ArticleNucleic acids research2005
ECgene: genome annotation for alternative splicing.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- The cobalamin processing enzyme of Trichoplax adhaerens.The Journal of biological chemistry · 2025Article
- Fragile X mental retardation protein recognizes a G quadruplex structure within the survival motor neuron domain containing 1 mRNA 5'-UTR.Molecular bioSystems · 2017Article
- Integrating genomic, transcriptomic, and interactome data to improve Peptide and protein identification in shotgun proteomics.Journal of proteome research · 2014Review
- SpliceVista, a tool for splice variant identification and visualization in shotgun proteomics data.Molecular & cellular proteomics : MCP · 2014Article
- Genomics of alternative splicing: evolution, development and pathophysiology.Human genetics · 2014Review
- Innovations in proteomic profiling of cancers: alternative splice variants as a new class of cancer biomarker candidates and bridging of proteomics with structural biology.Journal of proteomics · 2013Review
- C-terminal truncation of a bovine B(12) trafficking chaperone enhances the sensitivity of the glutathione-regulated thermostability.BMB reports · 2013Article
- Structural basis of multifunctionality in a vitamin B12-processing enzyme.The Journal of biological chemistry · 2011Article
- Different sequence signatures in the upstream regions of plant and animal tRNA genes shape distinct modes of regulation.Nucleic acids research · 2011Article
- PEPPI: a peptidomic database of human protein isoforms for proteomics experiments.BMC bioinformatics · 2010Article
- Testing the coding potential of conserved short genomic sequences.Advances in bioinformatics · 2010Article
- Comprehensive splicing graph analysis of alternative splicing patterns in chicken, compared to human and mouse.BMC genomics · 2009Article
- Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer.Cancer research · 2009Article
- A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data.BMC bioinformatics · 2008Article
- SpliceCenter: a suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies.BMC bioinformatics · 2008Article
- hsp70 genes in the human genome: Conservation and differentiation patterns predict a wide array of overlapping and specialized functions.BMC evolutionary biology · 2008Article
- A new advance in alternative splicing databases: from catalogue to detailed analysis of regulation of expression and function of human alternative splicing variants.BMC bioinformatics · 2007Article
- SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis.BMC bioinformatics · 2007Article
- The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.Nucleic acids research · 2007Article
- Characterising alternate splicing and tissue specific expression in the chicken from ESTs.Cytogenetic and genome research · 2007Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
ECgene provides annotation for gene structure, function and expression, taking alternative splicing events into consideration. The gene-modeling algorithm combines the genome-based expressed sequence tag (EST) clustering and graph-theoretic transcript assembly procedures. The website provides several viewers and applications that have many unique features useful for the analysis of the transcript structure and gene expression. The summary viewer shows the gene summary and the essence of other annotation programs. The genome browser and the transcript viewer are available for comparing the gene structure of splice variants. Changes in the functional domains by alternative splicing can be seen at a glance in the transcript viewer. We also provide two unique ways of analyzing gene expression. The SAGE tags deduced from the assembled transcripts are used to delineate quantitative expression patterns from SAGE libraries available publically. Furthermore, the cDNA libraries of EST sequences in each cluster are used to infer qualitative expression patterns. It should be noted that the ECgene website provides annotation for the whole transcriptome, not just the alternatively spliced genes. Currently, ECgene supports the human, mouse and rat genomes. The ECgene suite of tools and programs is available at http://genome.ewha.ac.kr/ECgene/.
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