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| public:loadedtestcases:tc3 [2012/09/12 09:17] – andreas | public: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, | 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, | ||
| \\ | \\ | ||
| - | CORNET. | ||
| - | ATTED-II . | ||
| - | CressExpress. | ||
| - | CSB.DB | ||
| - | Patmatch in TAIR\\ | ||
| - | 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. | ||
| \\ | \\ | ||
| + | * CORNET. | ||
| + | * ATTED-II . | ||
| + | * CressExpress. | ||
| + | * CSB.DB | ||
| + | * Patmatch in TAIR\\ | ||
| + | * 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:// |