ECgene: an alternative splicing database update.
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.
Lee
Yeunsook
Y
Division of Molecular Life Sciences, Ewha Womans University, Seoul 120-750, Korea.
Lee
Younghee
Y
Kim
Bumjin
B
Shin
Youngah
Y
Nam
Seungyoon
S
Kim
Pora
P
Kim
Namshin
N
Chung
Won-Hyong
WH
Kim
Jaesang
J
Lee
Sanghyuk
S
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
D020033:Protein Isoforms; D012333:RNA, Messenger