README
The data.tgz file can be decompressed using software such as Winrar, Unrar or StuffIt Expander.
If you have a computer with MacOS or Linux, you can open a terminal window, change to the folder with the compressed file and copy and paste the following command in your prompt:
> tar zxvf data.tgz
The R-script.R file is the R script containing all the commands used in the chapter.
The affy_ATH1_array_elements-2010-12-20.txt file contains the probeset id to gene identifier relationships.
The id.genes.txt file contains an arbitrary list of genes selected to do the analysis.
The interaction.data.txt file contains interaction information obtained from the following databases and papers as described in the chapter text:
ATPID: http://www.megabionet.org/atpid/webfile/download.php
AtPIN: http://bioinfo.esalq.usp.br/atpin/atpin.pl
Pair: http://www.cls.zju.edu.cn/pair/public/downloads/Experimentally_Reported_Interactions/PAIR-V3.3-Experimentally-Reported-Interactions.txt.zip
PPIN-1, AI_interactions: http://interactome.dfci.harvard.edu/A_thaliana/index.php?page=download
Srivastava: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2982689/bin/1752-0509-4-S2-S2-S2.txt
Geisler_lee J. et al. : Plant Physiology October 2007 vol. 145 no. 2 317-329 Supplemental Data - Supplemental Table I
Barah P. et al.: BMC Genomics. 2013; 14: 722
The Agris file: families_data.tbl BindingSite.tbl, were download from http://arabidopsis.med.ohio-state.edu/
The file transcription_factor_family.agris.txt contains a list of transcriptions factor and families.
