miSolRNA
The economic importance of Solanaceae plant species is well documented and tomato has become a model for functional genomics studies. In plants, important processes are regulated by microRNAs (miRNA).
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Active
RPdb
Many cell lines can be reprogrammed to other cell lines by forced expression of a few transcription factors or by specifically designed culture methods, which have attracted a great interest in the field of regenerative medicine and stem cell research. Plenty of cell lines have been used to generate induced pluripotent stem cells (IPSCs) by expressing a group of genes and microRNAs. These IPSCs can differentiate into somatic cells to promote tissue regeneration. Similarly, many somatic cells can be directly reprogrammed to other cells without a stem cell state.
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MTide
Small RNA sequencing and degradome sequencing (also known as parallel analysis of RNA ends) have provided rich information on the microRNA (miRNA) and its cleaved mRNA targets on a genome-wide scale in plants, but no computational tools have been developed to effectively and conveniently deconvolute the miRNA-target interaction (MTI).
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CellMiner
High-throughput and high-content databases are increasingly important resources in molecular medicine, systems biology, and pharmacology. However, the information usually resides in unwieldy databases, limiting ready data analysis and integration. One resource that offers substantial potential for improvement in this regard is the NCI-60 cell line database compiled by the U.S. National Cancer Institute, which has been extensively characterized across numerous genomic and pharmacologic response platforms.
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miRNACon
MicroRNAs (miRNAs) measured from blood samples are promising minimally invasive biomarker candidates that have been extensively studied in several case-control studies. However, the influence of age and sex as confounding variables remains largely unknown.
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SylArray
A useful step for understanding the function of microRNAs (miRNA) or siRNAs is the detection of their effects on genome-wide expression profiles. Typically, approaches look for enrichment of words in the 3(')UTR sequences of the most deregulated genes. A number of tools are available for this purpose, but they require either in-depth computational knowledge, filtered 3(')UTR sequences for the genome of interest, or a set of genes acquired through an arbitrary expression cutoff.
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MiRmat
MicroRNAs are known to be generated from primary transcripts mainly through the sequential cleavages by two enzymes, Drosha and Dicer. The sequence of a mature microRNA, especially the 'seeding sequence', largely determines its binding ability and specificity to target mRNAs. Therefore, methods that predict mature microRNA sequences with high accuracy will benefit the identification and characterization of novel microRNAs and their targets, and contribute to inferring the post-transcriptional regulation network at a genome scale.
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miR-BAG
Non-coding elements such as miRNAs play key regulatory roles in living systems. These ultra-short, ~21 bp long, RNA molecules are derived from their hairpin precursors and usually participate in negative gene regulation by binding the target mRNAs. Discovering miRNA candidate regions across the genome has been a challenging problem. Most of the existing tools work reliably only for limited datasets.
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ISMARA
Accurate reconstruction of the regulatory networks that control gene expression is one of the key current challenges in molecular biology. Although gene expression and chromatin state dynamics are ultimately encoded by constellations of binding sites recognized by regulators such as transcriptions factors (TFs) and microRNAs (miRNAs), our understanding of this regulatory code and its context-dependent read-out remains very limited.
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ExcellmiRDB
A large number of studies have suggested extracellular microRNAs (microRNAs in biofluids) as potential noninvasive biomarkers for pathophysiological conditions such as cancer. However, reported differentially expressed signatures of extracellular miRNAs in diseases are not uniformly consistent among studies. Here, we present "ExcellmiRDB", a curated online database that provides integrated information about miRNAs levels in biofluids in a user-friendly way.
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