From phenotype to gene: Detecting disease-specific gene functional modules via a text-based human disease phenotype network construction
Currently, some efforts have been devoted to the text analysis of disease phenotype data, and their results indicated that similar disease phenotypes arise from functionally related genes. These related genes work together, as a functional module, to perform a desired cellular function. We construct...
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| Veröffentlicht in: | FEBS letters 2010-08, Vol.584 (16), p.3635-3643 |
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| creator | Zhang, Shi-Hua Wu, Chao Li, Xia Chen, Xi Jiang, Wei Gong, Bin-Sheng Li, Jiang Yan, Yu-Qing |
| description | Currently, some efforts have been devoted to the text analysis of disease phenotype data, and their results indicated that similar disease phenotypes arise from functionally related genes. These related genes work together, as a functional module, to perform a desired cellular function. We constructed a text-based human disease phenotype network and detected 82 disease-specific gene functional modules, each corresponding to a different phenotype cluster, by means of graph-based clustering and mapping from disease phenotype to gene. Since genes in such gene functional modules are functionally related and cause clinically similar diseases, they may share common genetic origin of their associated disease phenotypes. We believe the investigation may facilitate the ultimate understanding of the common pathophysiologic basis of associated diseases. |
| doi_str_mv | 10.1016/j.febslet.2010.07.038 |
| format | Article |
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We believe the investigation may facilitate the ultimate understanding of the common pathophysiologic basis of associated diseases.</description><subject>Cluster Analysis</subject><subject>Computational Biology</subject><subject>Databases, Genetic</subject><subject>Disease - genetics</subject><subject>Disease phenotype</subject><subject>Gene functional module</subject><subject>Gene Regulatory Networks</subject><subject>Genetic origin</subject><subject>Humans</subject><subject>Phenotype</subject><subject>Phenotype network</subject><subject>Text mining</subject><issn>0014-5793</issn><issn>1873-3468</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkcFu1DAQhi0EokvhEUC-ccpiJ05sc0G0dFukShwAqTfLdiatl8RebKdl34DHrre7RdzgZI3n__8ZzYfQa0qWlNDu3Xo5gEkj5GVNyh_hS9KIJ2hBBW-qhnXiKVoQQlnVctkcoRcprUmpBZXP0VFNulYWzQL9XsUw4c0N-JC3G8A54Gvw8B5_ggw2O3-Ne5dAJ6jSBqwbnH0Q4GH2pR28HvEU-nmEhG-dxhpn-JUrUww9vpkn7R_9fw3xkO9C_IFt8CnH-SHnJXo26DHBq8N7jL6vzr6dXlSXX84_n368rCzj3VXFBdPEGkOBMFILI2rDh8ZIWQutQUptiWR9A9yYutFtPRDasEHL0oG2q0VzjN7uczcx_JwhZTW5ZGEctYcwJ8WZkJxR1hZlu1faGFKKMKhNdJOOW0WJ2jFQa3VgoHYMFOGqMCi-N4cJs5mg_-N6PHoRXOwFd26E7f-lqtXZSf11B3THkxaUreyuStSHfRSUk906iCpZB95C72LBp_rg_rHtPYics34</recordid><startdate>20100820</startdate><enddate>20100820</enddate><creator>Zhang, Shi-Hua</creator><creator>Wu, Chao</creator><creator>Li, Xia</creator><creator>Chen, Xi</creator><creator>Jiang, Wei</creator><creator>Gong, Bin-Sheng</creator><creator>Li, Jiang</creator><creator>Yan, Yu-Qing</creator><general>Elsevier B.V</general><scope>6I.</scope><scope>AAFTH</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>7X8</scope></search><sort><creationdate>20100820</creationdate><title>From phenotype to gene: Detecting disease-specific gene functional modules via a text-based human disease phenotype network construction</title><author>Zhang, Shi-Hua ; Wu, Chao ; Li, Xia ; Chen, Xi ; Jiang, Wei ; Gong, Bin-Sheng ; Li, Jiang ; Yan, Yu-Qing</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c476X-784a0cbb1e04028b82b7f3b9928aae99ac094d3e7bb23a52f0134fa999ae56283</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Cluster Analysis</topic><topic>Computational Biology</topic><topic>Databases, Genetic</topic><topic>Disease - genetics</topic><topic>Disease phenotype</topic><topic>Gene functional module</topic><topic>Gene Regulatory Networks</topic><topic>Genetic origin</topic><topic>Humans</topic><topic>Phenotype</topic><topic>Phenotype network</topic><topic>Text mining</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zhang, Shi-Hua</creatorcontrib><creatorcontrib>Wu, Chao</creatorcontrib><creatorcontrib>Li, Xia</creatorcontrib><creatorcontrib>Chen, Xi</creatorcontrib><creatorcontrib>Jiang, Wei</creatorcontrib><creatorcontrib>Gong, Bin-Sheng</creatorcontrib><creatorcontrib>Li, Jiang</creatorcontrib><creatorcontrib>Yan, Yu-Qing</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>FEBS letters</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhang, Shi-Hua</au><au>Wu, Chao</au><au>Li, Xia</au><au>Chen, Xi</au><au>Jiang, Wei</au><au>Gong, Bin-Sheng</au><au>Li, Jiang</au><au>Yan, Yu-Qing</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>From phenotype to gene: Detecting disease-specific gene functional modules via a text-based human disease phenotype network construction</atitle><jtitle>FEBS letters</jtitle><addtitle>FEBS Lett</addtitle><date>2010-08-20</date><risdate>2010</risdate><volume>584</volume><issue>16</issue><spage>3635</spage><epage>3643</epage><pages>3635-3643</pages><issn>0014-5793</issn><eissn>1873-3468</eissn><abstract>Currently, some efforts have been devoted to the text analysis of disease phenotype data, and their results indicated that similar disease phenotypes arise from functionally related genes. 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| source | MEDLINE; EZB Free E-Journals; Wiley Online Library Journals Frontfile Complete; Wiley Online Library Free Content; Alma/SFX Local Collection; Elsevier ScienceDirect Journals Collection |
| subjects | Cluster Analysis Computational Biology Databases, Genetic Disease - genetics Disease phenotype Gene functional module Gene Regulatory Networks Genetic origin Humans Phenotype Phenotype network Text mining |
| title | From phenotype to gene: Detecting disease-specific gene functional modules via a text-based human disease phenotype network construction |
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