ArticleBMC bioinformatics2007
Computational analysis of biological functions and pathways collectively targeted by co-expressed microRNAs in cancer.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 72 citations in OpenAlex.
- Gra-CRC-miRTar: The pre-trained nucleotide-to-graph neural networks to identify potential miRNA targets in colorectal cancer.Computational and structural biotechnology journal · 2024Article
- Gra-CRC-miRTar: The pre-trained nucleotide-to-graph neural networks to identify potential miRNA targets in colorectal cancer.bioRxiv : the preprint server for biology · 2024Article
- Proposing new early detection indicators for pancreatic cancer: Combining machine learning and neural networks for serum miRNA-based diagnostic model.Frontiers in oncology · 2023Article
- miR-19b-3p promotes colon cancer proliferation and oxaliplatin-based chemoresistance by targeting SMAD4: validation by bioinformatics and experimental analyses.Journal of experimental & clinical cancer research : CR · 2017Article
- Review
- High-throughput sequencing of RNAs isolated by cross-linking immunoprecipitation (HITS-CLIP) reveals Argonaute-associated microRNAs and targets in Schistosoma japonicum.Parasites & vectors · 2015Article
- Bias in microRNA functional enrichment analysis.Bioinformatics (Oxford, England) · 2015Article
- Environmental exposures in utero and microRNA.Current opinion in pediatrics · 2014Review
- Distance-based classifiers as potential diagnostic and prediction tools for human diseases.BMC genomics · 2014Article
- The Diagnostic and Prognostic Role of microRNA in Colorectal Cancer - a Comprehensive review.Journal of Cancer · 2013Article
- A novel biclustering algorithm for the discovery of meaningful biological correlations between microRNAs and their target genes.BMC bioinformatics · 2013Article
- Effects of oestrogen on microRNA expression in hormone-responsive breast cancer cells.Hormones & cancer · 2012Article
- Discovering dysfunction of multiple microRNAs cooperation in disease by a conserved microRNA co-expression network.PloS one · 2012Article
- Identification of links between small molecules and miRNAs in human cancers based on transcriptional responses.Scientific reports · 2012Article
- Article
- A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules.Bioinformatics (Oxford, England) · 2011Article
- MicroRNA in pancreatic cancer: pathological, diagnostic and therapeutic implications.Cancer letters · 2010Review
- Clustered microRNAs' coordination in regulating protein-protein interaction network.BMC systems biology · 2009Article
- Estrogen Regulation of MicroRNA Expression.Current genomics · 2009Article
- Estradiol downregulates miR-21 expression and increases miR-21 target gene expression in MCF-7 breast cancer cells.Nucleic acids research · 2009Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMultiple recent studies have found aberrant expression profiles of microRNAome in human cancers. While several target genes have been experimentally identified for some microRNAs in various tumors, the global pattern of cellular functions and pathways affected by co-expressed microRNAs in cancer remains elusive. The goal of this study was to develop a computational approach to global analysis of the major biological processes and signaling pathways that are most likely to be affected collectively by co-expressed microRNAs in cancer cells.
resultsWe report results of computational analysis of five datasets of aberrantly expressed microRNAs in five human cancers published by the authors (pancreatic cancer) and others (breast cancer, colon cancer, lung cancer and lymphoma). Using the combinatorial target prediction algorithm miRgate and a two-step data reduction procedure we have determined Gene Ontology categories as well as biological functions, disease categories, toxicological categories and signaling pathways that are: targeted by multiple microRNAs; statistically significantly enriched with target genes; and known to be affected in specific cancers.
conclusionOur global analysis of predicted miRNA targets suggests that co-expressed miRNAs collectively provide systemic compensatory response to the abnormal phenotypic changes in cancer cells by targeting a broad range of functional categories and signaling pathways known to be affected in a particular cancer. Such systems biology based approach provides new avenues for biological interpretation of miRNA profiling data and generation of experimentally testable hypotheses regarding collective regulatory functions of miRNA in cancer.
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