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public:loadedtestcases:tc3 [2012/09/12 09:16] – created andreaspublic:loadedtestcases:tc3 [2019/02/12 09:04] (current) – external edit 127.0.0.1
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 There are various tools available allow for coexpression analysis, motif ifentification (e.g. Patmatch), the extraction of promoters from different plant specie (e.g. phytozome), phylogenetic footprinting, cis element databases, etc. However, it is extremely time-consuming to transfer data from A to B and extract the information that is needed to establish a GRN.  There are various tools available allow for coexpression analysis, motif ifentification (e.g. Patmatch), the extraction of promoters from different plant specie (e.g. phytozome), phylogenetic footprinting, cis element databases, etc. However, it is extremely time-consuming to transfer data from A to B and extract the information that is needed to establish a GRN. 
 \\ \\
-CORNET.         https://cornet.psb.ugent.be/main/precalc +\\ 
-ATTED-II .       http://atted.jp/top_search.shtml#CoExSearch +  * CORNET.         https://cornet.psb.ugent.be/main/precalc\\ 
-CressExpress.   http://cressexpress.org/ +  * ATTED-II .       http://atted.jp/top_search.shtml#CoExSearch\\ 
-CSB.DB           http://csbdb.mpimp-golm.mpg.de/ +  * CressExpress.   http://cressexpress.org/\\ 
-Patmatch in TAIR +  * CSB.DB           http://csbdb.mpimp-golm.mpg.de/\\ 
-AGRIS, TransFac, PLACE for the identification of known cis elements in promoters of interest (e.g. of coexpressed genes). +  * Patmatch in TAIR\\ 
-MEME for the identification of motifs overrepresented in a set of promoters.+  * AGRIS, TransFac, PLACE for the identification of known cis elements in promoters of interest (e.g. of coexpressed genes).\\ 
 +  * MEME for the identification of motifs overrepresented in a set of promoters.
 \\ \\
 Drawbacks: Drawbacks:
- 
 The main drawback is that it is extremely time-consuming to combine the different data into one single scheme that displays the GRN. The main drawback is that it is extremely time-consuming to combine the different data into one single scheme that displays the GRN.
 ==Desired final state of the Test Case== ==Desired final state of the Test Case==
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   - Suggest a GRN in a good schematic presentation that highlights various aspects of the interaction of the TF with its downstream target genes (e.g. cis elements in the promoters to which it might bind; expression induction or repression curve of the target gene);   - Suggest a GRN in a good schematic presentation that highlights various aspects of the interaction of the TF with its downstream target genes (e.g. cis elements in the promoters to which it might bind; expression induction or repression curve of the target gene);
 ==Discussion== ==Discussion==
-nd+LF: Possible person to invite: Chris J Needham C.Needham@leeds.ac.uk (see http://www.biomedcentral.com/1752-0509/3/85)
public/loadedtestcases/tc3.1347441390.txt.gz · Last modified: 2019/02/12 09:04 (external edit)
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