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:
This record last updated: 03-05-2007