From 2010.igem.org
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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:
| Environmental Condition (EV)
| #genes selectively expressed in this EV
| Reference
|
| Conduritol B Epoxide treatment
| 57
| [1]
|
| Gammaherpesvirus
| 103
| [2]
|
| HIV integration
| 1
| [3]
|
| HLTV-1 p30
| 2291
| [4]
|
| Hypoxia
| 2
| [5]
|
| RCAS-beta-cateinS37A
| 55
| [6]
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[1] Reference one Geo
[1] Reference one Geo
[1] Reference one Geo
[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 was downloaded from [http://www.introni.it/transcription_factors.html here] and [http://www.nature.com/nrg/journal/v10/n4/extref/nrg2538-s3.txt here].
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