Team:LMU-Munich/ProSearch/Schedule

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(Environmental Conditions)
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In order to understand gene regulation of apoptosis regulated genes we used the Transcriptional Regulatory Element Database [http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=searchPromForm (TRED)] to extract known promoters and the [http://string-db.org/ STRING] database for known interactions between genes and their transcription factors.  
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In order to understand gene regulation of apoptosis regulated genes we used the [http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=searchPromForm Transcriptional Regulatory Element Database (TRED)] to extract known promoters and the [http://string-db.org/ STRING] database for known and predicted protein-protein interactions. The list 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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Revision as of 10:34, 26 September 2010


Cell Line

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

Databases Search

The NCBI GEO and 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]


[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 we used the Transcriptional Regulatory Element Database (TRED) to extract known promoters and the STRING database for known and predicted protein-protein interactions. The list of all known human transcription factors was downloaded from here and here.