H-DBAS: Human-transcriptome database for alternative splicing: Update 2010

Integrated Database and Systems Biology Team, Biomedicinal Information Research Center National Institute of Advanced Industrial Science and Technology, AIST Bio-IT Research Bldg Aomi 2-4-7, Koto-ku, Tokyo 135-0064, Japan.
Nucleic Acids Research (Impact Factor: 9.11). 12/2009; 38(Database issue):D86-90. DOI: 10.1093/nar/gkp984
Source: PubMed


H-DBAS (http://h-invitational.jp/h-dbas/) is a specialized database for human alternative splicing (AS) based on H-Invitational full-length cDNAs. In this update, for better annotations of AS events, we correlated RNA-Seq tag information to the AS exons and splice junctions. We generated a total of 148,376,598 RNA-Seq tags from RNAs extracted from cytoplasmic, nuclear and polysome fractions. Analysis of the RNA-Seq tags allowed us to identify 90,900 exons that are very likely to be used for protein synthesis. On the other hand, 254 AS junctions of human RefSeq transcripts are unique to nuclear RNA and may not have any translational consequences. We also present a new comparative genomics viewer so that users can empirically understand the evolutionary turnover of AS. With the unique experimental data closely connected with intensively curated cDNA information, H-DBAS provides a unique platform for the analysis of complex AS.

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Available from: Yoshiharu Sato, Aug 21, 2014
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    • "Additionally, several comprehensive databases for alternative splicing have been developed such as HOLLYWOOD [113], ASD [114], BIPASS [117], ECgene [118], ASPicDB [121], AspAlt [125], H-DBAS [128], SPLOOCE [129], and APPRIS [130]. For example, the ECgene provides EST and serial analysis of gene expression (SAGE) data-based annotation and visualization for alternative splicing (AS). "
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    ABSTRACT: Alternative splicing is a major diversification mechanism in the human transcriptome and proteome. Several diseases, including cancers, have been associated with dysregulation of alternative splicing. Thus, correcting alternative splicing may restore normal cell physiology in patients with these diseases. This paper summarizes several alternative splicing-related diseases, including cancers and their target genes. Since new cancer drugs often target spliceosomes, several clinical drugs and natural products or their synthesized derivatives were analyzed to determine their effects on alternative splicing. Other agents known to have modulating effects on alternative splicing during therapeutic treatment of cancer are also discussed. Several commonly used bioinformatics resources are also summarized.
    The Scientific World Journal 05/2013; 2013:703568. DOI:10.1155/2013/703568 · 1.73 Impact Factor
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    • "Mammal transcripts were obtained from the Human-transcriptome Database for Alternative Splicing (H-DBAS) [29] and fish transcripts from the Ensembl database [22]. In the H-DBAS database, we considered only transcripts that were present in both the cDNA and mRNA databases, except in the case of R. norvegicus, where only the mRNA database was available. "
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    ABSTRACT: Alternative splicing, an unknown mechanism 20 years ago, is now recognized as a major mechanism for proteome and transcriptome diversity, particularly in mammals--some researchers conjecture that up to 90% of human genes are alternatively spliced. Despite much research on exon and intron evolution, little is known about the evolution of transcripts. In this paper, we present a model of transcript evolution and an associated algorithm to reconstruct transcript phylogenies. The evolution of the gene structure--exons and introns--is used as basis for the reconstruction of transcript phylogenies. We apply our model and reconstruction algorithm on two well-studied genes, MAG and PAX6, obtaining results consistent with current knowledge and thereby providing evidence that a phylogenetic analysis of transcripts is feasible and likely to be informative.
    BMC Bioinformatics 06/2012; 13 Suppl 9(Suppl 9):S1. DOI:10.1109/BIBM.2011.11 · 2.58 Impact Factor
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    • "The human ASPicDB isoform d47ccf3a53:7 has a structure identical to mouse NM_134050. Orthologous isoforms not included in the RefSeq database but supported by transcript evidences and collected in ASPicDB [13] as well as in other alternative splicing databases [38] are indicated in blue by their unique signature ID [39]. "
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    ABSTRACT: Recent discoveries have highlighted the fact that alternative splicing and alternative transcripts are the rule, rather than the exception, in metazoan genes. Since multiple transcript and protein variants expressed by the same gene are, by definition, structurally distinct and need not to be functionally equivalent, the concept of gene orthology should be extended to the transcript level in order to describe evolutionary relationships between structurally similar transcript variants. In other words, the identification of true orthology relationships between gene products now should progress beyond primary sequence and "splicing orthology", consisting in ancestrally shared exon-intron structures, is required to define orthologous isoforms at transcript level. As a starting step in this direction, in this work we performed a large scale human- mouse gene comparison with a twofold goal: first, to assess if and to which extent traditional gene annotations such as RefSeq capture genuine splicing orthology; second, to provide a more detailed annotation and quantification of true human-mouse orthologous transcripts defined as transcripts of orthologous genes exhibiting the same splicing patterns. We observed an identical exon/intron structure for 32% of human and mouse orthologous genes. This figure increases to 87% using less stringent criteria for gene structure similarity, thus implying that for about 13% of the human RefSeq annotated genes (and about 25% of the corresponding transcripts) we could not identify any mouse transcript showing sufficient similarity to be confidently assigned as a splicing ortholog. Our data suggest that current gene and transcript data may still be rather incomplete - with several splicing variants still unknown. The observation that alternative splicing produces large numbers of alternative transcripts and proteins, some of them conserved across species and others truly species-specific, suggests that, still maintaining the conventional definition of gene orthology, a new concept of "splicing orthology" can be defined at transcript level.
    BMC Genomics 10/2010; 11(1):534. DOI:10.1186/1471-2164-11-534 · 3.99 Impact Factor
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