title: QServer: a biclustering server for prediction and assessment of co-expressed gene clusters.
abstract: BACKGROUND
  Biclustering is a powerful technique for identification of co-expressed gene groups under any (unspecified) substantial subset of given experimental conditions, which can be used for elucidation of transcriptionally co-regulated genes.
  
  
  RESULTS
  We have previously developed a biclustering algorithm, QUBIC, which can solve more general biclustering problems than previous biclustering algorithms. To fully utilize the analysis power the algorithm provides, we have developed a web server, QServer, for prediction, computational validation and analyses of co-expressed gene clusters. Specifically, the QServer has the following capabilities in addition to biclustering by QUBIC: (i) prediction and assessment of conserved cis regulatory motifs in promoter sequences of the predicted co-expressed genes; (ii) functional enrichment analyses of the predicted co-expressed gene clusters using Gene Ontology (GO) terms, and (iii) visualization capabilities in support of interactive biclustering analyses. QServer supports the biclustering and functional analysis for a wide range of organisms, including human, mouse, Arabidopsis, bacteria and archaea, whose underlying genome database will be continuously updated.
  
  
  CONCLUSIONS
  We believe that QServer provides an easy-to-use and highly effective platform useful for hypothesis formulation and testing related to transcription co-regulation.
authors.affiliation: Research Center for Biomedical Information Technology, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China.
authors.forename: Fengfeng
authors.initials: F
authors.lastname: Zhou
authors.forename: Qin
authors.initials: Q
authors.lastname: Ma
authors.forename: Guojun
authors.initials: G
authors.lastname: Li
authors.forename: Ying
authors.initials: Y
authors.lastname: Xu
mesh_terms: D000465:Algorithms; D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D005810:Multigene Family / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D014584:User-Computer Interface