Updated CRACR Algorithm and
Associated Files
Page last updated: 5/21/2010
CRACR, an algorithm to predict condition-specific TF function by integrating TF binding specifities with gene expression data, was first published in McCord, et al. Molecular Systems Biology, 3:100. The scripts and programs used in that publication are available on the original CRACR Supplementary Website.
The data files, scripts, and programs below reflect updates to CRACR and associated data since this original publication. These updated algorithms were used in the analysis of Protein Binding Microarray (PBM) data for 89 yeast TFs as published in Zhu, Byers, McCord et al. Genome Research, 19:556-66.
Changes in these updated files include:
- 1693 yeast expression conditions and condition annotations instead of the original 1327. This set now includes a larger number of TF perturbation datasets (deletion, mutation, overexpression, etc.)
- CRACR_v2.m does not include a length correction since it assumes that TF binding scoring will have been performed over sequences of approximately the same length
-
Programs and Scripts Necessary to Run
CRACR_v2:
CRACR algorithm: Requires MATLAB and Perl.
Subsidiary scripts necessary to run the above program—make sure
to place all these in the same folder as the above CRACR MATLAB script:
Script to create graphs of CRACR results: graphconds.m
CRACR readme: A text file explaining how to run the CRACR algorithm and associated scripts.
Scripts to score genes by PBM data for CRACR: *coming soon*
Example data files for running CRACR and associated scripts for yeast:
Yeast Genes Scored by Pbf1 PBM data: Pbf1-avgv9v11-0.35bgdsub_lteq600.txt
Heat shock expression data only: heatshockexpr.txt
Gene IDs for yeast genes: gene_IDs_1693.txt
Expression
Data: A tab-delimited file containing data from all 1693 yeast expression
conditions that can be used with CRACR.
All data is presented as log2 expression ratios. Genes with no data in a particular
expression experiment are assigned an expression value of “
Expression Condition Annotations: An Excel file containing the condition annotation terms for all 1693 yeast expression conditions.
Expression Data Sources: An Excel file with the Pubmed IDs for the original publications of all yeast expression data.
Questions? Rachel Patton McCord, Martha Bulyk.