title: GeneSense: a new approach for human gene annotation integrated with protein-protein interaction networks.
abstract: Virtually all cellular functions involve protein-protein interactions (PPIs). As an increasing number of PPIs are identified and vast amount of information accumulated, researchers are finding different ways to interrogate the data and understand the interactions in context. However, it is widely recognized that a significant portion of the data is scattered, redundant, not considered high quality, and not readily accessible to researchers in a systematic fashion. In addition, it is challenging to identify the optimal protein targets in the current PPI networks. The GeneSense server was developed to integrate gene annotation and PPI networks in an expandable architecture that incorporates selected databases with the aim to assemble, analyze, evaluate and disseminate protein-protein association information in a comprehensive and user-friendly manner. Three network models including nodenet, leafnet and loopnet are used to identify the optimal protein targets in the complex networks. GeneSense is freely available at www.biomedsense.org/genesense.php.
authors.affiliation: BioMedSense Laboratory, Shanghai 200433, China.
authors.forename: Zhongzhong
authors.initials: Z
authors.lastname: Chen
authors.affiliation: Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital, Harbin Medical University, Harbin 150081, China.
authors.forename: Tianhong
authors.initials: T
authors.lastname: Zhang
authors.affiliation: Department of Biotechnology, Guilin Medical University, Guilin 541004, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Lin
authors.affiliation: Shanghai Yingyun Biotech Inc., Shanghai 200433, China.
authors.forename: Zidan
authors.initials: Z
authors.lastname: Yan
authors.affiliation: College of Basic Science, Zhejiang Chinese Medical University, Hangzhou 310053, China.
authors.forename: Yongren
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Pathology, Changhai Hospital, Shanghai 200433, China.
authors.forename: Weiqiang
authors.initials: W
authors.lastname: Zheng
authors.affiliation: Nplex Laboratory, San Jose, CA 95134, USA.
authors.forename: Kevin C
authors.initials: KC
authors.lastname: Weng
mesh_terms: D019295:Computational Biology; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D058977:Molecular Sequence Annotation; D060066:Protein Interaction Maps / Q000235:genetics*; D012984:Software