| DIANA-miRGen v3.0 provides the accurate cell-line-specific miRNA gene transcription start sites (TSSs), coupled with genome-wide maps of transcription factor (TF) binding sites in order to unveil the mechanisms of miRNA transcription regulation. To this end, more than 7.3 billion RNA-, ChIP- and DNase-Seq next generation sequencing reads were analyzed/assembled and combined with state-of-the-art miRNA TSS prediction and TF binding site identification algorithms. |
| Search by miRNA or TF name |
| CircuitsDB 2 is an improvement and extension of our previous work, CircuitsDB, in which we systematically study, by computational means, the combined role of microRNAs and lncRNAs within the human regulatory network and their impact on cancer-related genes. CircuitsDB 2 contains a large number of regulatory circuits, composed by Transcription Factors, target genes, microRNAs and lincRNAs interacting together, in the human genome. |
| Combined role of microRNAs and lncRNAs within the human regulatory network Regulatory circuits, composed by Transcription Factors, target genes, microRNAs and lncRNAs interacting together |
| miReg is a manually curated microRNA Regulation Resource that represents regulatory relationships among validated upstream regulators (Transcription factors or TFs, drugs, physical, and chemical), downstream targets, associated biological process, experimental condition or disease state, and up/down regulation of the miR in that condition in a graphical and user friendly manner along with corresponding published references. |
| Containing validated upstream regulators as transcription factor, drug, physical, and chemical |
| MIR@NT@N is an effective computational approach to identify novel molecular regulations and to predict gene regulatory networks and sub-networks including conserved motifs within a given biological context. MIR@NT@N uses a graph-based approach to predict novel molecular actors across multiple regulatory processes (i.e. TFs acting on protein-coding or miRNA genes, or miRNAs acting on messenger RNAs). Exploiting these predictions, the user can generate networks and further analyze them to identify sub-networks, including motifs such as feedback and feedforward loops. |
| Provides a user-friendly graph-based application connected to a large scale database |
| miRStart is a novel resource of human microRNA TSSs (transcription start sites), systematically incorporates significant datasets derived from TSS-relevant experiments to identify transcription start sites of microRNAs. The distribution patterns of these experimental features within 50 k upstream region of microRNA precursors provides an insight into determining reliable microRNA TSSs. |
| Systematically incorporates datasets to identify transcription start sites of microRNAs |
| miRT is a novel database of validated miRNA TSSs prepared by collecting data from several experimental studies that validate miRNA TSSs and are available for full download. miRT is a web server and it is also possible to convert the TSS loci between different genome built. miRT might be a valuable resource for advanced research on miRNA regulation. |
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Search by miRNA name |
| PMMR constructed the miRNA and TF induced regulatory network for humans by combining all possible regulations between miRNAs and TFs. Topological analysis of the network revealed some of its non-trivial and intrinsic properties. The concept of topological overlap has been extended to formulate a novel dissimilarity measure that is capable of mining groups of closely interacting molecules from a weighted digraph such that the molecules in each group regulate each other to a large extent. Many of the identified TF modules are found to be enriched in different functional categories or displayed significant associations with common diseases. |
| Showing regulated and regulating miRNAs |
| PuTmiR provides an important resource for analyzing the direct and indirect regulation of human miRNAs. While it is already an established fact that miRNAs are regulated by TFs binding to their USR, this database might possibly help to study whether a miRNA can also be regulated by the TFs binding to their downstream region. |
| In 10 kb or custom regions Searching upstream or downstream reigons |
| RegRNA is an integrated web server for identifying the homologs of regulatory RNA motifs and elements against an input mRNA sequence. Both sequence homologs and structural homologs of regulatory RNA motifs can be recognized. |
| Sequence homologs or structural homologs of regulatory RNA motifs can be identified |
| TransmiR contains TFs and miRNAs with regulatory pairs between TFs and miRNAs. TransmiR included references to the published literature (PubMed ID) information about the organism in which the relationship was found, whether the TFs and miRNAs are involved with tumors, miRNA function annotation and miRNA-associated disease annotation. TransmiR provides a user-friendly interface by which interested parties can easily retrieve TF–miRNA regulatory pairs by searching for either a miRNA or a TF. |
| Including 735 entries, which include 201 TFs, 209 miRNAs, 16 organisms |
| RegRNA 2.0 is an integrated web server for identifying functional RNA motifs in an input RNA sequence. RegRNA 2.0 extends our previvous work, RegRNA which is a widely used regulatory RNA motifs identification tool by incoporating more analytical methods and updated data sources. Through our integrated user-friendly interface, user can conveniently use these analytical approaches and observe results with good graphical visualization. |
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Functional RNA motifs in an input RNA sequence |
| DIANA-mirExTra v2.0 performs a combined DEA of mRNAs and microRNAs to uncover miRNAs and transcription factors (TFs) playing important regulatory roles between two investigated states. The web server uses as input miRNA/RNA-Seq read count data sets that can be uploaded for analysis. The web server utilizes miRNA:mRNA, TF:mRNA and TF:miRNA interactions derived from extensive experimental data sets. |
| Containing miRNA:mRNA, TF:mRNA and TF:miRNA interactions derived from extensive experimental data sets Including 450 000 miRNA interactions and 2 000 000 TF binding sites from specific or high-throughput techniques |
| miRNA expression |
| EpimiR database collects 1974 regulations between 19 kinds of epigenetic modifications (such as DNA methylation, histone acetylation, H3K4me3, H3S10p) and 617 miRNAs across seven species (including Homo sapiens, Mus musculus, Rattus norvegicus, Gallus gallus, Epstein-Barr virus, Canis familiaris and Arabidopsis thaliana) from >300 references in the literature. These regulations can be divided into two parts: miR2Epi (103 entries describing how miRNA regulates epigenetic modification) and Epi2miR (1871 entries describing how epigenetic modification affects miRNA). |
| miRNA regulated by epigenetics miRNA regulating epigenetics Search by miRNA or epigenetics |
| microPIR2 provides approximately 80 million human and 40 million mouse predicted target sites. microPIR2 is a tool for comparative analysis of target sites on the promoters of human-mouse orthologous genes. In particular, this new feature was designed to identify potential microRNA-promoter interactions conserved between species that could be stronger candidates for further experimental validation. microPIR2 includes nuclear and cytoplasmic localization of microRNAs and miRNA-disease association. |
| Search by gene, miRNA, disease or phenotype |
| TMREC integrated curated transcriptional and post-transcriptional regulations to construct the TF and miRNA regulatory network. Next, this database identified all linear paths using the Breadth First Search traversal method. Finally, we used known disease-related genes and miRNAs to measure the strength of association between cascades and diseases. Currently, TMREC consists of 74,248 cascades and 25,194 cascade clusters, involving in 412 TFs, 266 miRNAs and 545 diseases. |
| Understand the transcriptional and post-transcriptional regulatory mechanisms in specific disease Identify the potential therapeutic targets in the upstream of the cascades |
