Introduction

microRNAs, a class of non-coding 20-24nt small RNAs, play important roles in post-transcriptional gene regulation by targeting mRNAs for cleavage or repressing translation. Development, response to environmental stress, pathogen invasion and regulation of their own biogenesis etc. are finely tuned by microRNAs. A relatively small number of microRNAs can setup remarkably complex spatial and temporal patterns of gene expression by means of combinatorial or differential gene regulation, i.e. regulation of a gene by two or more microRNAs simultaneously or under different conditions. Though there are some specific molecular details of combinatorial regulations, we have little knowledge regarding combinatorial regulation on a genome scale. Here, we address this problem by using the C2Analyzer: cotarget-cofunction analyzer, a versatile and user-friendly web-server. This novel web server provides users with microRNA-mRNA, mRNA-GO relational data combined analysis tools and broad gene sets, microRNA set or GO set.

C2Analyzer requires two files as input: one mapping the microRNAs to the genes and other mapping each gene to the GO ids it belongs to. C2Analyzer offers five types of analysis using these data.
  1. mRNA & GO targeted by microRNA
  2. microRNA set targeting mRNA
  3. mRNA cotargeted by microRNA set
  4. Cofunctionally significant microRNA pair
  5. microRNA set regulating GO
Output for each types of analysis can be saved as .csv format. Aditionally the microRNA-microRNA cofunctional relationship can also be saved for using with other graph veiwing software.
This tool can be used for analyzing microRNA-mRNA-GO relationship. However one can also analyze other data like, microRNA-Gene-Disease. The user has to maintain the proper format (given below) while preparing input data.

How to use

Sample input

    Note: Right click on the links below and choose 'Save Link As...' or 'Save Target As...'

  1. Download microRNA - mRNA file
  2. Download mRNA - GO file

References

About us

Dr. Md. Aftabuddin

West Bengal University of Technology
BF - 142, Salt Lake, Kolkata, West Bengal 700064
India

Chittabrata Mal
Arindam Deb
Dr. Sudip Kundu

University of Calcutta
Department of Biophysics, Molecular Biology & Bioinformatics
92, A.P.C. Road, Kolkata 700009
India








To cite this tool please cite
Md. Aftabuddin, Chittabrata Mal, Arindam Deb, Sudip Kundu, C2Analyzer: Co-target- Co-function Analyzer, Genomics, Proteomics & Bioinformatics, Available online 24 May 2014, ISSN 1672-0229