title: ECgene: an alternative splicing database update.
abstract: ECgene (http://genome.ewha.ac.kr/ECgene) was developed to provide functional annotation for alternatively spliced genes. The applications encompass the genome-based transcript modeling for alternative splicing (AS), domain analysis with Gene Ontology (GO) annotation and expression analysis based on the EST and SAGE data. We have expanded the ECgene's AS modeling and EST clustering to nine organisms for which sufficient EST data are available in the GenBank. As for the human genome, we have also introduced several new applications to analyze differential expression. ECprofiler is an ontology-based candidate gene search system that allows users to select an arbitrary combination of gene expression pattern and GO functional categories. DEGEST is a database of differentially expressed genes and isoforms based on the EST information. Importantly, gene expression is analyzed at three distinctive levels-gene, isoform and exon levels. The user interfaces for functional and expression analyses have been substantially improved. ASviewer is a dedicated java application that visualizes the transcript structure and functional features of alternatively spliced variants. The SAGE part of the expression module provides many additional features including SNP, differential expression and alternative tag positions.
authors.affiliation: Division of Molecular Life Sciences, Ewha Womans University, Seoul 120-750, Korea.
authors.forename: Yeunsook
authors.initials: Y
authors.lastname: Lee
authors.forename: Younghee
authors.initials: Y
authors.lastname: Lee
authors.forename: Bumjin
authors.initials: B
authors.lastname: Kim
authors.forename: Youngah
authors.initials: Y
authors.lastname: Shin
authors.forename: Seungyoon
authors.initials: S
authors.lastname: Nam
authors.forename: Pora
authors.initials: P
authors.lastname: Kim
authors.forename: Namshin
authors.initials: N
authors.lastname: Kim
authors.forename: Won-Hyong
authors.initials: WH
authors.lastname: Chung
authors.forename: Jaesang
authors.initials: J
authors.lastname: Kim
authors.forename: Sanghyuk
authors.initials: S
authors.lastname: Lee
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D016000:Cluster Analysis; D003196:Computer Graphics; D030541:Databases, Genetic; D004285:Dogs; D004331:Drosophila melanogaster / Q000235:genetics; D005091:Exons; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D023281:Genomics; D006801:Humans; D020407:Internet; D051379:Mice; D008957:Models, Genetic; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism; D051381:Rats; D014584:User-Computer Interface
chemical_list: D020033:Protein Isoforms; D012333:RNA, Messenger