Module 172 Residual: 0.14

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_0172 v02 0.14 -11.73

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 - 19 of 19
Cre01.g038400.t1.2 calreticulin 1b

Details for Cre01.g038400.t1.2 - calreticulin 1b

GO Terms: GO:0005509, GO:0051082, GO:0006457, GO:0005783

Go to Gene Page: Cre01.g038400.t1.2

Phytozome Genomic Region

Cre02.g084350.t1.2 Uncharacterized protein family (UPF0016)

Details for Cre02.g084350.t1.2 - Uncharacterized protein family (UPF0016)

GO Terms: GO:0016020

Go to Gene Page: Cre02.g084350.t1.2

Phytozome Genomic Region

Cre03.g144667.t1.1 ClpS-like protein

Details for Cre03.g144667.t1.1 - ClpS-like protein

GO Terms: NA

Go to Gene Page: Cre03.g144667.t1.1

Phytozome Genomic Region

Cre03.g188700.t1.2 Plastid-lipid associated protein PAP / fibrillin family protein

Details for Cre03.g188700.t1.2 - Plastid-lipid associated protein PAP / fibrillin family protein

GO Terms: GO:0005198, GO:0009507

Go to Gene Page: Cre03.g188700.t1.2

Phytozome Genomic Region

Cre03.g207000.t1.2 abscisic acid (aba)-deficient 4

Details for Cre03.g207000.t1.2 - abscisic acid (aba)-deficient 4

GO Terms: NA

Go to Gene Page: Cre03.g207000.t1.2

Phytozome Genomic Region

Cre03.g209841.t1.1

Details for Cre03.g209841.t1.1 -

GO Terms: NA

Go to Gene Page: Cre03.g209841.t1.1

Phytozome Genomic Region

Cre05.g233900.t1.2 ascorbate peroxidase 4

Details for Cre05.g233900.t1.2 - ascorbate peroxidase 4

GO Terms: GO:0004601, GO:0020037, GO:0006979, GO:0055114

Go to Gene Page: Cre05.g233900.t1.2

Phytozome Genomic Region

Cre06.g259401.t1.1 S-adenosyl-L-methionine-dependent methyltransferases superfamily protein

Details for Cre06.g259401.t1.1 - S-adenosyl-L-methionine-dependent methyltransferases superfamily protein

GO Terms: GO:0008168, GO:0008152

Go to Gene Page: Cre06.g259401.t1.1

Phytozome Genomic Region

Cre06.g267600.t2.1 Lycopene beta/epsilon cyclase protein

Details for Cre06.g267600.t2.1 - Lycopene beta/epsilon cyclase protein

GO Terms: GO:0016705, GO:0016117

Go to Gene Page: Cre06.g267600.t2.1

Phytozome Genomic Region

Cre07.g342150.t1.2 Glutamyl-tRNA reductase family protein

Details for Cre07.g342150.t1.2 - Glutamyl-tRNA reductase family protein

GO Terms: GO:0008883, GO:0050661, GO:0033014, GO:0055114

Go to Gene Page: Cre07.g342150.t1.2

Phytozome Genomic Region

Cre09.g397250.t1.2 fatty acid desaturase 5

Details for Cre09.g397250.t1.2 - fatty acid desaturase 5

GO Terms: GO:0006629

Go to Gene Page: Cre09.g397250.t1.2

Phytozome Genomic Region

Cre10.g424450.t1.2 translocase of the outer mitochondrial membrane 40

Details for Cre10.g424450.t1.2 - translocase of the outer mitochondrial membrane 40

GO Terms: GO:0055085, GO:0005741

Go to Gene Page: Cre10.g424450.t1.2

Phytozome Genomic Region

Cre10.g436050.t1.2 Fe superoxide dismutase 1

Details for Cre10.g436050.t1.2 - Fe superoxide dismutase 1

GO Terms: GO:0004784, GO:0046872, GO:0006801, GO:0055114

Go to Gene Page: Cre10.g436050.t1.2

Phytozome Genomic Region

Cre11.g467689.t1.1 photosynthetic electron transfer C

Details for Cre11.g467689.t1.1 - photosynthetic electron transfer C

GO Terms: GO:0016491, GO:0051537, GO:0055114, GO:0009496, GO:0042651

Go to Gene Page: Cre11.g467689.t1.1

Phytozome Genomic Region

Cre12.g497300.t2.1 calcium sensing receptor

Details for Cre12.g497300.t2.1 - calcium sensing receptor

GO Terms: NA

Go to Gene Page: Cre12.g497300.t2.1

Phytozome Genomic Region

Cre12.g510050.t1.2 dicarboxylate diiron protein, putative (Crd1)

Details for Cre12.g510050.t1.2 - dicarboxylate diiron protein, putative (Crd1)

GO Terms: GO:0016491, GO:0046872, GO:0055114

Go to Gene Page: Cre12.g510050.t1.2

Phytozome Genomic Region

Cre12.g544050.t1.1 poly(A) binding protein 8

Details for Cre12.g544050.t1.1 - poly(A) binding protein 8

GO Terms: GO:0003676

Go to Gene Page: Cre12.g544050.t1.1

Phytozome Genomic Region

Cre13.g588100.t1.2 rotamase cyclophilin 2

Details for Cre13.g588100.t1.2 - rotamase cyclophilin 2

GO Terms: GO:0003755, GO:0006457

Go to Gene Page: Cre13.g588100.t1.2

Phytozome Genomic Region

Cre14.g629800.t1.2

Details for Cre14.g629800.t1.2 -

GO Terms: NA

Go to Gene Page: Cre14.g629800.t1.2

Phytozome Genomic Region

motif_0172_1

e.value: 
2.3
Motif Bicluster: 
Width: 
15
Number of Sites: 
1
Consensus: 
AgGAAAGaagnAAaa

motif_0172_2

e.value: 
94000
Motif Bicluster: 
Width: 
21
Number of Sites: 
1
Consensus: 
tctGTAaTAcAtCTagGanaA
Displaying 1 - 4 of 4
Interaction Weight
up-regulates 0.051756
down-regulates 0.048563
down-regulates 0.058834
up-regulates 0.068551
Displaying 1 - 1 of 1
GO Terms Descriptions
GO:0016491 | GO:0016209 oxidoreductase activity | antioxidant activity
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