Cell Line

The cell line used in this project is the human embryonic kidney cell line 293T .

Databases Search

The [http://www.ncbi.nlm.nih.gov/sites/entrez?db=ncbisearch NCBI GEO] and [http://www.ebi.ac.uk/arrayexpress/browse.html ArrayExpress] databases were extensively searched for environmental conditions leading to apoptosis in 293T cells and genes differentially expressed under these conditions. The following data was obtained:

[1] Campeau PM, Rafei M, Boivin MN, Sun Y et al. Characterization of Gaucher disease bone marrow mesenchymal stromal cells reveals an altered inflammatory secretome. Blood 2009 Oct 8;114(15):3181-90. [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13675 GEO Link] [2] Gene Expression and Transcription Factor Profiling Reveal Inhibition of Transcription Factor cAMP-response Element-binding Protein by {gamma}-Herpesvirus Replication and Transcription Activator. Brown HJ, Peng L, Harada JN, Walker JR, Cole S, Lin SF, Zack JA, Chanda SK, Sun R. J Biol Chem 285(33):25139-53 [http://www.ebi.ac.uk/arrayexpress/browse.html?keywords=E-MEXP-1437&species=&array=&exptype[]=&exptype[]=&pagesize=25&sortby=releasedate&sortorder=descending&expandefo=on Array Express Link] [3] A role for LEDGF/p75 in targeting HIV DNA integration. Angela Ciuffi, Manuel Llano, Eric Poeschla, Christian Hoffmann, Jeremy Leipzig, Paul Shinn, Joseph R Ecker, Frederic Bushman. Nat Med 11(12):1287-9 [http://www.ebi.ac.uk/arrayexpress/browse.html?keywords=E-GEOD-3485&species=&array=&exptype[]=&exptype[]=&pagesize=25&sortby=releasedate&sortorder=descending&expandefo=on Array Express Link] [1] Reference one Geo [1] Reference one Geo [1] Reference one Geo

In order to understand gene regulation of apoptosis regulated genes the [http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=searchPromForm Transcriptional Regulatory Element Database (TRED)] was used to extract known promoters and the [http://string-db.org/ STRING] database for known and predicted protein-protein interactions. The lists of all known human transcription factors were downloaded from [http://www.introni.it/transcription_factors.html here] and [http://www.nature.com/nrg/journal/v10/n4/extref/nrg2538-s3.txt here].