ArticleGenome research2005
ECgene: genome-based EST clustering and gene modeling for alternative splicing.
Article in Genome research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Highly sensitive and multiplexed quantification of mRNA splice variants by the direct ligation of DNA probes at the exon junction and universal PCR amplification.Chemical science · 2017Article
- Survey of Programs Used to Detect Alternative Splicing Isoforms from Deep Sequencing Data In Silico.BioMed research international · 2015Review
- Onco-proteogenomics: cancer proteomics joins forces with genomics.Nature methods · 2014Article
- RCDA: a highly sensitive and specific alternatively spliced transcript assembly tool featuring upstream consecutive exon structures.Genomics · 2012Article
- PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text.BMC bioinformatics · 2012Article
- Bio301: A Web-Based EST Annotation Pipeline That Facilitates Functional Comparison Studies.ISRN bioinformatics · 2012Article
- A hybrid distance measure for clustering expressed sequence tags originating from the same gene family.PloS one · 2012Article
- An alternative polyadenylation signal in TCF7L2 generates isoforms that inhibit T cell factor/lymphoid-enhancer factor (TCF/LEF)-dependent target genes.Diabetologia · 2011Article
- Identification of alternatively spliced transcripts using a proteomic informatics approach.Methods in molecular biology (Clifton, N.J.) · 2011Article
- Complexity of bidirectional transcription and alternative splicing at human RCAN3 locus.PloS one · 2011Article
- Verifying expressed transcript variants by detecting and assembling stretches of consecutive exons.Nucleic acids research · 2010Article
- Identification of tumor-associated cassette exons in human cancer through EST-based computational prediction and experimental validation.Molecular cancer · 2010Article
- Quantitative gene expression profiles in real time from expressed sequence tag databases.Gene expression · 2010Article
- k-link EST clustering: evaluating error introduced by chimeric sequences under different degrees of linkage.Bioinformatics (Oxford, England) · 2009Article
- WebGMAP: a web service for mapping and aligning cDNA sequences to genomes.Nucleic acids research · 2009Article
- ESTPiper--a web-based analysis pipeline for expressed sequence tags.BMC genomics · 2009Article
- Highly diversified molecular evolution of downstream transcription start sites in rice and Arabidopsis.Plant physiology · 2009Article
- Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer.Cancer research · 2009Article
- A general definition and nomenclature for alternative splicing events.PLoS computational biology · 2008Article
- Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array.BMC genomics · 2008Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With the availability of the human genome map and fast algorithms for sequence alignment, genome-based EST clustering became a viable method for gene modeling. We developed a novel gene-modeling method, ECgene (Gene modeling by EST Clustering), which combines genome-based EST clustering and the transcript assembly procedure in a coherent and consistent fashion. Specifically, ECgene takes alternative splicing events into consideration. The position of splice sites (i.e., exon-intron boundaries) in the genome map is utilized as the critical information in the whole procedure. Sequences that share any splice sites are grouped together to define an EST cluster in a manner similar to that of the genome-based version of the UniGene algorithm. Transcript assembly is achieved using graph theory that represents the exon connectivity in each cluster as a directed acyclic graph (DAG). Distinct paths along exons correspond to possible gene models encompassing all alternative splicing events. EST sequences in each cluster are subclustered further according to the compatibility with gene structure of each splice variant, and they can be regarded as clone evidence for the corresponding isoform. The reliability of each isoform is assessed from the nature of cluster members and from the minimum number of clones required to reconstruct all exons in the transcript.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.