ECgene -- Genome annotation for alternative splicing

What you can do:
Search for annotated information about gene structure, function and expression, and alternative splicing events.
Highlights:
  • ECgene website provides annotation for the whole transcriptome, as well as the alternatively spliced genes.
  • The summary viewer shows the gene summary and the essence of other annotation programs.
  • The genome browser and the transcript viewer are available for comparing the gene structure of splice variants. Changes in the functional domains by alternative splicing can be seen at a glance in the transcript viewer.
  • Two unique ways of analyzing gene expression are provided: the SAGE tags deduced from the assembled transcripts are used to delineate quantitative expression patterns from SAGE libraries available publicly.
  • The cDNA libraries of EST sequences in each cluster are used to infer qualitative expression patterns.
  • In its 2007 update, the ECgene's AS modeling and EST clustering were expanded to nine organisms for which sufficient EST data are available in the GenBank.
  • New tools for differential expression analysis are introduced:
  • **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.
  • ** 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.
Keywords:
  • transcriptome analysis
  • transcriptome annotations
  • transcription analysis
  • expression patterns
  • genome browser
  • alternative splicing
  • alternatively spliced genes
  • gene splicing
  • introns
  • exons
  • splice variants
  • SAGE data analysis
  • SAGE tags
  • ESTs
  • expressed sequence tags
  • gene expression patterns
  • gene annotations
  • genome annotations
Literature & Tutorials:
PubMed Link: ECgene
PubMed Link of 2007 update: ECgene: an alternative splicing database update
This record last updated: 03-05-2007

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