ECgene: An alternative splicing database update

Cited 33 time in scopus
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Title
ECgene: An alternative splicing database update
Author(s)
Y Lee; Y Lee; B Kim; Y Shin; S Nam; P Kim; Namshin Kim; W H Chung; J Kim; S Lee
Bibliographic Citation
Nucleic Acids Research, vol. 35, no. S1, pp. D99-D103
Publication Year
2007
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.
ISSN
0305-1048
Publisher
Oxford Univ Press
DOI
http://dx.doi.org/10.1093/nar/gkl992
Type
Article
Appears in Collections:
1. Journal Articles > Journal Articles
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