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 contain the probeset id to gene identifier relation.

id.genes.txt contain a arbitrary list of genes selected to the analysis.

The interaction.data.txt file contains interaction information obtained from the following databases and papers 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: http://www.plantphysiol.org/content/145/2/317.full Supplemental Data - Supplemental Table I

Barah: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3829657/

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.