Module 189 Residual: 0.11

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_0189 v02 0.11 -14.19

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:
2 hour
Displaying 1 - 16 of 16
Cre01.g016514.t1.1 lipoamide dehydrogenase 1

Details for Cre01.g016514.t1.1 - lipoamide dehydrogenase 1

GO Terms: GO:0016491, GO:0050660, GO:0055114, GO:0045454

Go to Gene Page: Cre01.g016514.t1.1

Phytozome Genomic Region

Cre01.g016900.t1.2

Details for Cre01.g016900.t1.2 -

GO Terms: NA

Go to Gene Page: Cre01.g016900.t1.2

Phytozome Genomic Region

Cre01.g040300.t1.2 S-adenosyl-L-methionine-dependent methyltransferases superfamily protein

Details for Cre01.g040300.t1.2 - S-adenosyl-L-methionine-dependent methyltransferases superfamily protein

GO Terms: GO:0008171

Go to Gene Page: Cre01.g040300.t1.2

Phytozome Genomic Region

Cre01.g046652.t1.1 Nucleic acid-binding, OB-fold-like protein

Details for Cre01.g046652.t1.1 - Nucleic acid-binding, OB-fold-like protein

GO Terms: GO:0000049

Go to Gene Page: Cre01.g046652.t1.1

Phytozome Genomic Region

Cre02.g092400.t1.1 Nuclear transport factor 2 (NTF2) family protein with RNA binding (RRM-RBD-RNP motifs) domain

Details for Cre02.g092400.t1.1 - Nuclear transport factor 2 (NTF2) family protein with RNA binding (RRM-RBD-RNP motifs) domain

GO Terms: GO:0006810, GO:0005622

Go to Gene Page: Cre02.g092400.t1.1

Phytozome Genomic Region

Cre06.g250200.t1.2 methionine adenosyltransferase 3

Details for Cre06.g250200.t1.2 - methionine adenosyltransferase 3

GO Terms: GO:0004478, GO:0006556

Go to Gene Page: Cre06.g250200.t1.2

Phytozome Genomic Region

Cre06.g251900.t1.2 63 kDa inner membrane family protein

Details for Cre06.g251900.t1.2 - 63 kDa inner membrane family protein

GO Terms: GO:0051205, GO:0016021

Go to Gene Page: Cre06.g251900.t1.2

Phytozome Genomic Region

Cre06.g257601.t1.2 2-cysteine peroxiredoxin B

Details for Cre06.g257601.t1.2 - 2-cysteine peroxiredoxin B

GO Terms: GO:0016209, GO:0016491, GO:0055114, GO:0051920

Go to Gene Page: Cre06.g257601.t1.2

Phytozome Genomic Region

Cre06.g278195.t1.1

Details for Cre06.g278195.t1.1 -

GO Terms: NA

Go to Gene Page: Cre06.g278195.t1.1

Phytozome Genomic Region

Cre08.g359350.t1.2 acetyl Co-enzyme a carboxylase biotin carboxylase subunit

Details for Cre08.g359350.t1.2 - acetyl Co-enzyme a carboxylase biotin carboxylase subunit

GO Terms: GO:0003824, GO:0005524, GO:0008152, GO:0016874

Go to Gene Page: Cre08.g359350.t1.2

Phytozome Genomic Region

Cre08.g362900.t1.1 Photosystem II reaction center PsbP family protein

Details for Cre08.g362900.t1.1 - Photosystem II reaction center PsbP family protein

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

Go to Gene Page: Cre08.g362900.t1.1

Phytozome Genomic Region

Cre11.g467770.t1.1 Phosphoglycerate kinase family protein

Details for Cre11.g467770.t1.1 - Phosphoglycerate kinase family protein

GO Terms: GO:0004618, GO:0006096

Go to Gene Page: Cre11.g467770.t1.1

Phytozome Genomic Region

Cre12.g484000.t1.2 acetyl-CoA carboxylase carboxyl transferase subunit beta

Details for Cre12.g484000.t1.2 - acetyl-CoA carboxylase carboxyl transferase subunit beta

GO Terms: GO:0016874

Go to Gene Page: Cre12.g484000.t1.2

Phytozome Genomic Region

Cre12.g498550.t1.1 magnesium-protoporphyrin IX methyltransferase

Details for Cre12.g498550.t1.1 - magnesium-protoporphyrin IX methyltransferase

GO Terms: GO:0046406, GO:0015995

Go to Gene Page: Cre12.g498550.t1.1

Phytozome Genomic Region

Cre13.g562850.t1.2 photosystem II reaction center PSB29 protein

Details for Cre13.g562850.t1.2 - photosystem II reaction center PSB29 protein

GO Terms: GO:0010027, GO:0015979, GO:0009523

Go to Gene Page: Cre13.g562850.t1.2

Phytozome Genomic Region

Cre17.g701700.t2.1 Plant stearoyl-acyl-carrier-protein desaturase family protein

Details for Cre17.g701700.t2.1 - Plant stearoyl-acyl-carrier-protein desaturase family protein

GO Terms: GO:0045300, GO:0006631, GO:0055114

Go to Gene Page: Cre17.g701700.t2.1

Phytozome Genomic Region

motif_0189_1

e.value: 
31
Motif Bicluster: 
Width: 
21
Number of Sites: 
1
Consensus: 
TttacACnAaaAgaaaaagCA

motif_0189_2

e.value: 
87000
Motif Bicluster: 
Width: 
23
Number of Sites: 
1
Consensus: 
AGCCCCCAAcCCCCCcAAAaCgT
Displaying 1 - 1 of 1
Interaction Weight
Displaying 1 - 1 of 1
GO Terms Descriptions
GO:0044802 | GO:0061024 single-organism membrane organization | membrane organization
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