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Structural profiles of human miRNA families from pairwise clustering

B. Kaczkowski, E. Torarinsson, K. Reiche, J. H. Havgaard, P. F. Stadler, J. Gorodkin
2008 Bioinformatics  
We address this issue by clustering the human pre-miRNA sequences based on pairwise, sequence and secondary structure alignment using FOLDALIGN, followed by global multiple alignment of obtained clusters  ...  As a result, the common secondary structure was successfully determined for four FOLDALIGN clusters: the RF00027 structural family of the Rfam database and three clusters with previously undescribed consensus  ...  ACKNOWLEDGEMENTS The work on the Duda rule has been done by R.K. while she was a member of the Bioinformatics Group, University of Leipzig. Conflict of interest: none declared.  ... 
doi:10.1093/bioinformatics/btn628 pmid:19059941 fatcat:ctkvuhpm4fbd3kntx3kahnzcry

Structured RNAs and synteny regions in the pig genome

Christian Anthon, Hakim Tafer, Jakob H Havgaard, Bo Thomsen, Jakob Hedegaard, Stefan E Seemann, Sachin Pundhir, Stephanie Kehr, Sebastian Bartschat, Mathilde Nielsen, Rasmus O Nielsen, Merete Fredholm (+2 others)
2014 BMC Genomics  
Additional analysis of RNA-seq data from a pooled library from 10 different pig tissues added another 165 miRNA loci, yielding an overall annotation of 3,556 structured RNA loci.  ...  Currently, the human genome holds the best mammalian ncRNA annotation, a result of numerous efforts by several groups.  ...  This results in a total of 168 miRNAs from the human miRNA clusters that are considered conserved in pig.  ... 
doi:10.1186/1471-2164-15-459 pmid:24917120 pmcid:PMC4124155 fatcat:e7lm3yec2ndjnbtsc35hclnqca

The discovery potential of RNA processing profiles

Amadís Pagès, Ivan Dotu, Joan Pallarès-Albanell, Eulàlia Martí, Roderic Guigó, Eduardo Eyras
2017 Nucleic Acids Research  
Here we argue that read profiles from size-selected RNA sequencing capture the posttranscriptional processing specific to each RNA family, thereby providing functional information independently of sequence  ...  sncRNAs by harnessing the power of read profiles.  ...  Profiles are clustered into families according to pairwise distances using an improved density-based clustering algorithm ( Figure 1B ).  ... 
doi:10.1093/nar/gkx1115 pmid:29155959 pmcid:PMC5814818 fatcat:zdsghtvtwvgpnivv3yu637oc4y

A new method for measuring functional similarity of microRNAs

Guangchuang Yu, Chuan-Le Xiao, Xiaochen Bo, Chun-Hua Lu, Yide Qin, Sheng Zhan, Qing-Yu He
2011 Journal of Integrated OMICS  
The clustering of human miRNAs based on target genes molecular function annotation led to 44 significant clusters. The clustering results were coherent with biological knowledge.  ...  Our analysis suggests that systematic clustering based on target genes GO semantic similarities can aid to reveal the functional diversity of miRNA families.  ...  Human miRNAs have been grouped into 46 families on the basis of hairpin sequences conservation by Rfam [10] , and 60 families according to pre-miRNAs sequence and secondary structures by using FOLDALIGN  ... 
doi:10.5584/jiomics.v1i1.21 fatcat:la2b237a3vapvcgmfdz3avs7ce

Convolutional neural networks for classification of alignments of non-coding RNA sequences

Genta Aoki, Yasubumi Sakakibara
2018 Bioinformatics  
Results: We propose a novel application of CNNs to classification of pairwise alignments of sequences for accurate clustering of sequences and show the benefits of the CNN method of inputting pairwise  ...  After we combined the distributed representation of RNA nucleotides with the secondary-structure information specific to ncRNAs and furthermore with mapping profiles of next-generation sequence reads,  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/bty228 pmid:29949978 pmcid:PMC6022636 fatcat:egte4po4ibbfhe4ahaj72sgz3m

The discovery potential of RNA processing profiles [article]

Amadis Pages, Ivan Dotu, Joan Pallares-Albanell, Eulalia Marti, Roderic Guigo, Eduardo Eyras
2016 bioRxiv   pre-print
Here we argue that read profiles from size-selected RNA sequencing capture the post-transcriptional processing specific to each RNA family, thereby providing functional information independently of sequence  ...  and compare small non-coding RNAs (sncRNAs) by harnessing the power of read profiles.  ...  Profiles are clustered into families according to pairwise distances using an improved density-based clustering algorithm (Fig. 1B) .  ... 
doi:10.1101/049809 fatcat:2ghvl4htwjfyvhmwz6lgig4c4m

MicroRNA discovery by similarity search to a database of RNA-seq profiles

Sachin Pundhir, Jan Gorodkin
2013 Frontiers in Genetics  
On comparison of miRNA read profiles from plants and animals, we observed kingdom specific read profiles that are distinct in terms of both length and distribution of reads within the read profiles to  ...  We further analyzed known human and mouse miRNA read profiles and found two distinct classes; the first containing two blocks and the second containing >2 blocks of reads.  ...  ACKNOWLEDGMENTS We would like to thank the reviewers for their helpful comments and suggestions, Christian Anthon for the help in development of the web server and Betina Wingreen Jensen for proof-reading  ... 
doi:10.3389/fgene.2013.00133 pmid:23874353 pmcid:PMC3708161 fatcat:jgphucwlqzey7mrgzvoivji2ky

Modeling the asymmetric evolution of a mouse and rat-specific microRNA gene cluster intron 10 of the Sfmbt2 gene

Stefan Lehnert, Vladimir Kapitonov, Pushpike J Thilakarathne, Frans C Schuit
2011 BMC Genomics  
Recent data in humans and opossum indicate that retrotranspons of the class of short interspersed nuclear elements have contributed to the growth of microRNA gene clusters.  ...  The center of the mouse miRNA gene cluster consists of 13 copies of MLONG1.  ...  P41-LM006252 from the National Library of Medicine, National Institutes of Health, US (to VK).  ... 
doi:10.1186/1471-2164-12-257 pmid:21605348 pmcid:PMC3212979 fatcat:ysal4r3s6zhgzdwpzkg5ah2c4i

Understanding cooperativity of microRNAs via microRNA association networks

Young-Ji Na, Ju Han Kim
2013 BMC Genomics  
We showed that the secondary structures of pre-miRNAs in cooperatively regulating miRNAs are highly similar.  ...  Sequence and structural similarity analysis within miRNA association network showed that pre-miRNA secondary structure may be involved in the expression of mature miRNA's function.  ...  Although CMMs tend to include miRNA families as shown in Table 3 , structural similarity of pre-miRNAs within CMM cannot be explained by miRNA families because many of them originate from different precursors  ... 
doi:10.1186/1471-2164-14-s5-s17 pmid:24552551 pmcid:PMC3852507 fatcat:sg6nosv7lfaqjdfnsrdx467brm

BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles

Pavankumar Videm, Dominic Rose, Fabrizio Costa, Rolf Backofen
2014 Computer applications in the biosciences : CABIOS  
One prominent approach for putative function assignment is clustering of transcripts according to sequence and secondary structure.  ...  We propose a novel way to encode expression profiles in compact discrete structures, which can then be processed using fast graphkernel techniques.  ...  ncRNA expression profile clustering The similarity notion of NSPDK can be used directly by clustering algorithms that make use of pairwise similarity or distance information.  ... 
doi:10.1093/bioinformatics/btu270 pmid:24931994 pmcid:PMC4058930 fatcat:u665rdwwzvazxlwsmkrgqx7rqi

Characterization and Comparative Analysis of Small RNAs in Three Small RNA Libraries of the Brown Planthopper (Nilaparvata lugens)

Qiuhong Chen, Lin Lu, Hongxia Hua, Fei Zhou, Liaoxun Lu, Yongjun Lin, Neil R. Smalheiser
2012 PLoS ONE  
All the miRNAs had their own expression profiles in the three libraries. The phylogenic evolution of the miRNA families in BPH was consistent with other species.  ...  Many animal-conserved miRNA families as well as some novel miRNAs have been detected in our libraries. This is the first achievement to discover the small RNA world of BPH.  ...  expression profiles of miRNAs varied from highly specific to ubiquitous during the three developmental stages.  ... 
doi:10.1371/journal.pone.0032860 pmid:22412935 pmcid:PMC3295781 fatcat:iozy6yrztzaxbdx2yx4aib6uji

Predicting MicroRNA Biomarkers for Cancer Using Phylogenetic Tree and Microarray Analysis

Hsiuying Wang
2016 International Journal of Molecular Sciences  
One is the expression profiles for 114 human miRNAs, and the other one is the expression profiles for 16,063 mRNAs.  ...  Huang et al. (2007) published two datasets of miRNA and mRNA microarray expression profiles across 88 normal or cancerous tissue samples [14] .  ...  This work has been supported by: Ministry of Science and Technology 103-2118-M-009-001-MY2, Taiwan.  ... 
doi:10.3390/ijms17050773 pmid:27213352 pmcid:PMC4881592 fatcat:oyc3sjnubfdp7pnlsysb7shthy

Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish

Candida Vaz, Choon Wei Wee, Gek Ping Serene Lee, Philip W. Ingham, Vivek Tanavde, Sinnakaruppan Mathavan
2015 BMC Genomics  
Using the miRNA discovery tool (miRDeep2), we discovered novel miRNAs from the unannotated reads that ranged from 7.6 to 23.0 %, with exceptions of ovary (51.4 %) and testis (55.2 %).  ...  It appears that most of the miRNAs in zebrafish are yet to be discovered. Results: We sequenced small RNAs from brain, gut, liver, ovary, testis, eye, heart and embryo of zebrafish.  ...  the novel pre-miRNAs predicted from different tissues Tissue Samples Number of novel miRNAs (unique) Number of human seed homologs Number of tissue associated novel miRNAs Number of human seed  ... 
doi:10.1186/s12864-015-2135-7 pmid:26574018 pmcid:PMC4647824 fatcat:fz7f6gotgnatllpcyepwsgofsy

A Family of Human MicroRNA Genes from Miniature Inverted-Repeat Transposable Elements

Jittima Piriyapongsa, I. King Jordan, Alan Christoffels
2007 PLoS ONE  
In this report, we demonstrate that members of a recently discovered family of human miRNA genes, hsa-mir-548, are derived from Made1 transposable elements.  ...  Consistent with their origin from MITEs, hsa-mir-548 genes are primate-specific and have many potential paralogs in the human genome.  ...  Conclusion We report here a human miRNA gene family derived from TEs.  ... 
doi:10.1371/journal.pone.0000203 pmid:17301878 pmcid:PMC1784062 fatcat:cfg6t24xurejldp56qusoy4hsy

Large-scale analysis of microRNA expression, epi-transcriptomic features and biogenesis

Dimitrios M. Vitsios, Matthew P. Davis, Stijn van Dongen, Anton J. Enright
2016 Nucleic Acids Research  
Herein, we focus on Human and Mouse for which the majority of data are available. We reanalyse sequencing data from 461 samples into a coordinated catalog of microRNA expression.  ...  These analyses include global expression comparison, co-expression of miRNA clusters and the prediction of miRNA strand-specificity and underlying constraints.  ...  ACKNOWLEDGEMENTS We thank members of the Enright and Marioni laboratories (EMBL) for interesting and useful discussions and support.  ... 
doi:10.1093/nar/gkw1031 pmid:28180281 pmcid:PMC5388392 fatcat:bht5qmlavnadrk7qzb7alvgaoa
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