Team:LMU-Munich/ProSearch/Schedule

From 2010.igem.org

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=Cell Line=
=Cell Line=
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The cell line used in this project is the human embryonic kidney cell line 293T .
The cell line used in this project is the human embryonic kidney cell line 293T .
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=Environmental Conditions=
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=Databases Search=
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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:  
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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:  
{| class="wikitable" border="0" style="width: 600px;"
{| class="wikitable" border="0" style="width: 600px;"
|-
|-
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! Environmental Condition (EV)
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! align="left"|Environmental Condition (EV)
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! #genes selectively expressed in this EV
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! align="center"|Number of genes differentially expressed
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! Reference
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! align="center"|Reference
|-
|-
| Conduritol B Epoxide treatment
| Conduritol B Epoxide treatment
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| align="center|"57
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| align="center"|57
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| row 1, cell 3
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| align="center"|[1]
|-
|-
| Gammaherpesvirus
| Gammaherpesvirus
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| align="center|103
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| align="center"|103
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| row 1, cell 3
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| align="center"|[2]
|-
|-
| HIV integration
| HIV integration
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| align="center|1
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| align="center"|1
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| row 1, cell 3
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| align="center"|[3]
|-
|-
| HLTV-1 p30
| HLTV-1 p30
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| align="center|2291
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| align="center"|2291
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| row 1, cell 3
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| align="center"|[4]
|-
|-
| Hypoxia
| Hypoxia
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| align="center|2
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| align="center"|2
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| row 1, cell 3
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| align="center"|[5]
|-
|-
| RCAS-beta-cateinS37A
| RCAS-beta-cateinS37A
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| align="center|55
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| align="center"|55
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| row 1, cell 3
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| align="center"|[6]
|}
|}
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[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].
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[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'' 2010 Aug 13;285(33):25139-53. [http://www.ebi.ac.uk/arrayexpress/browse.html?keywords=E-MEXP-1437 Array Express].
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[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'' 2005 Dec;11(12):1287-9. [http://www.ebi.ac.uk/arrayexpress/browse.html?keywords=E-GEOD-3485 Array Express].
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[4] Taylor JM, Ghorbel S, Nicot C. Genome wide analysis of human genes transcriptionally and post-transcriptionally regulated by the HTLV-I protein p30. ''BMC Genomics'' 2009 Jul 14;10:311. [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16098 GEO].
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[5] An inducible autoregulatory loop between HIPK2 and Siah2 at the apex of the hypoxic response. Calzado MA, de la Vega L, Möller A, Bowtell DD, Schmitz ML. ''Nat Cell Biol'' 2009 Jan;11(1):85-91. [http://www.ebi.ac.uk/arrayexpress/browse.html?keywords=E-MEXP-1896 Array Express].
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[6] Chamorro MN, Schwartz DR, Vonica A, Brivanlou AH et al. FGF-20 and DKK1 are transcriptional targets of beta-catenin and FGF-20 is implicated in cancer and development. ''EMBO J'' 2005 Jan 12;24(1):73-84. [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1473 GEO].
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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].
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Latest revision as of 14:45, 25 October 2010


Logo

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) Number of genes differentially expressed 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] 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].

[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 2010 Aug 13;285(33):25139-53. [http://www.ebi.ac.uk/arrayexpress/browse.html?keywords=E-MEXP-1437 Array Express].

[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 2005 Dec;11(12):1287-9. [http://www.ebi.ac.uk/arrayexpress/browse.html?keywords=E-GEOD-3485 Array Express].

[4] Taylor JM, Ghorbel S, Nicot C. Genome wide analysis of human genes transcriptionally and post-transcriptionally regulated by the HTLV-I protein p30. BMC Genomics 2009 Jul 14;10:311. [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16098 GEO].

[5] An inducible autoregulatory loop between HIPK2 and Siah2 at the apex of the hypoxic response. Calzado MA, de la Vega L, Möller A, Bowtell DD, Schmitz ML. Nat Cell Biol 2009 Jan;11(1):85-91. [http://www.ebi.ac.uk/arrayexpress/browse.html?keywords=E-MEXP-1896 Array Express].

[6] Chamorro MN, Schwartz DR, Vonica A, Brivanlou AH et al. FGF-20 and DKK1 are transcriptional targets of beta-catenin and FGF-20 is implicated in cancer and development. EMBO J 2005 Jan 12;24(1):73-84. [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1473 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].

 

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