miRCancer: a microRNA-cancer association database constructed by text mining on literature
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TLDR
This work proposes to extract microRNA-cancer associations by text mining and store them in a database called miRCancer, which documents 878 relationships between 236 microRNAs and 79 human cancers through the processing of >26 000 published articles.Abstract:
Motivation: Research interests in microRNAs have increased rapidly in the past decade. Many studies have showed that microRNAs have close relationships with various human cancers, and they potentially could be used as cancer indicators in diagnosis or as a suppressor for treatment purposes. There are several databases that contain microRNA–cancer associations predicted by computational methods but few from empirical results. Despite the fact that abundant experiments investigating microRNA expressions in cancer cells have been carried out, the results have remain scattered in the literature. We propose to extract microRNA–cancer associations by text mining and store them in a database called miRCancer. Results: The text mining is based on 75 rules we have constructed, which represent the common sentence structures typically used to state microRNA expressions in cancers. The microRNA–cancer association database, miRCancer, is updated regularly by running the text mining algorithm against PubMed. All miRNA–cancer associations are confirmed manually after automatic extraction. miRCancer currently documents 878 relationships between 236 microRNAs and 79 human cancers through the processing of426 000 published articles. Availability: miRCancer is freely available on the web at http://mircanread more
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References
More filters
Journal ArticleDOI
The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
TL;DR: Two small lin-4 transcripts of approximately 22 and 61 nt were identified in C. elegans and found to contain sequences complementary to a repeated sequence element in the 3' untranslated region (UTR) of lin-14 mRNA, suggesting that lin- 4 regulates lin- 14 translation via an antisense RNA-RNA interaction.
Journal ArticleDOI
The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans
Brenda J. Reinhart,Frank J. Slack,Frank J. Slack,Michael Basson,Amy E. Pasquinelli,Bettinger Jc,Ann E. Rougvie,H R Horvitz,Gary Ruvkun +8 more
TL;DR: It is shown that let-7 is a heterochronic switch gene that encodes a temporally regulated 21-nucleotide RNA that is complementary to elements in the 3′ untranslated regions of the heteroch chronic genes lin-14, lin-28, Lin-41, lin -42 and daf-12, indicating that expression of these genes may be directly controlled by let- 7.
Journal ArticleDOI
miRBase: tools for microRNA genomics
TL;DR: The overlap of miRNA sequences with annotated transcripts, both protein- and non-coding, are described and graphical views of the locations of a wide range of genomic features in model organisms allow for the first time the prediction of the likely boundaries of many miRNA primary transcripts.
Journal ArticleDOI
MicroRNA gene expression deregulation in human breast cancer.
Marilena V. Iorio,Manuela Ferracin,Chang Gong Liu,Angelo Veronese,Riccardo Spizzo,Silvia Sabbioni,Eros Magri,Massimo Pedriali,Muller Fabbri,Manuela Campiglio,Sylvie Ménard,Juan P. Palazzo,Anne L. Rosenberg,Piero Musiani,Stefano Volinia,Italo Nenci,George A. Calin,Patrizia Querzoli,Massimo Negrini,Carlo M. Croce +19 more
TL;DR: It is shown that, compared with normal breast tissue, miRNAs are also aberrantly expressed in human breast cancer, and the overall miRNA expression could clearly separate normal versus cancer tissues, with the most significantly deregulated mi RNAs being mir-125b, mir-145, mir -21, and mir-155.
Journal ArticleDOI
MicroRNAs Modulate Hematopoietic Lineage Differentiation
TL;DR: The results indicate that microRNAs are components of the molecular circuitry that controls mouse hematopoiesis and suggest that other micro RNAs have similar regulatory roles during other facets of vertebrate development.