Nucleic Acids Research Advance Access originally published online on November 28, 2006
Nucleic Acids Research 2007 35(Database issue):D99-D103; doi:10.1093/nar/gkl992
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Nucleic Acids Research, 2007, Vol. 35, Database issue D99-D103
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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ECgene: an alternative splicing database update
1 Division of Molecular Life Sciences, Ewha Womans University Seoul 120-750, Korea 2 Interdisciplinary Program in Bioinformatics, Seoul National University Seoul 151-742, Korea 3 Bioinformatics Team, Electronics and Telecommunications Research Institute (ETRI) Gajeong-Dong, Yuseong-Gu, Daejeon 305-350, Korea 4 Department of Chemistry and Biochemistry, Center for Computational Biology, Institute for Genomics and Proteomics, Molecular Biology Institute, University of California Los Angeles Los Angeles, CA 90095-1570, USA 5 Korean Bioinformation Center, Korea Research Institute of Bioscience & Biotechnology 52 Eoeun, Yuseong, Daejeon 305-333, Korea
*To whom correspondence should be addressed. Tel: +82 2 3277 2888; Fax: +82 2 3277 3760; Email: sanghyuk{at}ewha.ac.kr
Received September 15, 2006. Revised October 28, 2006. Accepted October 30, 2006.
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.
The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors
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