• psRNATarget

  • Referenced in 1 article [sw34140]
  • small RNAs (20–24 nt), including microRNAs (miRNAs) and a subset of small interfering RNAs ... regulatory small RNAs. Although a number of miRNA target prediction algorithms and programs have been ... most of them were designed for animal miRNAs which are significantly different from plant miRNAs ... differences demand the development of separate plant miRNA (and ta-siRNA) target analysis tool...
  • miRSystem

  • Referenced in 1 article [sw13902]
  • database which integrates seven well known miRNA target gene prediction programs: DIANA, miRanda, miRBridge, PicTar ... from TarBase and miRecords on interaction between miRNA and its target genes. Several new features ... from others: 1) miRSystem allows querying multiple miRNAs in one step for the associations between ... miRNAs and their target genes. 2) Two algorithms are incorporated to characterize the enriched biological...
  • MiRonTop

  • Referenced in 1 article [sw29581]
  • expression studies. Summary: Current challenges in microRNA (miRNA) research are to improve the identification ... complex interplay existing between a specific miRNA and multiple biological networks. MiRonTop is an online ... data to identify the potential implication of miRNAs on a specific biological system. It allows ... pertinent mRNA targets according to several existing miRNA target prediction approaches. It also provides useful...
  • miRNAkey

  • Referenced in 1 article [sw29585]
  • obtain a more accurate depiction of miRNA expression profiles in living cells. This type ... understanding of the complexity and mode of miRNA regulation. miRNAkey is a software package designed ... base-station for the analysis of miRNA deep sequencing data. Our package implements common steps ... novel platform for the analysis of miRNA expression. Through the use of a simple graphical...
  • LncmiRSRN

  • Referenced in 1 article [sw34139]
  • analysis of long non-coding RNA related miRNA sponge regulatory network in human cancer. Results ... novel method to construct lncRNA related miRNA sponge regulatory networks (LncmiRSRNs) by integrating matched lncRNA ... expression profiles with clinical information and putative miRNA-target interactions. Using the method, we have ... discover that after being released from miRNA control, the target mRNAs are normally up-regulated...
  • ComiRNet

  • Referenced in 1 article [sw34289]
  • based system for the analysis of miRNA-gene regulatory networks. ComiRNet is a database ... miRNA target predictions and predicted miRNA regulatory networks. ComiRNet stores approximately 5 million predicted interactions ... between 934 human miRNAs and 30,875 gene transcripts (mRNAs) which are exploited ... hierarchies of overlapping biclusters representing potential miRNA regulatory networks...
  • DIANA-mirExTra

  • Referenced in 1 article [sw29578]
  • Data to MicroRNA Function. Methodology/Principal Findings: Although miRNA expression levels may not be routinely measured ... high-throughput experiments, a possible involvement of miRNAs in the deregulation of gene expression ... that allows the comparison of frequencies of miRNA associated motifs between sets of genes that ... lead to the identification of miRNAs responsible for the deregulation of large numbers of genes...
  • SeqBuster

  • Referenced in 1 article [sw29583]
  • analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells. High-throughput ... bioinformatic tool offering a deep characterization of miRNA variants (isomiRs). The application of SeqBuster ... human embryonic stem cells revealed that most miRNAs present different types of isomiRs, some ... provided by SeqBuster could help to identify miRNA-variants that are relevant in physiological...
  • Mirsynergy

  • Referenced in 1 article [sw34555]
  • Mirsynergy: detecting synergistic miRNA regulatory modules by overlapping neighbourhood expansion. Motivation: Identification of microRNA regulatory ... forms MiRMs based on co-occurring microRNA (miRNA) targets and then expands each MiRM ... synergy score, which is a function of miRNA–mRNA and gene–gene interactions. Using expression ... significantly higher functional enrichment and more coherent miRNA–mRNA expression anti-correlation. Based on Kaplan...
  • SpidermiR

  • Referenced in 1 article [sw19416]
  • R/Bioconductor package for integrative network analysis with miRNA data. The aims of SpidermiR ... appropriate gene nomenclature, iii) integration of miRNA data in a specific network, iv) provide different ... integration with validated and predicted miRNA data (mirWalk, miR2Disease,miRTar, miRandola,Pharmaco-miR,DIANA, Miranda...
  • TAPIR

  • Referenced in 1 article [sw34141]
  • offers the possibility to search for plant miRNA targets using a fast and a precise ... guarantees to find less perfectly paired miRNA-target duplexes. Furthermore, the precise option allows ... target mimics, which are characterized by a miRNA-target duplex having a large loop, making...
  • CAP-miRSeq

  • Referenced in 1 article [sw34371]
  • both a small and large number of miRNA-seq samples quickly. The results of both ... known and novel miRNAs are presented in the merged and convenient format for investigators ... called variants in the coding regions of miRNAs can be used to investigate gene regulation...
  • SylArray

  • Referenced in 1 article [sw35229]
  • server for automated detection of miRNA effects from expression data. A useful step for understanding ... function of microRNAs (miRNA) or siRNAs is the detection of their effects on genome-wide ... applies the Sylamer algorithm for detection of miRNA or siRNA signatures in those sequences...
  • Chippeakanno

  • Referenced in 2 articles [sw18996]
  • terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements...
  • ipflasso

  • Referenced in 2 articles [sw31364]
  • predicted based on, say, mRNA data, miRNA data, methylation data, CNV data, clinical data...
  • LncDisease

  • Referenced in 2 articles [sw34250]
  • based on the crosstalk between lncRNAs and miRNAs. Using LncDisease, we predicted the lncRNAs associated...
  • LVSmiRNA

  • Referenced in 1 article [sw20390]
  • Bioconductor package LVSmiRNA: LVS normalization for Agilent miRNA data. Normalization of Agilent miRNA arrays...
  • DisSetSim

  • Referenced in 1 article [sw33494]
  • applied for calculating the functional similarity of miRNAs based on their induced disease sets ... were further used to predict potential disease-miRNA relationships. The high area under the receiver...
  • TFGD

  • Referenced in 1 article [sw18850]
  • pathways from gene expression data sets and miRNA targets, and to integrate transcript and metabolite...
  • Omics Pipe

  • Referenced in 1 article [sw26801]
  • best practice published pipelines for RNA-seq, miRNA-seq, Exome-seq, Whole-Genome sequencing, ChIP...