Target Functional AnalysisTools for miRNA targets functional analysis
| # | Name | Description | Online/Local | Organism Specific |
NGS Data Needed |
Target Prediction Data Needed |
Analysis Features |
References |
|---|---|---|---|---|---|---|---|---|
| 1 | BioVLAB-MMIA-NGS | BioVLAB-MMIA-NGS is Cloud-based miRNA mRNA integraed analysis system using NGS data. System computes differentially/significantly expressed miRNAs (DEmiRNAs) and mRNAs/genes (DEGs), and with targeting information, DEGs targeted by DEmiRNAs and having negative correlation between them are extracted. | / | Homepage Publication Sept. 29, 2014 Citations: 8 | ||||
| 2 | BUFET | BUFET (Bitset-based Unbiased Functional Enrichment Tool) is a tool that performs the unbiased miRNA functional enrichment analysis (Bleazard et al.) requiring significantly reduced execution times (less than 10 minutes for 1 million random permutations). Users can provide their own interaction and annotation data in CSV files, making it a flexible tool for miRNA functional enrichment analysis. | / | Homepage Publication Sept. 6, 2017 Citations: 4 | ||||
| 3 | CPSS | CPSS is (a computational platform for the analysis of small RNA deep sequencing data), designed to completely annotate and functionally analyse microRNAs (miRNAs) from NGS data on one platform with a single data submission. | / | Homepage Publication May 9, 2012 Citations: 25 | ||||
| 4 | DeAnnIso | DeAnnIso, is an online tool, that is designed for Detection and Annotation of IsomiR from small RNA sequencing data. The detected isomiRs will be classified into different categories. The isomiRs will be aligned with canonical miRNA, and will be annotated with expression, constitution, SNP, and an in-house dataset. It can also extract differentially expressing isomiR between two samples. In addition, IsomiR Bank provides targets prediction and enrichment analysis to evaluate the effects of isomiRs on target selection. | / | Homepage Publication May 13, 2016 Citations: 20 | ||||
| 5 | DIANA-microT-CDS | DIANA-microT-CDS is the 5th version of the microT algorithm. It is specifically trained on a positive and a negative set of miRNA Recognition Elements (MREs) located in both the 3'-UTR and CDS regions. DIANA-microT-CDS provides a significant increase in sensitivity compared to the previous version (65% vs 52%), when compared against experimental proteomics data. | / | Homepage Publication May 16, 2013 Citations: 613 | ||||
| 6 | DIANA-mirPath v3 | DIANA-mirPath is a miRNA pathway analysis web-server, providing accurate statistics, while being able to accommodate advanced pipelines. mirPath can utilize predicted miRNA targets (in CDS or 3’-UTR regions) provided by the DIANA-microT-CDS algorithm or even experimentally validated miRNA interactions derived from DIANA-TarBase. These interactions (predicted and/or validated) can be subsequently combined with sophisticated merging and meta-analysis algorithms. | / | Homepage Publication May 14, 2015 Citations: 969 | ||||
| 7 | ElMMo3 | A Bayesian target prediction algorithm without any tunable parameters, that can be applied to sequences from any clade of species. The algorithm automatically infers the phylogenetic distribution of functional sites for each miRNA, and assigns a posterior probability to each putative target site. | / | Homepage Publication March 1, 2007 Citations: 176 | ||||
| 8 | IntaRNA | IntaRNA is a program for the fast and accurate prediction of interactions between two RNA molecules. It has been designed to predict mRNA target sites for given non-coding RNAs (ncRNAs) like eukaryotic microRNAs (miRNAs) or bacterial small RNAs (sRNAs), but it can also be used to predict other types of RNA-RNA interactions. | / | Homepage Publication Oct. 21, 2008 Citations: 260 | ||||
| 9 | isomiR2Function | somiR2Function allows for the high-throughput detection of plant isomiRs from any miRNA-seq profiling study. isomiR2Function not only allows for the identification of the templated and non-templated 5′- isomiRs and 3′- isomiRs but also allows for the expression quantification. Since, the prediction of biologically relevant target is an important criterion for the identification of isomiRs and their targets - isomiR2Function identifies target as well. Following target prediction, it allows for functional enrichment of the identified targets. In parallel, isomiR2Function provides support for the visualization of read mapping on corresponding precursor sequences. | / | Homepage Publication March 21, 2017 Citations: 11 | ||||
| 10 | miR2GO | miR2GO is a web-based platform for comparative analyses of human miRNA functions. It includes two programs: miRmut2GO and miRpair2GO. miRmut2GO implements a knowledge-based method to assess the functional effects of genetic and somatic mutations in microRNA seed regions. The functional effects of a mutation are analysed by semantic comparison of enriched gene ontology (GO) annotations of the target gene sets for the wild-type and mutated alleles. miRpair2GO compares the functions of two different miRNAs based on the enriched functional annotations of their target gene sets. | / | Homepage Publication March 10, 2015 Citations: 16 | ||||
| 11 | miRGator | Aims to be the microRNA (miRNA) portal encompassing microRNA diversity, expression profiles, target relationships, and various supporting tools. By keeping datasets and analytic tools up-to-date, miRGator should continue to serve as an integrated resource for biogenesis and functional investigation of miRNAs. | / | Homepage Publication Nov. 27, 2012 Citations: 81 | ||||
| 12 | miRNet | miRNet is an easy-to-use web-based tool with comprehensive supports for statistical analysis and functional interpretation of various datasets generated in miRNAs studies. Users can explore the results in miRNA-target interaction networks with powerful features to assist in biological understanding. | / | Homepage Publication April 21, 2016 Citations: 230 | ||||
| 13 | miRSystem | A database which integrates seven well known miRNA target gene prediction programs: DIANA, miRanda, miRBridge, PicTar, PITA, rna22, and TargetScan. This database contains validated data from TarBase and miRecords on interaction between miRNA and its target genes. | / | Homepage Publication Aug. 1, 2012 Citations: 165 | ||||
| 14 | mirTools 2.0 | MirTools 2.0 is updated version of mirTools, which was developed to comprehensive characterize the small RNA transcriptome obtained from high-throughput sequencing. It enables user to: detect and profile non-coding RNA (tRNA, snRNA, snoRNA, rRNA ans piRNA); obtain detailed annotation ifmromation about known miRNA (absolute/realtive reds count and most abundant tags); identify the microRNA targeted genes and their detailed functional annotate; perform the comparison of many samples and identify the differentially expressed non-coding RNAs between experimental groups; discovery the novel miRNAs. | / | Homepage Publication May 29, 2013 Citations: 40 | ||||
| 15 | MTide | MTide is an integrated pipeline designed to parse sRNA-seq and degradome data for miRNA-target identification in plant. It can quantify the known miRNA expression and identify novel miRNA from sRNA-seq data, identify the target of miRNA from degradome data signature, predict target of miRNA precisely, prioritize predicted target according to GO similarity to known or validated target, and identify the expressed miRNA between two samples. | / | Homepage Publication Sept. 24, 2014 Citations: 42 | ||||
| 16 | Oasis 2.0 | Oasis is a web application that allows for the fast and flexible online analysis of small-RNA-seq (sRNA-seq) data. Oasis’ exclusive selling points are a differential expression module that allows for the multivariate analysis of samples, a classification module for robust biomarker detection and an advanced programming interface that supports the batch submission of jobs. Both modules include the analysis of novel miRNAs, miRNA targets and functional analyses including GO and pathway enrichment. | / | Homepage Publication Feb. 19, 2015 Citations: 33 | ||||
| 17 | PPImiRFS | PPImiRFS, a novel method to obtain the functional similarity scores of plant miRNA pairs based on a PPIN with semantic similarity weights generated using GO terms and graph theoretic properties. | / | Homepage Publication Nov. 4, 2015 Citations: 4 | ||||
| 18 | sRNAtoolbox | sRNAtoolbox is aimed to provide small RNA researchers with several useful tools including sRNA expression profiling from deep sequencing experiments and several downstream analysis tools. The center piece of sRNAtoolbox is sRNAbench, which allows the expression profiling and prediction of novel microRNAs in deep sequencing experiments. The other tools can be either launched on sRNAbench results, or independently using the appropriate file formats. | / | Homepage Publication May 27, 2015 Citations: 118 | ||||
| 19 | sRNAtools | sRNAtools can be used to identify and functionally annotate diverse kinds of sncRNA for up to 21 model species (including human, mouse, Arabidopsis, rice, etc.), including (i) profiling of miRNAs, Piwi-interacting RNA (piRNAs), piRNA-producing loci (piRNA cluster), tRNAs, natsiRNA, small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs) and rRNAs and (ii) discovering isomiRs, novel miRNAs, tRFs, plant-specific 24-nt siRNAs and phasiRNAs. sRNAtools also provides web-based approaches to detect sncRNAs in multiple transcriptomes. | / | Homepage Publication Jan. 18, 2021 Citations: 21 | ||||
| 20 | TaLasso | TaLasso algorithm combines the information of sequence databases with mRNA and miRNA expression to quantify the down-regulation between miRNAs and their putative targets. | / | Homepage Publication Feb. 14, 2012 Citations: 38 | ||||
| 21 | wapRNA | wapRNA provides an integrated tool for RNA sequence, refers to the use of High-throughput sequencing technologies to sequence cDNAs in order to get information about a sample's RNA content. wapRNA provides researchers with efficient ways to measure RNA sequence experimentally, allowing them to get information such as how different alleles of a gene are expressed, detect post-transcriptional mutations or identifying gene fusions, annotate the known miRNAs or predict the news and so on. | / | Homepage Publication Sept. 6, 2011 Citations: 26 |