Gene structure prediction and alternative splicing analysis using genomically aligned ESTs.

By Zhengyan Kan, E. Rouchka, W. Gish, D. States. Genome Research, 2001

425 citations recorded by the source corpus.

With the availability of a nearly complete sequence of the human genome, aligning expressed sequence tags (EST) to the genomic sequence has become a practical and powerful strategy for gene prediction. Elucidating gene structure is a complex problem requiring the identification of splice junctions, gene boundaries, and alternative splicing variants. We have developed a software tool, Transcript Assembly Program (TAP), to delineate gene structures using genomically aligned EST sequences. TAP assembles the joint gene structure of the entire genomic region from individual splice junction pairs, using a novel algorithm that uses the EST-encoded connectivity and redundancy information to sort out the complex alternative splicing patterns. A method called polyadenylation site scan (PASS) has been developed to detect poly-A sites in the genome. TAP uses these predictions to identify gene boundaries by segmenting the joint gene structure at polyadenylated terminal exons. Reconstructing 1007 known transcripts, TAP scored a sensitivity (Sn) of 60% and a specificity (Sp) of 92% at the exon level. The gene boundary identification process was found to be accurate 78% of the time. also reports alternative splicing patterns in EST alignments. An analysis of alternative splicing in 1124 genic regions suggested that more than half of human genes undergo alternative splicing. Surprisingly, we saw an absolute majority of the detected alternative splicing events affect the coding region. Furthermore, the evolutionary conservation of alternative splicing between human and mouse was analyzed using an EST-based approach. (See http://stl.wustl.edu/~zkan/TAP/)

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/58349675deea7764313f83c573d23e4df9acc244

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Citations in the corpus

A hitchhiker's guide to expressed sequence tag (EST) analysis (2006, methodology): “With the exponential rise in genomic data from global sequencing projects, EST databases are used for gene structure prediction [20, 76], to investigate alternative splicing [77–80], to discriminate between genes exhibiting tissue or disease-specific expression [81] and for the discovery and charact”
GMAP: a genomic mapping and alignment program for mRNA and EST sequence (2005, background): “…phenomena as alternative splicing, single nucleotide polymorphisms, and cDNA insertions and deletions (Jiang and Jacob, 1998; Irizarryet al., 2000; Kanet al., 2001, 2002; Zavolan et al., 2002; Modrek and Lee, 2002; Clampet al., 2003; Wheeler et al., 2003; Drabenstotet al., 2003; Kimet al., 2004;…”
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. (2003, methodology): “Abundantly expressed genes provide a high level of redundancy in the EST populations and, in many cases, yield evidence for the existence of alternative splicing isoforms (4,5).”
A genomic view of alternative splicing (2002, background): “Kan et al. (2001)17 Aligned EST and genomic sequence to create transcript.”
Physiology and molecular biology of stress tolerance in plants (2006, background): “ESTs are also found to be useful in understanding gene structure (Kan et al., 2001) and cloning of agronomically important genes using ESTs based physical maps (Kurata et al., 1997).”
Nonsense-mediated mRNA decay: splicing, translation and mRNP dynamics (2004, background): “For example, the advantages that are afforded by proteome diversity, which arises from the alternative splicing of more than 55% of human pre-mRNA”
Current methods of gene prediction, their strengths and weaknesses. (2002, methodology): “The approach adopted is rather different for programs which try to elucidate the gene structure from EST matches, like EbEST (73), Est2genome (74) or, more recently, TAP (75) and PAGAN (http://ismb01.”
EGASP: the human ENCODE Genome Annotation Assessment Project (2006, result): “In line with earlier estimates [43], 86% of the multi-exon loci exhibit alternative splicing in either the coding or non-coding transcripts.”
Function of alternative splicing. (2005, positive): “The high frequency of alternative splicing in humans is also supported by ESTbased database analysis, indicating that 35–60% of all human gene products are alternatively spliced (Mironov et al., 1999; Brett et al., 2000; Kan et al., 2001; Modrek et al., 2001), suggesting that alternative splicing of”