Module 8 Residual: 0.13

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_0008 v02 0.13 -13.79

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 - 24 of 24
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.g095097.t1.1 FKBP-like peptidyl-prolyl cis-trans isomerase family protein

Details for Cre02.g095097.t1.1 - FKBP-like peptidyl-prolyl cis-trans isomerase family protein

GO Terms: GO:0006457

Go to Gene Page: Cre02.g095097.t1.1

Phytozome Genomic Region

Cre02.g100050.t1.2 Oxoglutarate/iron-dependent oxygenase

Details for Cre02.g100050.t1.2 - Oxoglutarate/iron-dependent oxygenase

GO Terms: NA

Go to Gene Page: Cre02.g100050.t1.2

Phytozome Genomic Region

Cre02.g114400.t1.2 Radical SAM superfamily protein

Details for Cre02.g114400.t1.2 - Radical SAM superfamily protein

GO Terms: GO:0003824, GO:0051536

Go to Gene Page: Cre02.g114400.t1.2

Phytozome Genomic Region

Cre02.g147302.t1.1 aspartate aminotransferase

Details for Cre02.g147302.t1.1 - aspartate aminotransferase

GO Terms: GO:0030170, GO:0009058

Go to Gene Page: Cre02.g147302.t1.1

Phytozome Genomic Region

Cre03.g207601.t1.1

Details for Cre03.g207601.t1.1 -

GO Terms: NA

Go to Gene Page: Cre03.g207601.t1.1

Phytozome Genomic Region

Cre04.g213100.t1.1 alpha/beta-Hydrolases superfamily protein

Details for Cre04.g213100.t1.1 - alpha/beta-Hydrolases superfamily protein

GO Terms: NA

Go to Gene Page: Cre04.g213100.t1.1

Phytozome Genomic Region

Cre04.g213251.t1.1 Peptidase M1 family protein

Details for Cre04.g213251.t1.1 - Peptidase M1 family protein

GO Terms: NA

Go to Gene Page: Cre04.g213251.t1.1

Phytozome Genomic Region

Cre04.g232902.t1.1

Details for Cre04.g232902.t1.1 -

GO Terms: GO:0003723, GO:0003746, GO:0043022, GO:0006452, GO:0045901, GO:0045905

Go to Gene Page: Cre04.g232902.t1.1

Phytozome Genomic Region

Cre06.g252650.t1.2 Aconitase/3-isopropylmalate dehydratase protein

Details for Cre06.g252650.t1.2 - Aconitase/3-isopropylmalate dehydratase protein

GO Terms: GO:0008152

Go to Gene Page: Cre06.g252650.t1.2

Phytozome Genomic Region

Cre06.g297950.t1.2

Details for Cre06.g297950.t1.2 -

GO Terms: NA

Go to Gene Page: Cre06.g297950.t1.2

Phytozome Genomic Region

Cre09.g388356.t1.1 Translation factor for chloroplast psbC mRNA

Details for Cre09.g388356.t1.1 - Translation factor for chloroplast psbC mRNA

GO Terms: NA

Go to Gene Page: Cre09.g388356.t1.1

Phytozome Genomic Region

Cre09.g389801.t1.1

Details for Cre09.g389801.t1.1 -

GO Terms: NA

Go to Gene Page: Cre09.g389801.t1.1

Phytozome Genomic Region

Cre10.g429200.t1.1 Rubisco methyltransferase family protein

Details for Cre10.g429200.t1.1 - Rubisco methyltransferase family protein

GO Terms: GO:0005515

Go to Gene Page: Cre10.g429200.t1.1

Phytozome Genomic Region

Cre10.g433000.t1.1 glycine-tRNA ligases

Details for Cre10.g433000.t1.1 - glycine-tRNA ligases

GO Terms: GO:0000166, GO:0004820, GO:0005524, GO:0006426, GO:0005737

Go to Gene Page: Cre10.g433000.t1.1

Phytozome Genomic Region

Cre12.g490350.t1.1 4-hydroxy-3-methylbut-2-enyl diphosphate synthase

Details for Cre12.g490350.t1.1 - 4-hydroxy-3-methylbut-2-enyl diphosphate synthase

GO Terms: GO:0046429, GO:0016114, GO:0055114

Go to Gene Page: Cre12.g490350.t1.1

Phytozome Genomic Region

Cre12.g496700.t1.2 thioredoxin F-type 1

Details for Cre12.g496700.t1.2 - thioredoxin F-type 1

GO Terms: GO:0045454

Go to Gene Page: Cre12.g496700.t1.2

Phytozome Genomic Region

Cre12.g500650.t1.2 Ribonuclease II/R family protein

Details for Cre12.g500650.t1.2 - Ribonuclease II/R family protein

GO Terms: GO:0003723, GO:0004540

Go to Gene Page: Cre12.g500650.t1.2

Phytozome Genomic Region

Cre12.g537100.t1.2 valyl-tRNA synthetase / valine--tRNA ligase (VALRS)

Details for Cre12.g537100.t1.2 - valyl-tRNA synthetase / valine--tRNA ligase (VALRS)

GO Terms: GO:0000166, GO:0004812, GO:0005524, GO:0006418

Go to Gene Page: Cre12.g537100.t1.2

Phytozome Genomic Region

Cre13.g564050.t1.1 Mog1/PsbP/DUF1795-like photosystem II reaction center PsbP family protein

Details for Cre13.g564050.t1.1 - Mog1/PsbP/DUF1795-like photosystem II reaction center PsbP family protein

GO Terms: NA

Go to Gene Page: Cre13.g564050.t1.1

Phytozome Genomic Region

Cre13.g570550.t1.2 cytidine deaminase 1

Details for Cre13.g570550.t1.2 - cytidine deaminase 1

GO Terms: GO:0008270, GO:0016787, GO:0004126, GO:0009972

Go to Gene Page: Cre13.g570550.t1.2

Phytozome Genomic Region

Cre14.g614800.t1.2

Details for Cre14.g614800.t1.2 -

GO Terms: NA

Go to Gene Page: Cre14.g614800.t1.2

Phytozome Genomic Region

Cre15.g635067.t1.1

Details for Cre15.g635067.t1.1 -

GO Terms: NA

Go to Gene Page: Cre15.g635067.t1.1

Phytozome Genomic Region

Cre17.g732250.t1.1

Details for Cre17.g732250.t1.1 -

GO Terms: NA

Go to Gene Page: Cre17.g732250.t1.1

Phytozome Genomic Region

motif_0008_1

e.value: 
0.0000042
Motif Bicluster: 
Width: 
15
Number of Sites: 
1
Consensus: 
CACatGCAaACAngC

motif_0008_2

e.value: 
0.0000021
Motif Bicluster: 
Width: 
21
Number of Sites: 
1
Consensus: 
gctGccgcTGCTaCtGCCgCn
Displaying 1 - 1 of 1
Interaction Weight
down-regulates 0.043771
Displaying 1 - 1 of 1
GO Terms Descriptions
GO:0006418 | GO:0043038 | GO:0043039 | GO:0004812 | GO:0016875 | GO:0016876 | GO:0004126 | GO:0004820 | GO:0046429 | GO:0052592 tRNA aminoacylation for protein translat... | amino acid activation | tRNA aminoacylation | aminoacyl-tRNA ligase activity | ligase activity, forming carbon-oxygen b... | ligase activity, forming aminoacyl-tRNA ... | cytidine deaminase activity | glycine-tRNA ligase activity | 4-hydroxy-3-methylbut-2-en-1-yl diphosph... | oxidoreductase activity, acting on CH or...
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