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AltTrans: Transcript pattern variants annotated for both alternative splicing and alternative polyadenylation

Le Texier V, Riethoven JJ, Kumanduri V, Gopalakrishnan C, Lopez F, Gautheret D, Thanaraj TA - BMC Bioinformatics (2006)

Bottom Line: We now extend these pipelines and integrate the resultant data sets to facilitate an integrated view of the contributions from splicing and polyadenylation in the formation of transcript variants.Resultant polyA sites from both AltTrans and AltPAS are merged.The generated database reports data on alternative splicing, alternative polyadenylation and the resultant alternate transcript patterns; the basal data is annotated for various biological features.

Affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. texier@ebi.ac.uk

ABSTRACT

Background: The three major mechanisms that regulate transcript formation involve the selection of alternative sites for transcription start (TS), splicing, and polyadenylation. Currently there are efforts that collect data & annotation individually for each of these variants. It is important to take an integrated view of these data sets and to derive a data set of alternate transcripts along with consolidated annotation. We have been developing in the past computational pipelines that generate value-added data at genome-scale on individual variant types; these include AltSplice on splicing and AltPAS on polyadenylation. We now extend these pipelines and integrate the resultant data sets to facilitate an integrated view of the contributions from splicing and polyadenylation in the formation of transcript variants.

Description: The AltSplice pipeline examines gene-transcript alignments and delineates alternative splice events and splice patterns; this pipeline is extended as AltTrans to delineate isoform transcript patterns for each of which both introns/exons and 'terminating' polyA site are delineated; EST/mRNA sequences that qualify the transcript pattern confirm both the underlying splicing and polyadenylation. The AltPAS pipeline examines gene-transcript alignments and delineates all potential polyA sites irrespective of underlying splicing patterns. Resultant polyA sites from both AltTrans and AltPAS are merged. The generated database reports data on alternative splicing, alternative polyadenylation and the resultant alternate transcript patterns; the basal data is annotated for various biological features. The data (named as integrated AltTrans data) generated for both the organisms of human and mouse is made available through the Alternate Transcript Diversity web site at http://www.ebi.ac.uk/atd/.

Conclusion: The reported data set presents alternate transcript patterns that are annotated for both alternative splicing and alternative polyadenylation. Results based on current transcriptome data indicate that the contribution of alternative splicing is larger than that of alternative polyadenylation.

Inset A: Example of transcript pattern view. Exons are indicated by boxes and introns by lines. Exons/introns that are variants are indicated in blue colour. Browsing the cursor over various elements of a pattern displays pop-up's giving detailed information on the elements. The displayed pop-up in this example shows information on the polyA sites that maps to the alternate transcript pattern AT2; of these two polyA sites, the first one (located at gene position 9317) terminates the transcript pattern while the second one (located at gene position 9189) is skipped and is not used as a terminating polyA in the formation of this pattern. Inset B: Example snapshot of a portion of Ensembl gene display page to illustrate the integration of the AltTrans data in Ensembl genome annotation project.
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Figure 6: Inset A: Example of transcript pattern view. Exons are indicated by boxes and introns by lines. Exons/introns that are variants are indicated in blue colour. Browsing the cursor over various elements of a pattern displays pop-up's giving detailed information on the elements. The displayed pop-up in this example shows information on the polyA sites that maps to the alternate transcript pattern AT2; of these two polyA sites, the first one (located at gene position 9317) terminates the transcript pattern while the second one (located at gene position 9189) is skipped and is not used as a terminating polyA in the formation of this pattern. Inset B: Example snapshot of a portion of Ensembl gene display page to illustrate the integration of the AltTrans data in Ensembl genome annotation project.

Mentions: Pattern viewers that give visual presentation of the observed isoform splice pattern structures and of the observed transcript pattern structures are provided. An example of transcript pattern view is presented in Fig. 6A. Each element of the pattern such as exon/intron/polyA site and the pattern as such is hyperlinked to pages giving detailed information (including nucleotide sequence, and detected signals).

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AltTrans: Transcript pattern variants annotated for both alternative splicing and alternative polyadenylation

Le Texier V, Riethoven JJ, Kumanduri V, Gopalakrishnan C, Lopez F, Gautheret D, Thanaraj TA - BMC Bioinformatics (2006)

Inset A: Example of transcript pattern view. Exons are indicated by boxes and introns by lines. Exons/introns that are variants are indicated in blue colour. Browsing the cursor over various elements of a pattern displays pop-up's giving detailed information on the elements. The displayed pop-up in this example shows information on the polyA sites that maps to the alternate transcript pattern AT2; of these two polyA sites, the first one (located at gene position 9317) terminates the transcript pattern while the second one (located at gene position 9189) is skipped and is not used as a terminating polyA in the formation of this pattern. Inset B: Example snapshot of a portion of Ensembl gene display page to illustrate the integration of the AltTrans data in Ensembl genome annotation project.
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Figure 6: Inset A: Example of transcript pattern view. Exons are indicated by boxes and introns by lines. Exons/introns that are variants are indicated in blue colour. Browsing the cursor over various elements of a pattern displays pop-up's giving detailed information on the elements. The displayed pop-up in this example shows information on the polyA sites that maps to the alternate transcript pattern AT2; of these two polyA sites, the first one (located at gene position 9317) terminates the transcript pattern while the second one (located at gene position 9189) is skipped and is not used as a terminating polyA in the formation of this pattern. Inset B: Example snapshot of a portion of Ensembl gene display page to illustrate the integration of the AltTrans data in Ensembl genome annotation project.
Mentions: Pattern viewers that give visual presentation of the observed isoform splice pattern structures and of the observed transcript pattern structures are provided. An example of transcript pattern view is presented in Fig. 6A. Each element of the pattern such as exon/intron/polyA site and the pattern as such is hyperlinked to pages giving detailed information (including nucleotide sequence, and detected signals).

Bottom Line: We now extend these pipelines and integrate the resultant data sets to facilitate an integrated view of the contributions from splicing and polyadenylation in the formation of transcript variants.Resultant polyA sites from both AltTrans and AltPAS are merged.The generated database reports data on alternative splicing, alternative polyadenylation and the resultant alternate transcript patterns; the basal data is annotated for various biological features.

Affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. texier@ebi.ac.uk

ABSTRACT

Background: The three major mechanisms that regulate transcript formation involve the selection of alternative sites for transcription start (TS), splicing, and polyadenylation. Currently there are efforts that collect data & annotation individually for each of these variants. It is important to take an integrated view of these data sets and to derive a data set of alternate transcripts along with consolidated annotation. We have been developing in the past computational pipelines that generate value-added data at genome-scale on individual variant types; these include AltSplice on splicing and AltPAS on polyadenylation. We now extend these pipelines and integrate the resultant data sets to facilitate an integrated view of the contributions from splicing and polyadenylation in the formation of transcript variants.

Description: The AltSplice pipeline examines gene-transcript alignments and delineates alternative splice events and splice patterns; this pipeline is extended as AltTrans to delineate isoform transcript patterns for each of which both introns/exons and 'terminating' polyA site are delineated; EST/mRNA sequences that qualify the transcript pattern confirm both the underlying splicing and polyadenylation. The AltPAS pipeline examines gene-transcript alignments and delineates all potential polyA sites irrespective of underlying splicing patterns. Resultant polyA sites from both AltTrans and AltPAS are merged. The generated database reports data on alternative splicing, alternative polyadenylation and the resultant alternate transcript patterns; the basal data is annotated for various biological features. The data (named as integrated AltTrans data) generated for both the organisms of human and mouse is made available through the Alternate Transcript Diversity web site at http://www.ebi.ac.uk/atd/.

Conclusion: The reported data set presents alternate transcript patterns that are annotated for both alternative splicing and alternative polyadenylation. Results based on current transcriptome data indicate that the contribution of alternative splicing is larger than that of alternative polyadenylation.

View Similar Images In: Results  - Collection
View Article: PubMed Central - HTML -  PubMed
Show All Figures - Show MeSH
getmorefigures.php?pmc=1435940&rFormat=json&query=null&req=5