attract-package {attract} | R Documentation

## Methods to find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape

### Description

This package contains functions used to determine the gene expression modules that represent the drivers of Kauffman's attractor landscape.

### Details

Package: | attract
Type: | Package
Version: | 1.33.2
Date: | 2018-06-29
License: |
LazyLoad: | yes

The method can be summarized in the following key steps: (1) Determine core KEGG or reactome pathways that discriminate the most strongly between celltypes or experimental groups of interest (see `findAttractors)`). (2) Find the different synexpression groups that are present within a core attractor pathway (see `findSynexprs`). (3) Find sets of genes that show highly similar profiles to the synexpression groups within an attractor pathway module (see `findCorrPartners`). (4) Test for functional enrichment for each of the synexpression groups to detect any potentially shared biological themes (see `calcFuncSynexprs`).

### Author(s)

Jessica Mar <jess@jimmy.harvard.edu>

### References

Kauffman S. 2004. A proposal for using the ensemble approach to understand genetic regulatory networks. J Theor Biol. 230:581. Mar JC, Wells CA, Quackenbush J. 2010. Identifying Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape. To Appear. M\"uller F et al. 2008. Regulatory networks define phenotypic classes of human stem cell lines. Nature. 455(7211): 401. Mar JC, Wells CA, Quackenbush J. 2010. Defining an Informativeness Metric for Clustering Gene Expression Data. To Appear.

### Examples

    ## Not run:
    data(subset.loring.eset)
    attractor.states <- findAttractors(subset.loring.eset, "celltype", nperm=10, annotation="illuminaHumanv1.db")
    remove.these.genes <- removeFlatGenes(subset.loring.eset, "celltype", contrasts=NULL, limma.cutoff=0.05)
    mapk.syn <- findSynexprs("04010", attractor.states, remove.these.genes)
    mapk.cor <- findCorrPartners(mapk.syn, subset.loring.eset, remove.these.genes)
    mapk.func <- calcFuncSynexprs(mapk.syn, attractor.states, "CC", annotation="illuminaHumanv1.db")

    ## End(Not run)

[Package attract version 1.42.0 Index]