Module 62 Residual: 0.07

Module Page Help

What is a module?

Regulatory units (modules) in the Network Portal are based on the network inference algorithm used. For the current version, modules are based on cMonkey modules and Inferelator regulatory influences on these modules. More specifically, module refers to set of genes that are conditionally co-regulated under subset of the conditions. Identification of modules integrates co-expression, de-novo motif identification, and other functional associations such as operon information and protein-protein interactions.

Expression Profiles

Expression profiles is a plot of the expression ratios (log10) of the module's genes, over all subset of the conditions included in the module. The X-axis represent conditions and the Y-axis represents log10 expression ratios. Each gene is plotted as line plot with different colors. Colored legend for the lines are presented under the plot. This plot is dynamic. Clicking on the gene names in the legend will show/hide the plot for that particular gene. A tooltip will show expression ratio information if you mouseover the lines in the plot.

Motif Locations

Location of the Identified motifs for the module in the upstream regions of the member genes are shown under the expression profiles plot. This plot shows the diagram of the upstream positions of the motifs, colored red and green for motifs #1, and 2, respectively. Intensity of the color is proportional to the significance of the occurence of that motif at a given location. Motifs on the forward and reverse strand are represented over and under the line respectively.

Regulators

For each module, single or AND logic connected regulatory influences are listed under the regulators tab. These regulatory influences are identified by Inferelator. Table shows name of the regulator and its type. tf: Transcription factor, ef: Environmental factor and combiner:Combinatorial influence of a tf or an ef through logic gate. Tabel is sortable by clicking on the arrows next to column headers.

Motifs

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.
Title Model version Residual Score
bicluster_0062 v02 0.07 -16.62

Module Expression Profile Help

How this plot was built?

For the current module we plotted the expression values of the module along time in an ammonia starvation experiment [Boyle et al. 2012]. The thick black line represents the mean expression value for the members of the module. Specifically, it is the log2 fold change with respect to the initial conditions. The gray area specifies a region one standard deviation around the mean expression values. Finally, highlighted at the plot title, we show the first time at which the module mean expression is observed to be above the 2-fold change.
Differential Expression Time:
4 hour
Displaying 1 - 12 of 12
Cre01.g043350.t1.2 Pheophorbide a oxygenase family protein with Rieske [2Fe-2S] domain

Details for Cre01.g043350.t1.2 - Pheophorbide a oxygenase family protein with Rieske [2Fe-2S] domain

GO Terms: GO:0016491, GO:0051537, GO:0055114, GO:0010277

Go to Gene Page: Cre01.g043350.t1.2

Phytozome Genomic Region

Cre01.g051500.t1.2 Uncharacterized thykaloid lumenal polypeptide

Details for Cre01.g051500.t1.2 - Uncharacterized thykaloid lumenal polypeptide

GO Terms: GO:0005509, GO:0015979, GO:0009523, GO:0009654, GO:0019898

Go to Gene Page: Cre01.g051500.t1.2

Phytozome Genomic Region

Cre02.g082750.t1.2 photosystem II subunit X

Details for Cre02.g082750.t1.2 - photosystem II subunit X

GO Terms: GO:0015979, GO:0009523, GO:0016020

Go to Gene Page: Cre02.g082750.t1.2

Phytozome Genomic Region

Cre03.g165100.t1.2 photsystem I subunit I

Details for Cre03.g165100.t1.2 - photsystem I subunit I

GO Terms: GO:0015979, GO:0009522

Go to Gene Page: Cre03.g165100.t1.2

Phytozome Genomic Region

Cre03.g182551.t1.2 plastocyanin 1

Details for Cre03.g182551.t1.2 - plastocyanin 1

GO Terms: GO:0005507, GO:0009055

Go to Gene Page: Cre03.g182551.t1.2

Phytozome Genomic Region

Cre05.g238332.t1.1 photosystem I subunit D-2

Details for Cre05.g238332.t1.1 - photosystem I subunit D-2

GO Terms: GO:0015979, GO:0009522, GO:0009538

Go to Gene Page: Cre05.g238332.t1.1

Phytozome Genomic Region

Cre06.g294650.t1.2 alanine:glyoxylate aminotransferase

Details for Cre06.g294650.t1.2 - alanine:glyoxylate aminotransferase

GO Terms: GO:0008152

Go to Gene Page: Cre06.g294650.t1.2

Phytozome Genomic Region

Cre09.g396213.t1.1 PS II oxygen-evolving complex 1

Details for Cre09.g396213.t1.1 - PS II oxygen-evolving complex 1

GO Terms: GO:0005509, GO:0015979, GO:0042549, GO:0009523, GO:0009654, GO:0019898

Go to Gene Page: Cre09.g396213.t1.1

Phytozome Genomic Region

Cre12.g486300.t1.2 photosystem I subunit l

Details for Cre12.g486300.t1.2 - photosystem I subunit l

GO Terms: GO:0015979, GO:0009522, GO:0009538

Go to Gene Page: Cre12.g486300.t1.2

Phytozome Genomic Region

Cre12.g550850.t1.2 photosystem II subunit P-1

Details for Cre12.g550850.t1.2 - photosystem II subunit P-1

GO Terms: GO:0005509, GO:0015979, GO:0009523, GO:0009654, GO:0019898

Go to Gene Page: Cre12.g550850.t1.2

Phytozome Genomic Region

Cre17.g720250.t1.2 light harvesting complex photosystem II

Details for Cre17.g720250.t1.2 - light harvesting complex photosystem II

GO Terms: NA

Go to Gene Page: Cre17.g720250.t1.2

Phytozome Genomic Region

Cre17.g724300.t1.2 photosystem I subunit K

Details for Cre17.g724300.t1.2 - photosystem I subunit K

GO Terms: GO:0015979, GO:0009522, GO:0016020

Go to Gene Page: Cre17.g724300.t1.2

Phytozome Genomic Region

motif_0062_1

e.value: 
0.8
Motif Bicluster: 
Width: 
23
Number of Sites: 
1
Consensus: 
gCTgCtGttgctGCTGtcaCTGc

motif_0062_2

e.value: 
11000
Motif Bicluster: 
Width: 
11
Number of Sites: 
1
Consensus: 
ATGGGTGTTGc
Displaying 1 - 1 of 1
Interaction Weight
Displaying 1 - 1 of 1
GO Terms Descriptions
GO:0043234 | GO:0009522 | GO:0019898 | GO:0044425 | GO:0009654 protein complex | photosystem I | extrinsic component of membrane | membrane part | photosystem II oxygen evolving complex
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