Thaps_bicluster_0185 Residual: 0.25
Thalassiosira pseudonana

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 Residual Model version Organism
Thaps_bicluster_0185 0.25 Thalassiosira pseudonana
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Displaying 1 - 16 of 16
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24399 (DLDH2) PRK06416

24399 - (DLDH2) PRK06416

GO Terms:

GO:0006118, GO:0016491, GO:0050660, GO:0015036, GO:0005737, GO:0004148

CD Domains:

Go To Gene Page:

24399
24572 plant_peroxidase_like

24572 - plant_peroxidase_like

GO Terms:

GO:0004601, GO:0006979

CD Domains:

Go To Gene Page:

24572
261147 SUL1

261147 - SUL1

GO Terms:

NA

CD Domains:

Go To Gene Page:

261147
262753 (ApxS) ascorbate_peroxidase

262753 - (ApxS) ascorbate_peroxidase

GO Terms:

GO:0004601, GO:0006979, GO:0016688

CD Domains:

Go To Gene Page:

262753
269348 pyrophosphatase

269348 - pyrophosphatase

GO Terms:

GO:0000287, GO:0008152, GO:0016462, GO:0004427, GO:0005737

CD Domains:

Go To Gene Page:

269348
3113 hypothetical protein

3113 - hypothetical protein

GO Terms:

GO:0005515

CD Domains:

Go To Gene Page:

3113
31566 MBOAT superfamily

31566 - MBOAT superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

31566
33205 KefB

33205 - KefB

GO Terms:

NA

CD Domains:

Go To Gene Page:

33205
34447 Cyt-b5

34447 - Cyt-b5

GO Terms:

GO:0009703

CD Domains:

Go To Gene Page:

34447
38306 Chloroa_b-bind

38306 - Chloroa_b-bind

GO Terms:

GO:0009765, GO:0016020

CD Domains:

Go To Gene Page:

38306
38909 PLN02627

38909 - PLN02627

GO Terms:

GO:0004818, GO:0005524, GO:0006424, GO:0004812, GO:0006418, GO:0005737, GO:0009332

CD Domains:

Go To Gene Page:

38909
5219 (MCT1) PLN02752

5219 - (MCT1) PLN02752

GO Terms:

GO:0008152, GO:0016740, GO:0004314, GO:0006633

CD Domains:

Go To Gene Page:

5219
5815 hypothetical protein

5815 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

5815
6413 lipoyl_domain

6413 - lipoyl_domain

GO Terms:

NA

CD Domains:

Go To Gene Page:

6413
9720 hypothetical protein

9720 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

9720
GO ID Go Term p-value q-value Cluster
GO:0006633 fatty acid biosynthesis 0.000645694 1 Thaps_bicluster_0185
GO:0006979 response to oxidative stress 0.00103644 1 Thaps_bicluster_0185
GO:0006424 glutamyl-tRNA aminoacylation 0.00824653 1 Thaps_bicluster_0185
GO:0009765 photosynthesis light harvesting 0.0797569 1 Thaps_bicluster_0185
GO:0006418 tRNA aminoacylation for protein translation 0.111884 1 Thaps_bicluster_0185
GO:0008152 metabolism 0.203212 1 Thaps_bicluster_0185
GO:0006118 electron transport 0.432304 1 Thaps_bicluster_0185
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