Modeling the Human Genome Maintenance network

We present the Ontocancro Database ( www.ontocancro.org) illustrated with applications to network modeling and pathway functional analysis. The database compiles information on gene pathways involved in Human Genome Maintenance Mechanisms (GMM) whose dysfunction accounts for cancer and several genet...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Physica A 2010-10, Vol.389 (19), p.4188-4194
Hauptverfasser: Simão, Éder M., Cabral, Heleno B., Castro, Mauro A.A., Sinigaglia, Marialva, Mombach, José C.M., Librelotto, Giovani R.
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
container_end_page 4194
container_issue 19
container_start_page 4188
container_title Physica A
container_volume 389
creator Simão, Éder M.
Cabral, Heleno B.
Castro, Mauro A.A.
Sinigaglia, Marialva
Mombach, José C.M.
Librelotto, Giovani R.
description We present the Ontocancro Database ( www.ontocancro.org) illustrated with applications to network modeling and pathway functional analysis. The database compiles information on gene pathways involved in Human Genome Maintenance Mechanisms (GMM) whose dysfunction accounts for cancer and several genetic syndromes. Ontocancro is the most complete, manually curated information resource available providing genomics and interatomics data on 120 GMM pathways (comprising a total of 1435 genes) obtained from curated databases and the literature. It was developed to facilitate the GMM network and functional modeling for the integration of genomic, transcriptomic and interatomic data. The database’s main contribution is the Ontocancro pathways that are expanded versions of standard GMM pathways for including additional genes with evidences of functional involvement in GMM. Using these pathways we find the largest cluster of interacting proteins involving GMM and on it we project a microarray study of adenoma to identify the regions of the network that are highly altered. In the last application we present the dynamical alterations of the pathways in a study of the effect of Cadmium, a known carcinogenic substance, on prostate cells to find that it produces a strong decrease of the pathway activity.
doi_str_mv 10.1016/j.physa.2010.05.051
format Article
fullrecord <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_1671230977</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><els_id>S0378437110004814</els_id><sourcerecordid>1671230977</sourcerecordid><originalsourceid>FETCH-LOGICAL-c381t-a77ea939d6c194ff8d462d10be114a3002fbfa64fdd8b2c748766658c8f179623</originalsourceid><addsrcrecordid>eNp9kEFLAzEUhIMoWKu_wMsevWzNS7ZJ9uBBiraCxYueQ5q82NTdbE22Sv-9W-tZGBh4zPdghpBroBOgIG43k-16n82E0eFCp4PghIxASV4ygPqUjCiXqqy4hHNykfOGUgqSsxEpl53DJsT3ol9jsdi1JhZzjF2LxdKE2GM00WIRsf_u0sclOfOmyXj152Py9vjwOluUzy_zp9n9c2m5gr40UqKpee2EhbryXrlKMAd0hQCV4ZQyv_JGVN45tWJWVkoKIabKKg-yFoyPyc3x7zZ1nzvMvW5Dttg0JmK3yxqEBMZpLeUQ5ceoTV3OCb3eptCatNdA9WEcvdG_4-jDOJpOB8FA3R0pHFp8BUw624BDUxcS2l67LvzL_wA0sm0i</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1671230977</pqid></control><display><type>article</type><title>Modeling the Human Genome Maintenance network</title><source>Elsevier ScienceDirect Journals</source><creator>Simão, Éder M. ; Cabral, Heleno B. ; Castro, Mauro A.A. ; Sinigaglia, Marialva ; Mombach, José C.M. ; Librelotto, Giovani R.</creator><creatorcontrib>Simão, Éder M. ; Cabral, Heleno B. ; Castro, Mauro A.A. ; Sinigaglia, Marialva ; Mombach, José C.M. ; Librelotto, Giovani R.</creatorcontrib><description>We present the Ontocancro Database ( www.ontocancro.org) illustrated with applications to network modeling and pathway functional analysis. The database compiles information on gene pathways involved in Human Genome Maintenance Mechanisms (GMM) whose dysfunction accounts for cancer and several genetic syndromes. Ontocancro is the most complete, manually curated information resource available providing genomics and interatomics data on 120 GMM pathways (comprising a total of 1435 genes) obtained from curated databases and the literature. It was developed to facilitate the GMM network and functional modeling for the integration of genomic, transcriptomic and interatomic data. The database’s main contribution is the Ontocancro pathways that are expanded versions of standard GMM pathways for including additional genes with evidences of functional involvement in GMM. Using these pathways we find the largest cluster of interacting proteins involving GMM and on it we project a microarray study of adenoma to identify the regions of the network that are highly altered. In the last application we present the dynamical alterations of the pathways in a study of the effect of Cadmium, a known carcinogenic substance, on prostate cells to find that it produces a strong decrease of the pathway activity.</description><identifier>ISSN: 0378-4371</identifier><identifier>EISSN: 1873-2119</identifier><identifier>DOI: 10.1016/j.physa.2010.05.051</identifier><language>eng</language><publisher>Elsevier B.V</publisher><subject>Apoptosis ; Cadmium ; Cancer ; DNA repair ; Gene expression ; Genes ; Genomes ; Human ; Maintenance ; Microarray ; Networks ; Pathway ; Pathways ; Protein network</subject><ispartof>Physica A, 2010-10, Vol.389 (19), p.4188-4194</ispartof><rights>2010 Elsevier B.V.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c381t-a77ea939d6c194ff8d462d10be114a3002fbfa64fdd8b2c748766658c8f179623</citedby><cites>FETCH-LOGICAL-c381t-a77ea939d6c194ff8d462d10be114a3002fbfa64fdd8b2c748766658c8f179623</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0378437110004814$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,776,780,3537,27901,27902,65306</link.rule.ids></links><search><creatorcontrib>Simão, Éder M.</creatorcontrib><creatorcontrib>Cabral, Heleno B.</creatorcontrib><creatorcontrib>Castro, Mauro A.A.</creatorcontrib><creatorcontrib>Sinigaglia, Marialva</creatorcontrib><creatorcontrib>Mombach, José C.M.</creatorcontrib><creatorcontrib>Librelotto, Giovani R.</creatorcontrib><title>Modeling the Human Genome Maintenance network</title><title>Physica A</title><description>We present the Ontocancro Database ( www.ontocancro.org) illustrated with applications to network modeling and pathway functional analysis. The database compiles information on gene pathways involved in Human Genome Maintenance Mechanisms (GMM) whose dysfunction accounts for cancer and several genetic syndromes. Ontocancro is the most complete, manually curated information resource available providing genomics and interatomics data on 120 GMM pathways (comprising a total of 1435 genes) obtained from curated databases and the literature. It was developed to facilitate the GMM network and functional modeling for the integration of genomic, transcriptomic and interatomic data. The database’s main contribution is the Ontocancro pathways that are expanded versions of standard GMM pathways for including additional genes with evidences of functional involvement in GMM. Using these pathways we find the largest cluster of interacting proteins involving GMM and on it we project a microarray study of adenoma to identify the regions of the network that are highly altered. In the last application we present the dynamical alterations of the pathways in a study of the effect of Cadmium, a known carcinogenic substance, on prostate cells to find that it produces a strong decrease of the pathway activity.</description><subject>Apoptosis</subject><subject>Cadmium</subject><subject>Cancer</subject><subject>DNA repair</subject><subject>Gene expression</subject><subject>Genes</subject><subject>Genomes</subject><subject>Human</subject><subject>Maintenance</subject><subject>Microarray</subject><subject>Networks</subject><subject>Pathway</subject><subject>Pathways</subject><subject>Protein network</subject><issn>0378-4371</issn><issn>1873-2119</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><recordid>eNp9kEFLAzEUhIMoWKu_wMsevWzNS7ZJ9uBBiraCxYueQ5q82NTdbE22Sv-9W-tZGBh4zPdghpBroBOgIG43k-16n82E0eFCp4PghIxASV4ygPqUjCiXqqy4hHNykfOGUgqSsxEpl53DJsT3ol9jsdi1JhZzjF2LxdKE2GM00WIRsf_u0sclOfOmyXj152Py9vjwOluUzy_zp9n9c2m5gr40UqKpee2EhbryXrlKMAd0hQCV4ZQyv_JGVN45tWJWVkoKIabKKg-yFoyPyc3x7zZ1nzvMvW5Dttg0JmK3yxqEBMZpLeUQ5ceoTV3OCb3eptCatNdA9WEcvdG_4-jDOJpOB8FA3R0pHFp8BUw624BDUxcS2l67LvzL_wA0sm0i</recordid><startdate>20101001</startdate><enddate>20101001</enddate><creator>Simão, Éder M.</creator><creator>Cabral, Heleno B.</creator><creator>Castro, Mauro A.A.</creator><creator>Sinigaglia, Marialva</creator><creator>Mombach, José C.M.</creator><creator>Librelotto, Giovani R.</creator><general>Elsevier B.V</general><scope>AAYXX</scope><scope>CITATION</scope><scope>7U5</scope><scope>8FD</scope><scope>H8D</scope><scope>L7M</scope></search><sort><creationdate>20101001</creationdate><title>Modeling the Human Genome Maintenance network</title><author>Simão, Éder M. ; Cabral, Heleno B. ; Castro, Mauro A.A. ; Sinigaglia, Marialva ; Mombach, José C.M. ; Librelotto, Giovani R.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c381t-a77ea939d6c194ff8d462d10be114a3002fbfa64fdd8b2c748766658c8f179623</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Apoptosis</topic><topic>Cadmium</topic><topic>Cancer</topic><topic>DNA repair</topic><topic>Gene expression</topic><topic>Genes</topic><topic>Genomes</topic><topic>Human</topic><topic>Maintenance</topic><topic>Microarray</topic><topic>Networks</topic><topic>Pathway</topic><topic>Pathways</topic><topic>Protein network</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Simão, Éder M.</creatorcontrib><creatorcontrib>Cabral, Heleno B.</creatorcontrib><creatorcontrib>Castro, Mauro A.A.</creatorcontrib><creatorcontrib>Sinigaglia, Marialva</creatorcontrib><creatorcontrib>Mombach, José C.M.</creatorcontrib><creatorcontrib>Librelotto, Giovani R.</creatorcontrib><collection>CrossRef</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>Technology Research Database</collection><collection>Aerospace Database</collection><collection>Advanced Technologies Database with Aerospace</collection><jtitle>Physica A</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Simão, Éder M.</au><au>Cabral, Heleno B.</au><au>Castro, Mauro A.A.</au><au>Sinigaglia, Marialva</au><au>Mombach, José C.M.</au><au>Librelotto, Giovani R.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Modeling the Human Genome Maintenance network</atitle><jtitle>Physica A</jtitle><date>2010-10-01</date><risdate>2010</risdate><volume>389</volume><issue>19</issue><spage>4188</spage><epage>4194</epage><pages>4188-4194</pages><issn>0378-4371</issn><eissn>1873-2119</eissn><abstract>We present the Ontocancro Database ( www.ontocancro.org) illustrated with applications to network modeling and pathway functional analysis. The database compiles information on gene pathways involved in Human Genome Maintenance Mechanisms (GMM) whose dysfunction accounts for cancer and several genetic syndromes. Ontocancro is the most complete, manually curated information resource available providing genomics and interatomics data on 120 GMM pathways (comprising a total of 1435 genes) obtained from curated databases and the literature. It was developed to facilitate the GMM network and functional modeling for the integration of genomic, transcriptomic and interatomic data. The database’s main contribution is the Ontocancro pathways that are expanded versions of standard GMM pathways for including additional genes with evidences of functional involvement in GMM. Using these pathways we find the largest cluster of interacting proteins involving GMM and on it we project a microarray study of adenoma to identify the regions of the network that are highly altered. In the last application we present the dynamical alterations of the pathways in a study of the effect of Cadmium, a known carcinogenic substance, on prostate cells to find that it produces a strong decrease of the pathway activity.</abstract><pub>Elsevier B.V</pub><doi>10.1016/j.physa.2010.05.051</doi><tpages>7</tpages><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 0378-4371
ispartof Physica A, 2010-10, Vol.389 (19), p.4188-4194
issn 0378-4371
1873-2119
language eng
recordid cdi_proquest_miscellaneous_1671230977
source Elsevier ScienceDirect Journals
subjects Apoptosis
Cadmium
Cancer
DNA repair
Gene expression
Genes
Genomes
Human
Maintenance
Microarray
Networks
Pathway
Pathways
Protein network
title Modeling the Human Genome Maintenance network
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-02T01%3A30%3A49IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Modeling%20the%20Human%20Genome%20Maintenance%20network&rft.jtitle=Physica%20A&rft.au=Sim%C3%A3o,%20%C3%89der%20M.&rft.date=2010-10-01&rft.volume=389&rft.issue=19&rft.spage=4188&rft.epage=4194&rft.pages=4188-4194&rft.issn=0378-4371&rft.eissn=1873-2119&rft_id=info:doi/10.1016/j.physa.2010.05.051&rft_dat=%3Cproquest_cross%3E1671230977%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1671230977&rft_id=info:pmid/&rft_els_id=S0378437110004814&rfr_iscdi=true