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PeTMbase

Submitted by ChenLiang on Mon, 01/09/2017 - 11:31

MicroRNAs (miRNA) are small endogenous RNA molecules, which regulate target gene expression at post-transcriptional level. Besides, miRNA activity can be controlled by a newly discovered regulatory mechanism called endogenous target mimicry (eTM). In target mimicry, eTMs bind to the corresponding miRNAs to block the binding of specific transcript leading to increase mRNA expression. Thus, miRNA-eTM-target-mRNA regulation modules involving a wide range of biological processes; an increasing need for a comprehensive eTM database arose.

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ARTS

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

A fast growing number of non-coding RNAs have recently been discovered to play essential roles in many cellular processes. Similar to proteins, understanding the functions of these active RNAs requires methods for analyzing their tertiary structures. However, in contrast to the wide range of structure-based approaches available for proteins, there is still a lack of methods for studying RNA structures.

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AmphiEST

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Amphioxus has been an important model for understanding the evolution of chordates and origin of vertebrates. Comparative transcriptome analysis can facilitate delineation of gene expression patterns of amphioxus at different developmental stages. So far, however, few such analyses have been performed. Here we have systematically compared amphioxus ESTs from five developmental stages. For the egg, gastrula, neurula, larva and adult stages, amphioxus ESTs were assembled, respectively, into 3364, 3230, 10,299, 4052 and 3866 contigs, and 193, 183, 933, 178 and 151 singlets.

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MLSeq

Submitted by ChenLiang on Sun, 09/10/2017 - 17:14

RNA sequencing (RNA-Seq) is a powerful technique for the gene-expression profiling of organisms that uses the capabilities of next-generation sequencing technologies. Developing gene-expression-based classification algorithms is an emerging powerful method for diagnosis, disease classification and monitoring at molecular level, as well as providing potential markers of diseases. Most of the statistical methods proposed for the classification of gene-expression data are either based on a continuous scale (eg. microarray data) or require a normal distribution assumption.

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pigcirNet

Submitted by ChenLiang on Tue, 01/09/2018 - 18:56

The spatio-temporal expression patterns of Circular RNA (circRNA) across organs and developmental stages are critical for its function and evolution analysis. However, they remain largely unclear in mammals. Here, we comprehensively analysed circRNAs in nine organs and three skeletal muscles of Guizhou miniature pig (S. scrofa), a widely used biomedical model animal. We identified 5,934 circRNAs and analysed their molecular properties, sequence conservation, spatio-temporal expression pattern, potential function, and interaction with miRNAs. S.

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Tools4miRs

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MiRNAs are short, non-coding molecules that negatively regulate gene expression and thereby play several important roles in living organisms. Dozens of computational methods for miRNA-related research have been developed, which greatly differ in various aspects. The substantial availability of difficult-to-compare approaches makes it challenging for the user to select a proper tool and prompts the need for a solution that will collect and categorize all the methods.

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RISE

Submitted by ChenLiang on Tue, 01/09/2018 - 18:59

We present RISE (http://rise.zhanglab.net), a database of RNA Interactome from Sequencing Experiments. RNA-RNA interactions (RRIs) are essential for RNA regulation and function. RISE provides a comprehensive collection of RRIs that mainly come from recent transcriptome-wide sequencing-based experiments like PARIS, SPLASH, LIGR-seq, and MARIO, as well as targeted studies like RIA-seq, RAP-RNA and CLASH. It also includes interactions aggregated from other primary databases and publications.

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miRprimer

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNAs are small but biologically important RNA molecules. Although different methods can be used for quantification of microRNAs, quantitative PCR is regarded as the reference that is used to validate other methods. Several commercial qPCR assays are available but they often come at a high price and the sequences of the primers are not disclosed. An alternative to commercial assays is to manually design primers but this work is tedious and, hence, not practical for the design of primers for a larger number of targets.

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miRTP

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

We used a machine learning method, the nearest neighbor algorithm (NNA), to learn the relationship between miRNAs and their target proteins, generating a predictor which can then judge whether a new miRNA-target pair is true or not. We acquired 198 positive (true) miRNA-target pairs from Tarbase and the literature, and generated 4,888 negative (false) pairs through random combination. A 0/1 system and the frequencies of single nucleotides and di-nucleotides were used to encode miRNAs into vectors while various physicochemical parameters were used to encode the targets.

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MDTE DB

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNAs are crucial regulators of gene expression at post-transcriptional level. Understanding origin and evolution of miRNAs and their functions. Transposable elements (TEs) provide a natural mechanism for the origin of new miRNAs derived from TEs (MDTEs) were collected to contruct a database named MDTE database (MDTE DB) for storing, searching and analyzing MDTEs. The database proveds a convenient source for studying the origin and evolution of miRNAs.[1]

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