Topological patterns in microRNA-gene regulatory network: studies in colorectal and breast cancer

Debarka Sengupta, Sanghamitra Bandyopadhyay
Molecular BioSystems 2013, 9 (6): 1360-71
It is now widely accepted that microRNAs (miRNAs or miRs) along with transcription factors (TFs) weave a complex inter-regulatory network within the cell that is responsible for the combinatorial regulation of gene expression. Recently we have shown that miRNAs and TFs that form network clusters are also associated with a number of common diseases. However, the quest persists to find out topological structures that facilitate disease progression. In the current work we choose colorectal and breast cancers for our analysis. For this, the human genome wide TF-miRNA-gene network (TMG-net) is first built by combining experimentally validated and confidently predicted miRNA→gene (including TF genes), TF→gene and TF→miRNA interactions. Subnetworks active in colorectal and breast cancers are extracted from the TMG-net and then analyzed. Disease specific subnetworks are found to be significantly dense, having a pyramid shaped hierarchical backbone of interactions. Interestingly, most of the top level molecules (e.g., hsa-mir-210, hsa-mir-378) are found to be already established as oncomirs. TFs that are dysregulated in a particular cancer, are found to be well-linked via miRNAs and other TFs, with miRNAs being highly predominant. Analogous to density, a new measure called Inductive Converge (InCov) is proposed and used to analyze the natural association of molecules in the disease specific networks. Finally a web application called DisTMGneT (Disease Specific TF-miRNA-gene Network) is developed for disease specific subnetworks from the TMG-net, based on user supplied sets of dysregulated miRNAs, TFs and non TF genes. DisTMGneT is available at

Full Text Links

Find Full Text Links for this Article


You are not logged in. Sign Up or Log In to join the discussion.

Related Papers

Remove bar
Read by QxMD icon Read

Save your favorite articles in one place with a free QxMD account.


Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"