ArticleNucleic acids research2011
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity.Genome research · 2025Article
- Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity.bioRxiv : the preprint server for biology · 2024Article
- Exon nomenclature and classification of transcripts database (ENACTdb): a resource for analyzing alternative splicing mediated proteome diversity.Bioinformatics advances · 2024Article
- APPRIS: selecting functionally important isoforms.Nucleic acids research · 2022Article
- tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing.Genome biology · 2020Article
- Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources.Briefings in bioinformatics · 2019Review
- APPRIS 2017: principal isoforms for multiple gene sets.Nucleic acids research · 2018Article
- Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond.Briefings in bioinformatics · 2016Article
- Clusterin transcript variants expression in thyroid tumor: a potential marker of malignancy?BMC cancer · 2015Article
- RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application.BMC genomics · 2015Article
- Evolution of gene structural complexity: an alternative-splicing-based model accounts for intron-containing retrogenes.Plant physiology · 2014Article
- A survey of software for genome-wide discovery of differential splicing in RNA-Seq data.Human genomics · 2014Article
- Pathway analysis and transcriptomics improve protein identification by shotgun proteomics from samples comprising small number of cells--a benchmarking study.BMC genomics · 2014Article
- Tumor antigens as proteogenomic biomarkers in invasive ductal carcinomas.BMC medical genomics · 2014Article
- SGTA: a new player in the molecular co-chaperone game.Hormones & cancer · 2013Review
- Function of alternative splicing.Gene · 2013Review
- DBATE: database of alternative transcripts expression.Database : the journal of biological databases and curation · 2013Article
- APPRIS: annotation of principal and alternative splice isoforms.Nucleic acids research · 2013Article
- SpliceAid-F: a database of human splicing factors and their RNA-binding sites.Nucleic acids research · 2013Article
- HEXEvent: a database of Human EXon splicing Events.Nucleic acids research · 2013Article
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20 authors.
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Abstract
Alternative splicing is emerging as a major mechanism for the expansion of the transcriptome and proteome diversity, particularly in human and other vertebrates. However, the proportion of alternative transcripts and proteins actually endowed with functional activity is currently highly debated. We present here a new release of ASPicDB which now provides a unique annotation resource of human protein variants generated by alternative splicing. A total of 256,939 protein variants from 17,191 multi-exon genes have been extensively annotated through state of the art machine learning tools providing information of the protein type (globular and transmembrane), localization, presence of PFAM domains, signal peptides, GPI-anchor propeptides, transmembrane and coiled-coil segments. Furthermore, full-length variants can be now specifically selected based on the annotation of CAGE-tags and polyA signal and/or polyA sites, marking transcription initiation and termination sites, respectively. The retrieval can be carried out at gene, transcript, exon, protein or splice site level allowing the selection of data sets fulfilling one or more features settled by the user. The retrieval interface also enables the selection of protein variants showing specific differences in the annotated features. ASPicDB is available at http://www.caspur.it/ASPicDB/.
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