Module 105 Residual: 0.21

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_0105 v02 0.21 -13.29

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:
45 min
Displaying 1 - 22 of 22
Cre01.g016850.t1.2 Uncharacterised protein family SERF

Details for Cre01.g016850.t1.2 - Uncharacterised protein family SERF

GO Terms: NA

Go to Gene Page: Cre01.g016850.t1.2

Phytozome Genomic Region

Cre01.g039350.t1.2 P450 reductase 1

Details for Cre01.g039350.t1.2 - P450 reductase 1

GO Terms: GO:0016491, GO:0055114, GO:0010181

Go to Gene Page: Cre01.g039350.t1.2

Phytozome Genomic Region

Cre02.g077350.t1.2 histidinol dehydrogenase

Details for Cre02.g077350.t1.2 - histidinol dehydrogenase

GO Terms: GO:0004399, GO:0008270, GO:0051287, GO:0000105, GO:0055114

Go to Gene Page: Cre02.g077350.t1.2

Phytozome Genomic Region

Cre02.g078100.t1.1 eukaryotic translation initiation factor 2 (eIF-2) family protein

Details for Cre02.g078100.t1.1 - eukaryotic translation initiation factor 2 (eIF-2) family protein

GO Terms: GO:0003924, GO:0005525, GO:0000049

Go to Gene Page: Cre02.g078100.t1.1

Phytozome Genomic Region

Cre02.g081050.t1.2 Flagellar Associated Protein

Details for Cre02.g081050.t1.2 - Flagellar Associated Protein

GO Terms: NA

Go to Gene Page: Cre02.g081050.t1.2

Phytozome Genomic Region

Cre03.g189400.t1.2 seryl-tRNA synthetase / serine--tRNA ligase

Details for Cre03.g189400.t1.2 - seryl-tRNA synthetase / serine--tRNA ligase

GO Terms: GO:0000166, GO:0004812, GO:0005524, GO:0006418, GO:0004828, GO:0006434, GO:0005737

Go to Gene Page: Cre03.g189400.t1.2

Phytozome Genomic Region

Cre03.g206600.t1.2 dehydratase family

Details for Cre03.g206600.t1.2 - dehydratase family

GO Terms: GO:0003824, GO:0008152

Go to Gene Page: Cre03.g206600.t1.2

Phytozome Genomic Region

Cre04.g231222.t2.1 chaperonin-60alpha

Details for Cre04.g231222.t2.1 - chaperonin-60alpha

GO Terms: GO:0005524, GO:0044267, GO:0005044, GO:0016020

Go to Gene Page: Cre04.g231222.t2.1

Phytozome Genomic Region

Cre05.g245900.t1.2 branched-chain amino acid aminotransferase 5 / branched-chain amino acid transaminase 5 (BCAT5)

Details for Cre05.g245900.t1.2 - branched-chain amino acid aminotransferase 5 / branched-chain amino acid transaminase 5 (BCAT5)

GO Terms: GO:0003824, GO:0008152

Go to Gene Page: Cre05.g245900.t1.2

Phytozome Genomic Region

Cre06.g250902.t1.1 Homocysteine S-methyltransferase family protein

Details for Cre06.g250902.t1.1 - Homocysteine S-methyltransferase family protein

GO Terms: GO:0042558, GO:0031419, GO:0046872, GO:0008898, GO:0008705, GO:0009086, GO:0005622

Go to Gene Page: Cre06.g250902.t1.1

Phytozome Genomic Region

Cre06.g299000.t1.2 Ribosomal protein L21

Details for Cre06.g299000.t1.2 - Ribosomal protein L21

GO Terms: NA

Go to Gene Page: Cre06.g299000.t1.2

Phytozome Genomic Region

Cre10.g436350.t1.1 shikimate kinase 1

Details for Cre10.g436350.t1.1 - shikimate kinase 1

GO Terms: NA

Go to Gene Page: Cre10.g436350.t1.1

Phytozome Genomic Region

Cre10.g439900.t1.2 heat shock protein 70 (Hsp 70) family protein

Details for Cre10.g439900.t1.2 - heat shock protein 70 (Hsp 70) family protein

GO Terms: NA

Go to Gene Page: Cre10.g439900.t1.2

Phytozome Genomic Region

Cre11.g479150.t3.1

Details for Cre11.g479150.t3.1 -

GO Terms: NA

Go to Gene Page: Cre11.g479150.t3.1

Phytozome Genomic Region

Cre12.g494750.t1.2 chloroplast 30S ribosomal protein S20, putative

Details for Cre12.g494750.t1.2 - chloroplast 30S ribosomal protein S20, putative

GO Terms: GO:0003723, GO:0003735, GO:0006412, GO:0005622, GO:0005840

Go to Gene Page: Cre12.g494750.t1.2

Phytozome Genomic Region

Cre12.g501550.t1.2

Details for Cre12.g501550.t1.2 -

GO Terms: NA

Go to Gene Page: Cre12.g501550.t1.2

Phytozome Genomic Region

Cre13.g603900.t1.2 tRNA synthetase beta subunit family protein

Details for Cre13.g603900.t1.2 - tRNA synthetase beta subunit family protein

GO Terms: GO:0003723, GO:0004826, GO:0000287, GO:0005524, GO:0006432

Go to Gene Page: Cre13.g603900.t1.2

Phytozome Genomic Region

Cre14.g611450.t1.1 Plastid-lipid associated protein PAP / fibrillin family protein

Details for Cre14.g611450.t1.1 - Plastid-lipid associated protein PAP / fibrillin family protein

GO Terms: GO:0005198, GO:0009507

Go to Gene Page: Cre14.g611450.t1.1

Phytozome Genomic Region

Cre16.g651750.t1.2 tRNA synthetase class I (I, L, M and V) family protein

Details for Cre16.g651750.t1.2 - tRNA synthetase class I (I, L, M and V) family protein

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

Go to Gene Page: Cre16.g651750.t1.2

Phytozome Genomic Region

Cre16.g693850.t1.1

Details for Cre16.g693850.t1.1 -

GO Terms: NA

Go to Gene Page: Cre16.g693850.t1.1

Phytozome Genomic Region

Cre17.g697406.t1.2

Details for Cre17.g697406.t1.2 -

GO Terms: NA

Go to Gene Page: Cre17.g697406.t1.2

Phytozome Genomic Region

Cre17.g734450.t1.2 Ribosomal protein L19 family protein

Details for Cre17.g734450.t1.2 - Ribosomal protein L19 family protein

GO Terms: GO:0003735, GO:0006412, GO:0005622, GO:0005840

Go to Gene Page: Cre17.g734450.t1.2

Phytozome Genomic Region

motif_0105_1

e.value: 
0.000000014
Motif Bicluster: 
Width: 
21
Number of Sites: 
1
Consensus: 
CagCaGcAGCTGcTGgTGCaG

motif_0105_2

e.value: 
82
Motif Bicluster: 
Width: 
21
Number of Sites: 
1
Consensus: 
TcTtcatcatcacCTtcangT
Displaying 1 - 2 of 2
Interaction Weight
up-regulates 0.054978
up-regulates 0.05663
Displaying 1 - 1 of 1
GO Terms Descriptions
GO:0006520 | GO:0006082 | GO:0019752 | GO:0043436 | GO:0006399 | GO:0034645 | GO:0009059 | GO:0034660 | GO:0005737 cellular amino acid metabolic process | organic acid metabolic process | carboxylic acid metabolic process | oxoacid metabolic process | tRNA metabolic process | cellular macromolecule biosynthetic proc... | macromolecule biosynthetic process | ncRNA metabolic process | cytoplasm
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