MicroRNAs (miRNAs) regulate gene expression through translational repression and RNA degradation. Recently developed high-throughput proteomic methods measure gene expression changes at protein level and therefore can reveal the direct effects of miRNAs' translational repression. Here, we present a web server, ProteoMirExpress, that integrates proteomic and mRNA expression data together to infer miRNA-centered regulatory networks.
Our innate immune system recognizes a foreign RNA sequence of a pathogen and activates the immune system to eliminate the pathogen from our body. This immunomodulatory potential of RNA can be used to design RNA-based immunotherapy and vaccine adjuvants. In case of siRNA-based therapy, the immunomodulatory effect of an RNA sequence is unwanted as it may cause immunotoxicity. Thus, we developed a method for designing a single-stranded RNA (ssRNA) sequence with desired immunomodulatory potentials, for designing RNA-based therapeutics, immunotherapy and vaccine adjuvants.
BACKGROUND: The amount of scientific information about MicroRNAs (miRNAs) is growing exponentially, making it difficult for researchers to interpret experimental results. In this study, we present an automated text mining approach using Latent Semantic Indexing (LSI) for prioritization, clustering and functional annotation of miRNAs. RESULTS: For approximately 900 human miRNAs indexed in miRBase, text documents were created by concatenating titles and abstracts of MEDLINE citations which refer to the miRNAs.
Drug resistance is becoming a serious problem that leads to the failure of standard treatments, which is generally developed because of genetic mutations of certain molecules. Here, we present GEAR (A database of Genomic Elements Associated with drug Resistance) that aims to provide comprehensive information about genomic elements (including genes, single-nucleotide polymorphisms and microRNAs) that are responsible for drug resistance.
MicroRNAs (miRNAs) are small regulatory RNAs that play important roles in animals, plants, and viruses. Deep-sequencing technology has been widely adopted in miRNA investigations. However, it is still a big mysterious why nearly all sequencing data contain miRNA sequences from exogenous species, called exo-miRNAs. In this study, we developed a novel platform, exo-miRExplorer, for mining and identifying exo-miRNAs from high-throughput small RNA sequencing experiments which originated from tissues and cell lines of multiple organisms.
Experimental evidence indicates that about 60% of miRNA-binding activity does not follow the canonical rule about the seed matching between miRNA and target mRNAs, but rather a non-canonical miRNA targeting activity outside the seed or with a seed-like motifs. Here, we propose a new unbiased method to identify canonical and non-canonical miRNA-binding sites from peaks identified by Ago2 Cross-Linked ImmunoPrecipitation associated to high-throughput sequencing (CLIP-seq).
MicroRNAs are short RNAs that serve as regulators of gene expression and are essential components of normal development as well as modulators of disease. MicroRNAs generally act cell-autonomously, and thus their localization to specific cell types is needed to guide our understanding of microRNA activity. Current tissue-level data have caused considerable confusion, and comprehensive cell-level data do not yet exist. Here, we establish the landscape of human cell-specific microRNA expression.
Most human genes produce several transcripts with different exon contents by using alternative promoters, alternative polyadenylation sites and alternative splice sites. Much effort has been devoted to describing known gene transcripts through the development of numerous databases. Nevertheless, owing to the diversity of the transcriptome, there is a need for interactive databases that provide information about the potential function of each splicing variant, as well as its expression pattern.
Cis-antisense gene pairs (CASGPs) can transcribe mRNAs from an opposite strand of a given locus. To classify and understand diverse CASGP phenomena in the human we compiled a genome-wide catalog of CASGPs and integrated these sequences with microarray, SAGE and miRNA data. Using the concept of overlapping regions and clustering of SA transcripts by chromosome coordinates, we identified up to 9000 overlapping antisense loci. Four thousand three hundred and seventy-four of these CASGPs form 1759 complex gene architectures.
Host-virus interaction via host cellular components has been an important field of research in recent times. RNA interference mediated by short interfering RNAs and microRNAs (miRNA), is a widespread anti-viral defense strategy. Importantly, viruses also encode their own miRNAs. In recent times miRNAs were identified as key players in host-virus interaction. Furthermore, viruses were shown to exploit the host miRNA networks to suite their own need.
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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