ArticleBMC genomics2007
In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers, 1 of them a synthesis that pooled it.
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Who cites it
9 citing papers in PubMed, 1 synthesis or guideline pooled it, 30 citations in OpenAlex.
- Correlation of VEGF +405C/G Polymorphism with Gastrointestinal Tract Cancers Risk: An Updated Meta-Analysis.Asian Pacific journal of cancer prevention : APJCP · 2025Pooled it
- AStruct: detection of allele-specific RNA secondary structure in structuromic probing data.BMC bioinformatics · 2024Article
- The role of SPARC (secreted protein acidic and rich in cysteine) in the pathogenesis of obesity, type 2 diabetes, and non-alcoholic fatty liver disease.Journal of physiology and biochemistry · 2023Review
- IndelsRNAmute: predicting deleterious multiple point substitutions and indels mutations.BMC bioinformatics · 2022Article
- Identification of SHANK2 Pathogenic Variants in a Chinese Uygur Population with Schizophrenia.Journal of molecular neuroscience : MN · 2021Article
- Single nucleotide polymorphisms and cancer susceptibility.Oncotarget · 2017Review
- Single nucleotide polymorphisms in microRNA binding sites of oncogenes: implications in cancer and pharmacogenomics.Omics : a journal of integrative biology · 2014Article
- Article
- In silico gene expression analysis--an overview.Molecular cancer · 2007Review
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundA promising application of the huge amounts of genetic data currently available lies in developing a better understanding of complex diseases, such as cancer. Analysis of publicly available databases can help identify potential candidates for genes or mutations specifically related to the cancer phenotype. In spite of their huge potential to affect gene function, no systematic attention has been paid so far to the changes that occur in untranslated regions of mRNA.
resultsIn this study, we used Expressed Sequence Tag (EST) databases as a source for cancer-related sequence polymorphism discovery at the whole-genome level. Using a novel computational procedure, we focused on the identification of untranslated region (UTR)-localized non-coding Single Nucleotide Polymorphisms (UTR-SNPs) significantly associated with the tumoral state. To explore possible relationships between genetic mutation and phenotypic variation, bioinformatic tools were used to predict the potential impact of cancer-associated UTR-SNPs on mRNA secondary structure and UTR regulatory elements. We provide a comprehensive and unbiased description of cancer-associated UTR-SNPs that may be useful to define genotypic markers or to propose polymorphisms that can act to alter gene expression levels. Our results suggest that a fraction of cancer-associated UTR-SNPs may have functional consequences on mRNA stability and/or expression.
conclusionWe have undertaken a comprehensive effort to identify cancer-associated polymorphisms in untranslated regions of mRNA and to characterize putative functional UTR-SNPs. Alteration of translational control can change the expression of genes in tumor cells, causing an increase or decrease in the concentration of specific proteins. Through the description of testable candidates and the experimental validation of a number of UTR-SNPs discovered on the secreted protein acidic and rich in cysteine (SPARC) gene, this report illustrates the utility of a cross-talk between in silico transcriptomics and cancer genetics.
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