ArticleOncogene2004
Identification of alternatively spliced mRNA variants related to cancers by genome-wide ESTs alignment.
Article in Oncogene, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 68 citations in OpenAlex.
- Serine-arginine splicing factor 2 promotes oesophageal cancer progression by regulating alternative splicing of interferon regulatory factor 3.RNA biology · 2023Article
- A bioinformatic analysis identifies circadian expression of splicing factors and time-dependent alternative splicing events in the HD-MY-Z cell line.Scientific reports · 2019Article
- Temporal Splicing Switches in Elements of the TNF-Pathway Identified by Computational Analysis of Transcriptome Data for Human Cell Lines.International journal of molecular sciences · 2019Article
- "Dicing and Splicing" Sphingosine Kinase and Relevance to Cancer.International journal of molecular sciences · 2017Review
- Review
- Digital inventory of Arabidopsis transcripts revealed by 61 RNA sequencing samples.Plant physiology · 2014Article
- RRP1B is a metastasis modifier that regulates the expression of alternative mRNA isoforms through interactions with SRSF1.Oncogene · 2014Article
- Computational evidence of NAGNAG alternative splicing in human large intergenic noncoding RNA.BioMed research international · 2014Article
- Identification of novel splice variants and exons of human endothelial cell-specific chemotaxic regulator (ECSCR) by bioinformatics analysis.Computational biology and chemistry · 2012Article
- Meta-analytical biomarker search of EST expression data reveals three differentially expressed candidates.BMC genomics · 2012Article
- Article
- Increased levels of noisy splicing in cancers, but not for oncogene-derived transcripts.Human molecular genetics · 2011Article
- Alternative splicing enriched cDNA libraries identify breast cancer-associated transcripts.BMC genomics · 2010Article
- Identification of tumor-associated cassette exons in human cancer through EST-based computational prediction and experimental validation.Molecular cancer · 2010Article
- A study of alternative splicing in the pig.BMC research notes · 2010Article
- High-throughput binding analysis determines the binding specificity of ASF/SF2 on alternatively spliced human pre-mRNAs.Combinatorial chemistry & high throughput screening · 2010Article
- A global view of cancer-specific transcript variants by subtractive transcriptome-wide analysis.PloS one · 2009Article
- Global analysis of aberrant pre-mRNA splicing in glioblastoma using exon expression arrays.BMC genomics · 2008Article
- SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays.Genome biology · 2008Article
- Caffeine regulates alternative splicing in a subset of cancer-associated genes: a role for SC35.Molecular and cellular biology · 2008Article
Corrections and comments
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Authors and funding
7 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 hepatocellular carcinoma and in lung cancer. The possible involvement of alternative splicing in cancer is discussed.
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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.