Master regulator analysis
(MMRA)
Version 1.00
contents
MMRA
is a piepline aimed at discovering
which microRNAs potentially regualte which Cancer sutype.
The MMRA
pipeline is subdivided in four sequential filtering steps, each
aimed at progressively reduceing the number of candidate microRNAs:
- Differential
expression alaysis to highlight microRNAs with subtyoe-specific
expression
- Target transcript
Enrichment analysis, to further select those microRNAs with
subtype-specific expression
- Network analysis, in which
an mRNA network is constructed around each microRNA using ARACNE, and
tested for enrichment in signature genes
- Identification of microRNAs
whose expression "explains" the expression of subtype signature genes,
using stepwise linear regression (SLR).
The following software components are required to run MMRA:
- MMRA
- R
- R packages: preprocessCore, plyr, Matching
- Perl
- ARACNE
In principle, MMRA should run
under Linux and Mac.
All the instractions are also reported in the ReadMe.pdf file inside the
downloaded folder
MMRA is invoked from the command line using the following format:
>> cd MMRA_pipeline/codes
>> ./run_MMRA.sh
| version |
date |
description |
| 1.00 |
10.05.15 |
First public version |
The data suites used in the paper can be downloaded as Bioconductor
ExperimentData packages (www.bioconductor.org):
| name |
email |
| Laura Cantini |
cantinilaura88@gmail.com |
Fore every use of the MMRA pipeline original or modified cite us:
"microRNA/mRNA
interactions
underlying colorectal cancer molecular subtypes", L. Cantini et
al.
