2013-08-01T11:13:14-07:00
Resource:ASAP: the Alternative Splicing Annotation Project
ASAP
Molecular Biology Institute
Department of Chemistry and Biochemistry
University of California
Los Angeles
CA 90095-1570
USA
curated
http://bioinfo.mbi.ucla.edu/ASAP/
Database to access and mine alternative splicing information coming from genomics and proteomics based on genome-wide analyses of alternative splicing in human (30 793 alternative splice relationships found) from detailed alignment of expressed sequences onto the genomic sequence. ASAP provides precise gene exon-intron structure, alternative splicing, tissue specificity of alternative splice forms, and protein isoform sequences resulting from alternative splicing.
They developed an automated method for discovering human tissue-specific regulation of alternative splicing through a genome-wide analysis of expressed sequence tags (ESTs), which involves classifying human EST libraries according to tissue categories and Bayesian statistical analysis.
They use the UniGene clusters of human Expressed Sequence Tags (ESTs) to identify splices. The UniGene EST's are clustered so that a single cluster roughly corresponds to a gene (or at least a part of a gene). A single EST represents a portion of a processed (already spliced) mRNA. A given cluster contains many ESTs, each representing an outcome of a series of splicing events. The ESTs in UniGene contain the different mRNA isoforms transcribed from an alternatively spliced gene. They are not "predicting" alternative splicing, but locating it based on EST analysis. The discovered splices are further analyzed to determine alternative splicing events.<br />
They have identified 6201 alternative splice relationships in human genes, through a genome-wide analysis of expressed sequence tags (ESTs). Starting with 2.1 million human mRNA and EST sequences, they mapped expressed sequences onto the draft human genome sequence and only accepted splices that obeyed the standard splice site consensus.
After constructing a tissue list of 46 human tissues with 2 million human ESTs, they generated a database of novel human alternative splices that is four times larger than our previous report, and used Bayesian statistics to compare the relative abundance of every pair of alternative splices in these tissues. Using several statistical criteria for tissue specificity, they have identified 667 tissue-specific alternative splicing relationships and analyzed their distribution in human tissues. They have validated our results by comparison with independent studies. This genome-wide analysis of tissue specificity of alternative splicing will provide a useful resource to study the tissue-specific functions of transcripts and the association of tissue-specific variants with human diseases.
Server unavail. 7/31/13
Category:0082964
Category:DEFG0387ER60615
Category:DGE-9987641
nif-0000-33105
Resource:ASAP: the Alternative Splicing Annotation Project
2013-07-31T00:00:00
12519958
Resource
Alternative Splicing Annotation Project
Alternative Splicing Annotation Project database
Alternative Splicing
Resource
Synonym
United States Department of Energy
Supporting Agency
SuperCategory
Mouse
Species
Resource:Biositemaps
Resource:Alternative Splicing Annotation Project II Database
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PublicationLink
PMID
ModifiedDate
Label
Image
Cancer
Contig
Alternatively spliced isoform
Biological process
Alternative splicing
Microarray
Alternate splicing
Transcript
Transcription
Tissue specificity
Splice
Sequence
Protein
Process
Nucleus
MRNA
Molecular
Metazoa
Mechanism
Isoform
Human
Genome
Gene
Keywords
University of California at Los Angeles; California; USA
Is part of
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Database
Has role
Grant
EditorialNote
Definition
DefiningCitation
CurationStatus
CCB License
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Abbrev