ECgene: an alternative splicing database update

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.

[1]  Daniel Gautheret,et al.  AltTrans: Transcript pattern variants annotated for both alternative splicing and alternative polyadenylation , 2006, BMC Bioinformatics.

[2]  Yi Xing,et al.  An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs , 2006, Nucleic acids research.

[3]  Tin Wee Tan,et al.  DEDB: a database of Drosophila melanogaster exons in splicing graph form , 2004, BMC Bioinformatics.

[4]  Bosiljka Tasic,et al.  Alternative pre-mRNA splicing and proteome expansion in metazoans , 2002, Nature.

[5]  I. Pastan,et al.  Discovery of three genes specifically expressed in human prostate by expressed sequence tag database analysis. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Xiang-Dong Fu,et al.  ASF/SF2-Regulated CaMKIIδ Alternative Splicing Temporally Reprograms Excitation-Contraction Coupling in Cardiac Muscle , 2005, Cell.

[7]  Christopher B. Burge,et al.  Hollywood: a comparative relational database of alternative splicing , 2005, Nucleic Acids Res..

[8]  Ting Wang,et al.  The UCSC Genome Browser Database: update 2009 , 2008, Nucleic Acids Res..

[9]  R H Hruban,et al.  Gene expression profiles in normal and cancer cells. , 1997, Science.

[10]  Steffen Heber,et al.  The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome. , 2004, Nucleic acids research.

[11]  S. Altschul,et al.  SAGEmap: a public gene expression resource. , 2000, Genome research.

[12]  Yi Xing,et al.  ASAP: the Alternative Splicing Annotation Project , 2003, Nucleic Acids Res..

[13]  Gene W. Yeo,et al.  Variation in sequence and organization of splicing regulatory elements in vertebrate genes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[14]  Namshin Kim,et al.  ECgene: genome-based EST clustering and gene modeling for alternative splicing. , 2005, Genome research.

[15]  Thangavel Alphonse Thanaraj,et al.  ASD: a bioinformatics resource on alternative splicing , 2005, Nucleic Acids Res..

[16]  Peng Liang,et al.  SAGE Genie: A suite with panoramic view of gene expression , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[17]  Christopher B. Burge,et al.  RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons , 2004, Nucleic Acids Res..

[18]  Tin Wee Tan,et al.  ASGS: an alternative splicing graph web service , 2006, Nucleic Acids Res..

[19]  Christopher J. Lee,et al.  Discovery of novel splice forms and functional analysis of cancer-specific alternative splicing in human expressed sequences. , 2003, Nucleic acids research.

[20]  Terrence S. Furey,et al.  The UCSC Genome Browser Database: update 2006 , 2005, Nucleic Acids Res..

[21]  Martin Vingron,et al.  T-STAG: resource and web-interface for tissue-specific transcripts and genes , 2005, Nucleic Acids Res..

[22]  Barry J. Dickson,et al.  fruitless Splicing Specifies Male Courtship Behavior in Drosophila , 2005, Cell.

[23]  Madeline A. Crosby,et al.  FlyBase: genes and gene models , 2004, Nucleic Acids Res..

[24]  R. Myers,et al.  Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data , 2005, Nucleic acids research.

[25]  John Quackenbush,et al.  The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes , 2004, Nucleic Acids Res..

[26]  Andrey A Mironov,et al.  Evolution of exon-intron structure and alternative splicing in fruit flies and malarial mosquito genomes. , 2006, Genome research.

[27]  Christopher J. Lee,et al.  Genome-wide detection of tissue-specific alternative splicing in the human transcriptome. , 2002, Nucleic acids research.

[28]  J. Thierry-Mieg,et al.  AceView: a comprehensive cDNA-supported gene and transcripts annotation , 2006, Genome Biology.

[29]  Sumio Sugano,et al.  Intris: A Viewer for cDNA-Genome Alignments Enabling Efficient Detection of Splicing Variants and Expression Profiles , 2002 .

[30]  Sanghyuk Lee,et al.  ECgene: genome annotation for alternative splicing , 2004, Nucleic Acids Res..