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Biclustering

Biclustering, block clustering , co-clustering, or two-mode clustering is a data mining technique which allows simultaneous clustering of the rows and columns of a matrix. The term was first introduced by Mirkin, although the technique was originally introduced much earlier. [Source: Wikipedia ]

miRMAP (Visualization)

Submitted by ChenLiang on Sun, 01/08/2017 - 16:16

MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression at a post-transcriptional level. An miRNA may target many messenger RNA (mRNA) transcripts, and each transcript may be targeted by multiple miRNAs. Our understanding of miRNA regulation is evolving to consider modules of miRNAs that regulate groups of functionally related mRNAs. Here we expand the model of miRNA functional modules and use it to guide the integration of miRNA and mRNA expression and target prediction data.

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treebic

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

Clustering methods are a useful and common first step in gene expression studies, but the results may be hard to interpret. We bring in explicitly an indicator of which genes tie each cluster, changing the setup to biclustering. Furthermore, we make the indicators hierarchical, resulting in a hierarchy of progressively more specific biclusters. A non-parametric Bayesian formulation makes the model rigorous yet flexible and computations feasible. The model can additionally be used in information retrieval for relating relevant samples.

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ComiRNet

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

The understanding of mechanisms and functions of microRNAs (miRNAs) is fundamental for the study of many biological processes and for the elucidation of the pathogenesis of many human diseases. Technological advances represented by high-throughput technologies, such as microarray and next-generation sequencing, have significantly aided miRNA research in the last decade. Nevertheless, the identification of true miRNA targets and the complete elucidation of the rules governing their functional targeting remain nebulous.

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