Team:LMU-Munich/ProSearch/Schedule

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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 [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]


[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 [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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