01717nas a2200325 4500008004100000022001400041245012600055210006900181260000900250300000800259490000700267520073000274653001501004653001201019653001601031653002601047653002801073653003101101653002901132653001101161653001401172653003401186653003001220653001301250653002601263100001801289700002101307700001501328856004801343 2013 eng d a1474-760X00aSustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.0 aSustainedinput switches for transcription factors and microRNAs c2013 aR850 v143 a
WaRSwap is a randomization algorithm that for the first time provides a practical network motif discovery method for large multi-layer networks, for example those that include transcription factors, microRNAs, and non-regulatory protein coding genes. The algorithm is applicable to systems with tens of thousands of genes, while accounting for critical aspects of biological networks, including self-loops, large hubs, and target rearrangements. We validate WaRSwap on a newly inferred regulatory network from Arabidopsis thaliana, and compare outcomes on published Drosophila and human networks. Specifically, sustained input switches are among the few over-represented circuits across this diverse set of eukaryotes.
10aAlgorithms10aAnimals10aArabidopsis10aComputational Biology10aDrosophila melanogaster10aGene Expression Regulation10aGene Regulatory Networks10aHumans10aMicroRNAs10aMolecular Sequence Annotation10aNucleic Acid Conformation10aSoftware10aTranscription Factors1 aMegraw, Molly1 aMukherjee, Sayan1 aOhler, Uwe uhttp://megraw.cgrb.oregonstate.edu/node/32002128nas a2200421 4500008004100000022001400041245007500055210006900130260001300199300001200212490000700224520091800231653002801149653001501177653001201192653002101204653002601225653002301251653002801274653001101302653003801313653001301351653000901364653001401373653003601387653001301423653002601436100002401462700002401486700002301510700001901533700002401552700001801576700001601594700001801610700003001628856004801658 2010 eng d a1362-496200amiRGen 2.0: a database of microRNA genomic information and regulation.0 amiRGen 20 a database of microRNA genomic information and regulat c2010 Jan aD137-410 v383 aMicroRNAs are small, non-protein coding RNA molecules known to regulate the expression of genes by binding to the 3'UTR region of mRNAs. MicroRNAs are produced from longer transcripts which can code for more than one mature miRNAs. miRGen 2.0 is a database that aims to provide comprehensive information about the position of human and mouse microRNA coding transcripts and their regulation by transcription factors, including a unique compilation of both predicted and experimentally supported data. Expression profiles of microRNAs in several tissues and cell lines, single nucleotide polymorphism locations, microRNA target prediction on protein coding genes and mapping of miRNA targets of co-regulated miRNAs on biological pathways are also integrated into the database and user interface. The miRGen database will be continuously maintained and freely available at http://www.microrna.gr/mirgen/.
10a3' Untranslated Regions10aAlgorithms10aAnimals10aCell Line, Tumor10aComputational Biology10aDatabases, Genetic10aDatabases, Nucleic Acid10aHumans10aInformation Storage and Retrieval10aInternet10aMice10aMicroRNAs10aPolymorphism, Single Nucleotide10aSoftware10aTranscription Factors1 aAlexiou, Panagiotis1 aVergoulis, Thanasis1 aGleditzsch, Martin1 aPrekas, George1 aDalamagas, Theodore1 aMegraw, Molly1 aGrosse, Ivo1 aSellis, Timos1 aHatzigeorgiou, Artemis, G uhttp://megraw.cgrb.oregonstate.edu/node/32402434nas a2200385 4500008004100000022001400041245005900055210005800114260001300172300001200185490000700197520139400204653001401598653002401612653001201636653001801648653001001666653001101676653001201687653000901699653001401708653002801722653001601750653001901766653004101785653002501826100002001851700001801871700002001889700002001909700001901929700003001948700002201978856004802000 2008 eng d a1362-496200aFrequency and fate of microRNA editing in human brain.0 aFrequency and fate of microRNA editing in human brain c2008 Sep a5270-800 v363 aPrimary transcripts of certain microRNA (miRNA) genes (pri-miRNAs) are subject to RNA editing that converts adenosine to inosine (A-->I RNA editing). However, the frequency of the pri-miRNA editing and the fate of edited pri-miRNAs remain largely to be determined. Examination of already known pri-miRNA editing sites indicated that adenosine residues of the UAG triplet sequence might be edited more frequently. In the present study, therefore, we conducted a large-scale survey of human pri-miRNAs containing the UAG triplet sequence. By direct sequencing of RT-PCR products corresponding to pri-miRNAs, we examined 209 pri-miRNAs and identified 43 UAG and also 43 non-UAG editing sites in 47 pri-miRNAs, which were highly edited in human brain. In vitro miRNA processing assay using recombinant Drosha-DGCR8 and Dicer-TRBP (the human immuno deficiency virus transactivating response RNA-binding protein) complexes revealed that a majority of pri-miRNA editing is likely to interfere with the miRNA processing steps. In addition, four new edited miRNAs with altered seed sequences were identified by targeted cloning and sequencing of the miRNAs that would be processed from edited pri-miRNAs. Our studies predict that approximately 16% of human pri-miRNAs are subject to A-->I editing and, thus, miRNA editing could have a large impact on the miRNA-mediated gene silencing.
10aAdenosine10aAdenosine Deaminase10aAnimals10aBase Sequence10aBrain10aHumans10aInosine10aMice10aMicroRNAs10aMolecular Sequence Data10aRNA Editing10aRNA Precursors10aRNA Processing, Post-Transcriptional10aRNA-Binding Proteins1 aKawahara, Yukio1 aMegraw, Molly1 aKreider, Edward1 aIizasa, Hisashi1 aValente, Louis1 aHatzigeorgiou, Artemis, G1 aNishikura, Kazuko uhttp://megraw.cgrb.oregonstate.edu/node/32702198nas a2200301 4500008004100000022001400041245009100055210006900146260001300215300001200228490000700240520133700247653001201584653003701596653002801633653001301661653001101674653001301685653000901698653001401707653000901721653002801730100001801758700002401776700001801800700003001818856004801848 2007 eng d a1362-496200amiRGen: a database for the study of animal microRNA genomic organization and function.0 amiRGen a database for the study of animal microRNA genomic organ c2007 Jan aD149-550 v353 amiRGen is an integrated database of (i) positional relationships between animal miRNAs and genomic annotation sets and (ii) animal miRNA targets according to combinations of widely used target prediction programs. A major goal of the database is the study of the relationship between miRNA genomic organization and miRNA function. This is made possible by three integrated and user friendly interfaces. The Genomics interface allows the user to explore where whole-genome collections of miRNAs are located with respect to UCSC genome browser annotation sets such as Known Genes, Refseq Genes, Genscan predicted genes, CpG islands and pseudogenes. These miRNAs are connected through the Targets interface to their experimentally supported target genes from TarBase, as well as computationally predicted target genes from optimized intersections and unions of several widely used mammalian target prediction programs. Finally, the Clusters interface provides predicted miRNA clusters at any given inter-miRNA distance and provides specific functional information on the targets of miRNAs within each cluster. All of these unique features of miRGen are designed to facilitate investigations into miRNA genomic organization, co-transcription and targeting. miRGen can be freely accessed at http://www.diana.pcbi.upenn.edu/miRGen.
10aAnimals10aData Interpretation, Statistical10aDatabases, Nucleic Acid10aGenomics10aHumans10aInternet10aMice10aMicroRNAs10aRats10aUser-Computer Interface1 aMegraw, Molly1 aSethupathy, Praveen1 aCorda, Benoit1 aHatzigeorgiou, Artemis, G uhttp://megraw.cgrb.oregonstate.edu/node/32901507nas a2200301 4500008004100000022001400041245010700055210006900162260001300231300001000244490000600254520059300260653002800853653002800881653001200909653002600921653001900947653001100966653001400977653003000991653001901021653003201040653001301072100002401085700001801109700003001127856004801157 2006 eng d a1548-709100aA guide through present computational approaches for the identification of mammalian microRNA targets.0 aguide through present computational approaches for the identific c2006 Nov a881-60 v33 aComputational microRNA (miRNA) target prediction is a field in flux. Here we present a guide through five widely used mammalian target prediction programs. We include an analysis of the performance of these individual programs and of various combinations of these programs. For this analysis we compiled several benchmark data sets of experimentally supported miRNA-target gene interactions. Based on the results, we provide a discussion on the status of target prediction and also suggest a stepwise approach toward predicting and selecting miRNA targets for experimental testing.
10a3' Untranslated Regions10a5' Untranslated Regions10aAnimals10aComputational Biology10aGene Targeting10aHumans10aMicroRNAs10aPredictive Value of Tests10aRNA, Messenger10aSensitivity and Specificity10aSoftware1 aSethupathy, Praveen1 aMegraw, Molly1 aHatzigeorgiou, Artemis, G uhttp://megraw.cgrb.oregonstate.edu/node/330