The cell-specific information of transcriptional regulation on microRNAs (miRNAs) is crucial to the precise understanding of gene regulations in various physiological and pathological processes existed in different tissues and cell types. The database, mirTrans, provides comprehensive information about cell-specific transcription of miRNAs including the transcriptional start sites (TSSs) of miRNAs, transcription factor (TF) to miRNA regulations and miRNA promoter sequences.
The recent discovery of the first small modulatory RNA (smRNA) presents the challenge of finding other molecules of similar length and conservation level. Unlike short interfering RNA (siRNA) and micro-RNA (miRNA), effective computational and experimental screening methods are not currently known for this species of RNA molecule, and the discovery of the one known example was partly fortuitous because it happened to be complementary to a well-studied DNA binding motif (the Neuron Restrictive Silencer Element).
The whole-genome sequence of carnation (Dianthus caryophyllus L.) cv. 'Francesco' was determined using a combination of different new-generation multiplex sequencing platforms. The total length of the non-redundant sequences was 568,887,315 bp, consisting of 45,088 scaffolds, which covered 91% of the 622 Mb carnation genome estimated by k-mer analysis. The N50 values of contigs and scaffolds were 16,644 bp and 60,737 bp, respectively, and the longest scaffold was 1,287,144 bp. The average GC content of the contig sequences was 36%.
'Off-target' silencing effect hinders the development of siRNA-based therapeutic and research applications. Common solution to this problem is an employment of the BLAST that may miss significant alignments or an exhaustive Smith-Waterman algorithm that is very time-consuming. We have developed a Comprehensive Redundancy Minimizer (CRM) approach for mapping all unique sequences ("targets") 9-to-15 nt in size within large sets of sequences (e.g. transcriptomes). CRM outputs a list of potential siRNA candidates for every transcript of the particular species.
With the rapid accumulation of microRNA (miRNAs), a class of newly identified small noncoding RNAs, in silico inference of miRNA functions has become one of the central tasks in miRNA bioinformatics. Traditional methods have helped in the understanding of miRNAs, but they also have limitations.
Hepatocellular carcinoma (HCC) is one of the most common malignant cancers with a poor prognosis. For decades, more and more biomarkers were found to effect on HCC prognosis, but these studies were scattered and there were no unified identifiers. Therefore, we built the database of prognostic biomarkers and models for hepatocellular carcinoma (dbPHCC).
: Next-Generation Sequencing (NGS) technology has revealed that microRNAs (miRNAs) are capable of exhibiting frequent differences from their corresponding mature reference sequences, generating multiple variants: the isoforms of miRNAs (isomiRs). These isomiRs mainly originate via the imprecise and alternative cleavage during the pre-miRNA processing and post-transcriptional modifications that influence miRNA stability, their sub-cellular localization and target selection.
Exploring microRNA (miRNA) regulations and protein-protein interactions could reveal the molecular mechanisms responsible for complex biological processes. Mirin is a web-based application suitable for identifying functional modules from protein-protein interaction networks regulated by aberrant miRNAs under user-defined biological conditions such as cancers. The analysis involves combining miRNA regulations, protein-protein interactions between target genes, as well as mRNA and miRNA expression profiles provided by users.
MOTIVATION: PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs that are highly abundant in the germline. One important role of piRNAs is to defend genome integrity by guiding PIWI proteins to silence transposable elements (TEs), which have a high potential to cause deleterious effects on their host. The mechanism of piRNA-mediated post-transcriptional silencing was also observed to affect mRNAs, suggesting that piRNAs might play a broad role in gene expression regulation.
In plants, various phloem-mobile macromolecules including noncoding RNAs, mRNAs and proteins are suggested to act as important long-distance signals in regulating crucial physiological and morphological transition processes such as flowering, plant growth and stress responses. Given recent advances in high-throughput sequencing technologies, numerous mobile macromolecules have been identified in diverse plant species from different plant families.
Our database aim to make it easy for researchers to find the right tools or data source for their own specific study in miRNA field. Now we have collect >1000 tools. This database will update when every new 100 tools add in. Last update time 22nd April, 2018 (v1.2).
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