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Journal Article
ECgene: an alternative splicing database update
- Authors
- Yeun Sook Lee, Young Hee Lee, Bum Jin Kim, Young Ah Shin, Seung Yoon Nam, Po Ra Kim, Nam Shin Kim, Won-Hyong Chung, Jae Sang Kim, Sang Hyuk Lee
- Issue Date
- 2007-01
- Citation
- Nucleic Acids Research, v.35, pp.D99-D103
- ISSN
- 0305-1048
- Publisher
- Oxford Univ. Press
- Language
- English
- Type
- Journal Article
- 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. © 2007 Oxford University Press.
- KSP Keywords
- Alternative splicing(AS), Candidate genes, Differential Expression, Expression analyses, Expression analysis, Functional features, Gene expression pattern, Gene ontology, Java application, Spliced variants, User interface
This work is distributed under the term of Creative Commons License (CCL)
(CC BY NC)
(CC BY NC)
