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Resource:ASAP: the Alternative Splicing Annotation Project

Name: Resource:ASAP: the Alternative Splicing Annotation Project
Description: THIS RESOURCE IS NO LONGER IN SERVICE, documented on 8/12/13.

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.

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.[1]
Other Name(s): Alternative Splicing Annotation Project, Alternative Splicing Annotation Project database, Alternative Splicing
Abbreviation: ASAP
Parent Organization: University of California at Los Angeles; California; USA
Supporting Agency: NSF, DOE
Grant: 0082964, DEFG0387ER60615, DGE-9987641
Resource Type(s): Database
Resource: Resource
URL: http://bioinfo.mbi.ucla.edu/ASAP/
*Id: nif-0000-33105
PMID: PMID 12519958
Publication link: http://nar.oxfordjournals.org/content/31/1/101.long
Related to: Resource:Alternative Splicing Annotation Project II Database, Resource:Biositemaps
Availability: THIS RESOURCE IS NO LONGER IN SERVICE, documented on 8/12/13, CCB License
Address: Molecular Biology Institute, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1570, USA
Keywords: gene, genome, human, isoform, mechanism, metazoa, molecular, mRNA, nucleus, process, protein, sequence, splice, tissue specificity, transcription, transcript, alternate splicing, microarray, alternative splicing, biological process, alternatively spliced isoform, contig, cancer, Image
Organism: Human, Mouse
Link to OWL / RDF: Download this content as OWL/RDF

Curation status: Uncurated

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References

  1. Lee C et al. (2003) ASAP: the Alternative Splicing Annotation Project. Nucleic Acids Res 31: 101-5 PubMed

Notes

This page uses this default form:Resource

Contributors

Aarnaud, Ccdbuser, Yazin, Zaidaziz



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Facts about Resource:ASAP: the Alternative Splicing Annotation ProjectRDF feed
AbbrevASAP  +
AddressMolecular Biology Institute  +, Department of Chemistry and Biochemistry  +, University of California  +, Los Angeles  +, CA 90095-1570  +, and USA  +
AvailabilityTHIS RESOURCE IS NO LONGER IN SERVICE  +, Documented on 8/12/13  +, and CCB License  +
CurationStatuscurated  +
DefiningCitationhttp://bioinfo.mbi.ucla.edu/ASAP/  +
DefinitionTHIS RESOURCE IS NO LONGER IN SERVICE, doc THIS RESOURCE IS NO LONGER IN SERVICE, documented on 8/12/13.

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.

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.
sue-specific variants with human diseases.
GrantCategory:0082964   +, Category:DEFG0387ER60615   +, and Category:DGE-9987641   +
Has default formThis property is a special property in this wiki.Resource  +
Has roleDatabase  +
Idnif-0000-33105  +
Is part ofUniversity of California at Los Angeles; California; USA  +
KeywordsGene  +, Genome  +, Human  +, Isoform  +, Mechanism  +, Metazoa  +, Molecular  +, MRNA  +, Nucleus  +, Process  +, Protein  +, Sequence  +, Splice  +, Tissue specificity  +, Transcription  +, Transcript  +, Alternate splicing  +, Microarray  +, Alternative splicing  +, Biological process  +, Alternatively spliced isoform  +, Contig  +, Cancer  +, and Image  +
LabelResource:ASAP: the Alternative Splicing Annotation Project  +
ModifiedDate12 August 2013  +
PMID12519958  +
Page has default formThis property is a special property in this wiki.Resource  +
PublicationLinkhttp://nar.oxfordjournals.org/content/31/1/101.long  +
RelatedToResource:Alternative Splicing Annotation Project II Database  +, and Resource:Biositemaps  +
SpeciesHuman  +, and Mouse  +
SuperCategoryResource  +
Supporting AgencyNSF  +, and DOE  +
SynonymAlternative Splicing Annotation Project  +, Alternative Splicing Annotation Project database  +, and Alternative Splicing  +