PALS db: Putative Alternative Splicing database

Huang, Ying; Chen, Y.-T.; Lai, Jiun-I; Yang, Shangdong; Yang, Ueng Cheng

doi:10.1093/nar/30.1.186

Cited by 57 publications

(29 citation statements)

References 16 publications

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“…Identification of alternative splicing is generally based on cDNA or EST evidence (Kan et al, 2001;Coward et al, 2002;Huang et al, 2002;Modrek and Lee, 2002). Based on strict criteria and manual inspection (see "Materials and Methods"), we identified 327 cases of alternative splicing among Arabidopsis genes and categorized them into five groups: (a) alternative donor sites (102 cases), (b) alternative acceptor sites (190 cases), (c) alternative introns that are shifted in position at both sites (three cases), (d) exon skipping (21 cases), and (e) composite alternative splicing (different combinations of several alternative splicing events, 11 cases).…”

Section: Alternative Splicingmentioning

confidence: 99%

Refined Annotation of the Arabidopsis Genome by Complete Expressed Sequence Tag Mapping

2003

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Expressed sequence tags (ESTs) currently encompass more entries in the public databases than any other form of sequence data. Thus, EST data sets provide a vast resource for gene identification and expression profiling. We have mapped the complete set of 176,915 publicly available Arabidopsis EST sequences onto the Arabidopsis genome using GeneSeqer, a spliced alignment program incorporating sequence similarity and splice site scoring. About 96% of the available ESTs could be properly aligned with a genomic locus, with the remaining ESTs deriving from organelle genomes and non-Arabidopsis sources or displaying insufficient sequence quality for alignment. The mapping provides verified sets of EST clusters for evaluation of EST clustering programs. Analysis of the spliced alignments suggests corrections to current gene structure annotation and provides examples of alternative and non-canonical pre-mRNA splicing. All results of this study were parsed into a database and are accessible via a flexible Web interface at http://www.plantgdb.org/AtGDB/.The efforts of an international collaboration to obtain the complete genome sequence of the flowering plant Arabidopsis resulted in the release and annotation of 115.4 Mb of the genome (estimated at 125 Mb) in December of 2000 (Arabidopsis Genome Initiative, 2000). At that time, 25,498 protein-coding genes were identified in the five haploid chromosomes, but only 9% of these genes had been characterized experimentally, and only 69% could be functionally classified by similarity to proteins of known functions. In the interim, sequencing and annotation has progressed. The most current release of the Arabidopsis genome available at GenBank provides 117.3 Mb and 27,288 annotated protein-coding genes (see Data Sets in "Materials and Methods"). Annotation of the Arabidopsis genome and functional characterization of all the genes is an ongoing effort. Initial, high-throughput computational gene structure prediction has likely been successful in identifying most gene locations; however, these methods still suffer from limitations in predicting the precise gene structure for an entire gene, detection of intergenic regions, and identification of non-coding exon sequences (Pavy et al., 1999;Brendel and Zhu, 2002). Recent studies have concentrated on sequencing of full-length cDNAs to improve genome annotation Seki et al., 2002).Expressed sequence tags (ESTs) are single-pass sequencing reads of cDNA clones that have become a widely employed method for gene identification, expression profiling, and polymorphism analysis. Presently, more than 13.4 million EST entries have been deposited into the National Center for Biotechnology Information (NCBI) dbEST public database, including Arabidopsis with 176,915 ESTs and 21 other species with EST sets of more than 100,000 entries (http://www.ncbi.nlm.nih.gov/dbEST/ dbEST_summary.html). In the absence of a wholegenome sequencing project for a particular species, clustering of ESTs into contigs that represent unique genes is one of the most promi...

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Section: Alternative Splicingmentioning

confidence: 99%

Refined Annotation of the Arabidopsis Genome by Complete Expressed Sequence Tag Mapping

2003

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“…Figure 1 and Figure S1 give some examples of AS patterns observed in the manually curated RefSeq annotation [12]. Despite the ever growing availability of gene annotations the lack of a universal reference definition of AS and hence of the corresponding categories of AS events prevent AS databases (e.g., AEdb [13], ASD [14], ATD [15], Hollywood [16], PASDB [17], SpliceNest [18], PALS db [19], SpliceDB [20], AsMamDB [21], HASDB [22], ProSplicer [23], EuSplice [24], ASAPII [25] etc. …), from the automatic identification and update of the AS landscape that characterizes the transcriptome from a particular cell type or condition.…”

Section: Introductionmentioning

confidence: 99%

A General Definition and Nomenclature for Alternative Splicing Events

Sammeth¹,

Foissac²,

Guigó³

2008

SciVee

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Understanding the molecular mechanisms responsible for the regulation of the transcriptome present in eukaryotic cells is one of the most challenging tasks in the postgenomic era. In this regard, alternative splicing (AS) is a key phenomenon contributing to the production of different mature transcripts from the same primary RNA sequence. As a plethora of different transcript forms is available in databases, a first step to uncover the biology that drives AS is to identify the different types of reflected splicing variation. In this work, we present a general definition of the AS event along with a notation system that involves the relative positions of the splice sites. This nomenclature univocally and dynamically assigns a specific ''AS code'' to every possible pattern of splicing variation. On the basis of this definition and the corresponding codes, we have developed a computational tool (AStalavista) that automatically characterizes the complete landscape of AS events in a given transcript annotation of a genome, thus providing a platform to investigate the transcriptome diversity across genes, chromosomes, and species. Our analysis reveals that a substantial part-in human more than a quarter-of the observed splicing variations are ignored in common classification pipelines. We have used AStalavista to investigate and to compare the AS landscape of different reference annotation sets in human and in other metazoan species and found that proportions of AS events change substantially depending on the annotation protocol, species-specific attributes, and coding constraints acting on the transcripts. The AStalavista system therefore provides a general framework to conduct specific studies investigating the occurrence, impact, and regulation of AS.

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“…Recently, a software tool, Transcript Assembly Program (TAP), which deduces the gene structure by genomic EST alignments, was developed (Kan et al, 2001;Kan et al, 2002). Databases for alternatively spliced mRNAs including AsMamDB, HASDB, PALS and SpliceNest, all of which are based on UniGene clusters, have been constructed Modrek et al, 2001;Coward et al, 2002;Huang et al, 2002). The EST database would give detailed information of cDNA libraries and make it possible to predict tissue expression.…”

Section: Introductionmentioning

confidence: 99%

Identification of alternatively spliced mRNA variants related to cancers by genome-wide ESTs alignment

Hui

Zhang

et al. 2004

Oncogene

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Several databases have been published to predict alternative splicing of mRNAs by analysing the exon linkage relationship by alignment of expressed sequence tags (ESTs) to the genome sequence; however, little effort has been made to investigate the relationship between cancers and alternative splicing. We developed a program, Alternative Splicing Assembler (ASA), to look for splicing variants of human gene transcripts by genome-wide ESTs alignment. Using ASA, we constructed the biosino alternative splicing database (BASD), which predicted splicing variants for reference sequences from the reference sequence database (RefSeq) and presented them in both graph and text formats. EST clusters that differ from the reference sequences in at least one splicing site were counted as splicing variants. Of 4322 genes screened, 3490 (81%) were observed with at least one alternative splicing variants. To discover the variants associated with cancers, tissue sources of EST sequences were extracted from the UniLib database and ESTs from the same tissue type were counted. These were regarded as the indicators for gene expression level. Using Fisher's exact test, alternative splicing variants, of which EST counts were significantly different between cancer tissues and their counterpart normal tissues, were identified. It was predicted that 2149 variants, or 383 variants after Bonferroni correction, of 26 812 variants were likely tumor-associated. By reverse transcription-PCR, 11 of 13 novel alternative splicing variants and eight of nine variants' tissue specificity were confirmed in hepatocelluar carcinoma and in lung cancer. The possible involvement of alternative splicing in cancer is discussed.

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PALS db: Putative Alternative Splicing database

Cited by 57 publications

References 16 publications

Refined Annotation of the Arabidopsis Genome by Complete Expressed Sequence Tag Mapping

Refined Annotation of the Arabidopsis Genome by Complete Expressed Sequence Tag Mapping

A General Definition and Nomenclature for Alternative Splicing Events

Identification of alternatively spliced mRNA variants related to cancers by genome-wide ESTs alignment

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