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Resource:ASAP: the Alternative Splicing Annotation Project
| Name: | Resource:ASAP: the Alternative Splicing Annotation Project |
| Description: | An online database to access and mine alternative splicing information coming from genomics and proteomics. ASAP is 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.
We 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. We 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. We are not "predicting" alternative splicing, but locating it based on EST analysis. The discovered splices are further analyzed to determine alternative splicing events. We 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, we 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, we 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, we have identified 667 tissue-specific alternative splicing relationships and analyzed their distribution in human tissues. We 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 |
| Parent Organization: | University of California at Los Angeles; California; USA |
| Supporting Agency: | National Science Foundation, U.S. Department of Energy |
| Related to: | Resource:Alternative Splicing Annotation Project II Database, Resource:Biositemaps |
| Resource Type(s): | Web accessible database, Downloadable database, Image |
| 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 |
| Grant: | 0082964, DEFG0387ER60615, DGE-9987641 |
| Abbreviation: | ASAP |
| Resource: | Resource |
| URL: | http://bioinfo.mbi.ucla.edu/ASAP/ |
| PMID: | PMID 12519958 |
| Publication link: | http://nar.oxfordjournals.org/content/31/1/101.long |
| Availability: | CCB License |
| Address: | Molecular Biology Institute, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1570, USA |
| Id: | nif-0000-33105 |
| Organism: | Human, Mouse |
| Link to OWL / RDF: | Download this content as OWL/RDF |
Curation status: Curated
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References
- ↑ 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
| Abbrev | ASAP + |
| Address | Molecular Biology Institute +, Department of Chemistry and Biochemistry +, University of California +, Los Angeles +, CA 90095-1570 +, and USA + |
| Availability | CCB License + |
| CurationStatus | curated + |
| DefiningCitation | http://bioinfo.mbi.ucla.edu/ASAP/ + |
| Definition | An online database to access and mine alte … An online database to access and mine alternative splicing information coming from genomics and proteomics. ASAP is 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.
We 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. We 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. We are not "predicting" alternative splicing, but locating it based on EST analysis. The discovered splices are further analyzed to determine alternative splicing events. We 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, we 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, we 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, we have identified 667 tissue-specific alternative splicing relationships and analyzed their distribution in human tissues. We 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. |
| Grant | Category:0082964 +, Category:DEFG0387ER60615 +, and Category:DGE-9987641 + |
| Has default formThis property is a special property in this wiki. | Resource + |
| Has role | Web accessible database +, Downloadable database +, and Image + |
| Id | nif-0000-33105 + |
| Is part of | University of California at Los Angeles; California; 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 +, and Cancer + |
| Label | Resource:ASAP: the Alternative Splicing Annotation Project + |
| ModifiedDate | 12 February 2013 + |
| PMID | 12519958 + |
| Page has default formThis property is a special property in this wiki. | Resource + |
| PublicationLink | http://nar.oxfordjournals.org/content/31/1/101.long + |
| RelatedTo | Resource:Alternative Splicing Annotation Project II Database +, and Resource:Biositemaps + |
| Species | Human +, and Mouse + |
| SuperCategory | Resource + |
| Supporting Agency | National Science Foundation +, and U.S. Department of Energy + |
| Synonym | Alternative Splicing Annotation Project +, Alternative Splicing Annotation Project database +, and Alternative Splicing + |