miRWalk - Database: Prediction of possible miRNA binding sites by walking the genes of three genomes
TL;DR: The miRWalk database as mentioned in this paper is a comprehensive database on miRNAs, which hosts predicted as well as validated miRNA binding sites, information on all known genes of human, mouse and rat.
About: This article is published in Journal of Biomedical Informatics.The article was published on 2011-10-01 and is currently open access. It has received 1603 citations till now. The article focuses on the topics: MiRNA binding & Untranslated region.
Citations
More filters
TL;DR: All of the major steps in RNA-seq data analysis are reviewed, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping.
Abstract: RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping. We highlight the challenges associated with each step. We discuss the analysis of small RNAs and the integration of RNA-seq with other functional genomics techniques. Finally, we discuss the outlook for novel technologies that are changing the state of the art in transcriptomics.
1,963 citations
TL;DR: An updated database containing 422 517 curated MTIs from 4076 miRNAs and 23 054 target genes collected from over 8500 articles is described, which serves as more comprehensively annotated, experimentally validated miRNA-target interactions databases in the field of miRNA related research.
Abstract: MicroRNAs (miRNAs) are small non-coding RNAs of ∼ 22 nucleotides that are involved in negative regulation of mRNA at the post-transcriptional level. Previously, we developed miRTarBase which provides information about experimentally validated miRNA-target interactions (MTIs). Here, we describe an updated database containing 422 517 curated MTIs from 4076 miRNAs and 23 054 target genes collected from over 8500 articles. The number of MTIs curated by strong evidence has increased ∼1.4-fold since the last update in 2016. In this updated version, target sites validated by reporter assay that are available in the literature can be downloaded. The target site sequence can extract new features for analysis via a machine learning approach which can help to evaluate the performance of miRNA-target prediction tools. Furthermore, different ways of browsing enhance user browsing specific MTIs. With these improvements, miRTarBase serves as more comprehensively annotated, experimentally validated miRNA-target interactions databases in the field of miRNA related research. miRTarBase is available at http://miRTarBase.mbc.nctu.edu.tw/.
1,394 citations
Cites background from "miRWalk - Database: Prediction of p..."
...Type of resources Database names Well-known databases miRBase (1), GeneCards (2), Ensembl (3), MGI (4) Information databases for MTIs Tarbase (5), starBase (6), miRGator (7), TSmiR (8) MiRNA target prediction databases miRWalk (9), miRGate (10), mirMark (11) SNP or mutation related databases PolymiRTS (12), SomamiR (13) Pathway related resources MiRPathDB (14), DIANA-miRPath (15), miRNet (16) Others Database or Web tools HMDD (17), MAGIA2 (18), NCG (19)...
[...]
...verified MTI information collected from miRTarBase (9)....
[...]
1,138 citations
TL;DR: The miRTarBase database (http://mirtarbase.mbc.nctu.edu.tw/) provides the most current and comprehensive information of experimentally validated miRNA-target interactions, with a 14-fold increase to mi RNA-target interaction entries and recent improvements.
Abstract: MicroRNAs (miRNAs) are small non-coding RNA molecules capable of negatively regulating gene expression to control many cellular mechanisms. The miRTarBase database (http://mirtarbase.mbc.nctu.edu.tw/) provides the most current and comprehensive information of experimentally validated miRNA-target interactions. The database was launched in 2010 with data sources for >100 published studies in the identification of miRNA targets, molecular networks of miRNA targets and systems biology, and the current release (2013, version 4) includes significant expansions and enhancements over the initial release (2010, version 1). This article reports the current status of and recent improvements to the database, including (i) a 14-fold increase to miRNA-target interaction entries, (ii) a miRNA-target network, (iii) expression profile of miRNA and its target gene, (iv) miRNA target-associated diseases and (v) additional utilities including an upgrade reminder and an error reporting/user feedback system.
756 citations
Cites background from "miRWalk - Database: Prediction of p..."
...miRWalk (27) presents predicted and validated information on miRNA-target interactions and enables researches to validate new targets of miRNA not only on 30 untranslated regions but also on other regions of all known genes....
[...]
TL;DR: A novel antimiR delivery platform that targets the acidic tumour microenvironment, evades systemic clearance by the liver, and facilitates cell entry via a non-endocytic pathway is introduced.
Abstract: MicroRNAs are short non-coding RNAs expressed in different tissue and cell types that suppress the expression of target genes. As such, microRNAs are critical cogs in numerous biological processes, and dysregulated microRNA expression is correlated with many human diseases. Certain microRNAs, called oncomiRs, play a causal role in the onset and maintenance of cancer when overexpressed. Tumours that depend on these microRNAs are said to display oncomiR addiction. Some of the most effective anticancer therapies target oncogenes such as EGFR and HER2; similarly, inhibition of oncomiRs using antisense oligomers (that is, antimiRs) is an evolving therapeutic strategy. However, the in vivo efficacy of current antimiR technologies is hindered by physiological and cellular barriers to delivery into targeted cells. Here we introduce a novel antimiR delivery platform that targets the acidic tumour microenvironment, evades systemic clearance by the liver, and facilitates cell entry via a non-endocytic pathway. We find that the attachment of peptide nucleic acid antimiRs to a peptide with a low pH-induced transmembrane structure (pHLIP) produces a novel construct that could target the tumour microenvironment, transport antimiRs across plasma membranes under acidic conditions such as those found in solid tumours (pH approximately 6), and effectively inhibit the miR-155 oncomiR in a mouse model of lymphoma. This study introduces a new model for using antimiRs as anti-cancer drugs, which can have broad impacts on the field of targeted drug delivery.
684 citations
References
More filters
TL;DR: Although they escaped notice until relatively recently, miRNAs comprise one of the more abundant classes of gene regulatory molecules in multicellular organisms and likely influence the output of many protein-coding genes.
32,946 citations
"miRWalk - Database: Prediction of p..." refers background in this paper
...protein-coding genes, leading to downregulation or repression of the target genes [1]....
[...]
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.
11,932 citations
"miRWalk - Database: Prediction of p..." refers background in this paper
...In the past couple of years, research groups demonstrated the involvement of miRNAs in complicated biological processes/pathways, including the control of developmental timing, haematopoietic cell differentiation, apoptosis, cell proliferation, organ development [10,11,46,47], as well as cancerogenesis [48–51] and other human diseases [40,52–57]....
[...]
TL;DR: In a four-genome analysis of 3' UTRs, approximately 13,000 regulatory relationships were detected above the estimate of false-positive predictions, thereby implicating as miRNA targets more than 5300 human genes, which represented 30% of the gene set.
11,624 citations
TL;DR: A new, bead-based flow cytometric miRNA expression profiling method is used to present a systematic expression analysis of 217 mammalian miRNAs from 334 samples, including multiple human cancers, and finds the miRNA profiles are surprisingly informative, reflecting the developmental lineage and differentiation state of the tumours.
Abstract: Recent work has revealed the existence of a class of small non-coding RNA species, known as microRNAs (miRNAs), which have critical functions across various biological processes. Here we use a new, bead-based flow cytometric miRNA expression profiling method to present a systematic expression analysis of 217 mammalian miRNAs from 334 samples, including multiple human cancers. The miRNA profiles are surprisingly informative, reflecting the developmental lineage and differentiation state of the tumours. We observe a general downregulation of miRNAs in tumours compared with normal tissues. Furthermore, we were able to successfully classify poorly differentiated tumours using miRNA expression profiles, whereas messenger RNA profiles were highly inaccurate when applied to the same samples. These findings highlight the potential of miRNA profiling in cancer diagnosis.
9,470 citations
"miRWalk - Database: Prediction of p..." refers background in this paper
...In the past couple of years, research groups demonstrated the involvement of miRNAs in complicated biological processes/pathways, including the control of developmental timing, haematopoietic cell differentiation, apoptosis, cell proliferation, organ development [10,11,46,47], as well as cancerogenesis [48–51] and other human diseases [40,52–57]....
[...]
TL;DR: The predicted regulatory targets of mammalian miRNAs were enriched for genes involved in transcriptional regulation but also encompassed an unexpectedly broad range of other functions.
5,246 citations
"miRWalk - Database: Prediction of p..." refers background in this paper
...…Both authors contributed equally to this work. a b s t r a c t MicroRNAs are small, non-coding RNA molecules that can complementarily bind to the mRNA 30-UTR region to regulate the gene expression by transcriptional repression or induction of mRNA degradation....
[...]