRasNazgzRbS1r0QDuOJWisxqwsVYKa7mQXd1AK1vatqw1nRFAiJGC7heHS-44txtrdB4mwqDG6DYQb1QAp_784t1a9eGbIoxwVtc54MUuIIavs02T2rik7TCAt2FOqsaCE0rwfyFBdVNzzDJ89he8DHPM17s1iEvJiczo5YJ0biBF292OjJHatq1y22ppO-Mnvx_yF93Vm8HzBYR5_HdQtbhthde3EuKVEjWtuTr5_EWJs-Nz-v4TVU32TxffQVDQR5fUxTnJP0RIIoolpz8AzVnQBA</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>200599529</pqid></control><display><type>article</type><title>Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach</title><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>Access via Oxford University Press (Open Access Collection)</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Li, Lei ; Wu, Chenggang ; Huang, Haiming ; Zhang, Kaizhong ; Gan, Jacob ; Li, Shawn S.-C</creator><creatorcontrib>Li, Lei ; Wu, Chenggang ; Huang, Haiming ; Zhang, Kaizhong ; Gan, Jacob ; Li, Shawn S.-C</creatorcontrib><description>Systematic identification of binding partners for modular domains such as Src homology 2 (SH2) is important for understanding the biological function of the corresponding SH2 proteins. We have developed a worldwide web-accessible computer program dubbed SMALI for scoring matrix-assisted ligand identification for SH2 domains and other signaling modules. The current version of SMALI harbors 76 unique scoring matrices for SH2 domains derived from screening oriented peptide array libraries. These scoring matrices are used to search a protein database for short peptides preferred by an SH2 domain. An experimentally determined cut-off value is used to normalize an SMALI score, therefore allowing for direct comparison in peptide-binding potential for different SH2 domains. SMALI employs distinct scoring matrices from Scansite, a popular motif-scanning program. Moreover, SMALI contains built-in filters for phosphoproteins, Gene Ontology (GO) correlation and colocalization of subject and query proteins. Compared to Scansite, SMALI exhibited improved accuracy in identifying binding peptides for SH2 domains. Applying SMALI to a group of SH2 domains identified hundreds of interactions that overlap significantly with known networks mediated by the corresponding SH2 proteins, suggesting SMALI is a useful tool for facile identification of signaling networks mediated by modular domains that recognize short linear peptide motifs.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkn161</identifier><identifier>PMID: 18424801</identifier><identifier>CODEN: NARHAD</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Computational Biology ; Humans ; Ligands ; Peptides - chemistry ; Phosphotyrosine - metabolism ; Protein Array Analysis ; Signal Transduction ; Software ; src Homology Domains</subject><ispartof>Nucleic acids research, 2008-06, Vol.36 (10), p.3263-3273</ispartof><rights>2008 The Author(s) 2008</rights><rights>2008 The Author(s)</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c526t-26c6bcd4b54d2cb79768a1f5396feca1dee96ee569f78ab9b3bb4bdfd6a22d963</citedby><cites>FETCH-LOGICAL-c526t-26c6bcd4b54d2cb79768a1f5396feca1dee96ee569f78ab9b3bb4bdfd6a22d963</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2425477/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2425477/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,1604,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18424801$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Li, Lei</creatorcontrib><creatorcontrib>Wu, Chenggang</creatorcontrib><creatorcontrib>Huang, Haiming</creatorcontrib><creatorcontrib>Zhang, Kaizhong</creatorcontrib><creatorcontrib>Gan, Jacob</creatorcontrib><creatorcontrib>Li, Shawn S.-C</creatorcontrib><title>Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Systematic identification of binding partners for modular domains such as Src homology 2 (SH2) is important for understanding the biological function of the corresponding SH2 proteins. We have developed a worldwide web-accessible computer program dubbed SMALI for scoring matrix-assisted ligand identification for SH2 domains and other signaling modules. The current version of SMALI harbors 76 unique scoring matrices for SH2 domains derived from screening oriented peptide array libraries. These scoring matrices are used to search a protein database for short peptides preferred by an SH2 domain. An experimentally determined cut-off value is used to normalize an SMALI score, therefore allowing for direct comparison in peptide-binding potential for different SH2 domains. SMALI employs distinct scoring matrices from Scansite, a popular motif-scanning program. Moreover, SMALI contains built-in filters for phosphoproteins, Gene Ontology (GO) correlation and colocalization of subject and query proteins. Compared to Scansite, SMALI exhibited improved accuracy in identifying binding peptides for SH2 domains. Applying SMALI to a group of SH2 domains identified hundreds of interactions that overlap significantly with known networks mediated by the corresponding SH2 proteins, suggesting SMALI is a useful tool for facile identification of signaling networks mediated by modular domains that recognize short linear peptide motifs.</description><subject>Computational Biology</subject><subject>Humans</subject><subject>Ligands</subject><subject>Peptides - chemistry</subject><subject>Phosphotyrosine - metabolism</subject><subject>Protein Array Analysis</subject><subject>Signal Transduction</subject><subject>Software</subject><subject>src Homology Domains</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2008</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNqF0V1r1TAYB_AiijtOb_wAWgS9EOry3uZmIEM3YehgDsWb8DRJe7L1JDVpdfv25tjDfLnQi9CU_vj3Sf5F8RijVxhJeuAhHvRXHgt8p1hhKkjFpCB3ixWiiFcYsWaveJDSJUKYYc7uF3u4YYQ1CK-KcBatcXpywZehK8d1SHlNNzEk522ZXO9hcL4vvZ2-h3iVyjltX6FMOsTtbgNTdNcVpOTSZE05uB68KZ2xfnKd0_AzG8YxBtDrh8W9DoZkH-2e-8XF2zcfj06q0w_H745en1aaEzFVRGjRasNazgzRbS1r0QDuOJWisxqwsVYKa7mQXd1AK1vatqw1nRFAiJGC7heHS-44txtrdB4mwqDG6DYQb1QAp_784t1a9eGbIoxwVtc54MUuIIavs02T2rik7TCAt2FOqsaCE0rwfyFBdVNzzDJ89he8DHPM17s1iEvJiczo5YJ0biBF292OjJHatq1y22ppO-Mnvx_yF93Vm8HzBYR5_HdQtbhthde3EuKVEjWtuTr5_EWJs-Nz-v4TVU32TxffQVDQR5fUxTnJP0RIIoolpz8AzVnQBA</recordid><startdate>20080601</startdate><enddate>20080601</enddate><creator>Li, Lei</creator><creator>Wu, Chenggang</creator><creator>Huang, Haiming</creator><creator>Zhang, Kaizhong</creator><creator>Gan, Jacob</creator><creator>Li, Shawn S.-C</creator><general>Oxford University Press</general><general>Oxford Publishing Limited (England)</general><scope>FBQ</scope><scope>BSCLL</scope><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QO</scope><scope>7QP</scope><scope>7QR</scope><scope>7SS</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20080601</creationdate><title>Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach</title><author>Li, Lei ; Wu, Chenggang ; Huang, Haiming ; Zhang, Kaizhong ; Gan, Jacob ; Li, Shawn S.-C</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c526t-26c6bcd4b54d2cb79768a1f5396feca1dee96ee569f78ab9b3bb4bdfd6a22d963</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2008</creationdate><topic>Computational Biology</topic><topic>Humans</topic><topic>Ligands</topic><topic>Peptides - chemistry</topic><topic>Phosphotyrosine - metabolism</topic><topic>Protein Array Analysis</topic><topic>Signal Transduction</topic><topic>Software</topic><topic>src Homology Domains</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Li, Lei</creatorcontrib><creatorcontrib>Wu, Chenggang</creatorcontrib><creatorcontrib>Huang, Haiming</creatorcontrib><creatorcontrib>Zhang, Kaizhong</creatorcontrib><creatorcontrib>Gan, Jacob</creatorcontrib><creatorcontrib>Li, Shawn S.-C</creatorcontrib><collection>AGRIS</collection><collection>Istex</collection><collection>Access via Oxford University Press (Open Access Collection)</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Li, Lei</au><au>Wu, Chenggang</au><au>Huang, Haiming</au><au>Zhang, Kaizhong</au><au>Gan, Jacob</au><au>Li, Shawn S.-C</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2008-06-01</date><risdate>2008</risdate><volume>36</volume><issue>10</issue><spage>3263</spage><epage>3273</epage><pages>3263-3273</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><coden>NARHAD</coden><abstract>Systematic identification of binding partners for modular domains such as Src homology 2 (SH2) is important for understanding the biological function of the corresponding SH2 proteins. We have developed a worldwide web-accessible computer program dubbed SMALI for scoring matrix-assisted ligand identification for SH2 domains and other signaling modules. The current version of SMALI harbors 76 unique scoring matrices for SH2 domains derived from screening oriented peptide array libraries. These scoring matrices are used to search a protein database for short peptides preferred by an SH2 domain. An experimentally determined cut-off value is used to normalize an SMALI score, therefore allowing for direct comparison in peptide-binding potential for different SH2 domains. SMALI employs distinct scoring matrices from Scansite, a popular motif-scanning program. Moreover, SMALI contains built-in filters for phosphoproteins, Gene Ontology (GO) correlation and colocalization of subject and query proteins. Compared to Scansite, SMALI exhibited improved accuracy in identifying binding peptides for SH2 domains. Applying SMALI to a group of SH2 domains identified hundreds of interactions that overlap significantly with known networks mediated by the corresponding SH2 proteins, suggesting SMALI is a useful tool for facile identification of signaling networks mediated by modular domains that recognize short linear peptide motifs.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>18424801</pmid><doi>10.1093/nar/gkn161</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
fulltext | fulltext |
identifier | ISSN: 0305-1048 |
ispartof | Nucleic acids research, 2008-06, Vol.36 (10), p.3263-3273 |
issn | 0305-1048 1362-4962 |
language | eng |
recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_2425477 |
source | MEDLINE; DOAJ Directory of Open Access Journals; Access via Oxford University Press (Open Access Collection); PubMed Central; Free Full-Text Journals in Chemistry |
subjects | Computational Biology Humans Ligands Peptides - chemistry Phosphotyrosine - metabolism Protein Array Analysis Signal Transduction Software src Homology Domains |
title | Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach |
url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-24T18%3A56%3A51IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Prediction%20of%20phosphotyrosine%20signaling%20networks%20using%20a%20scoring%20matrix-assisted%20ligand%20identification%20approach&rft.jtitle=Nucleic%20acids%20research&rft.au=Li,%20Lei&rft.date=2008-06-01&rft.volume=36&rft.issue=10&rft.spage=3263&rft.epage=3273&rft.pages=3263-3273&rft.issn=0305-1048&rft.eissn=1362-4962&rft.coden=NARHAD&rft_id=info:doi/10.1093/nar/gkn161&rft_dat=%3Cproquest_pubme%3E71652321%3C/proquest_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=200599529&rft_id=info:pmid/18424801&rft_oup_id=10.1093/nar/gkn161&rfr_iscdi=true |