Thaps_bicluster_0193 Residual: 0.22
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_0193 0.22 Thalassiosira pseudonana
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Displaying 1 - 15 of 15
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20985 COG5593

20985 - COG5593

GO Terms:

NA

CD Domains:

Go To Gene Page:

20985
21050 Ras_like_GTPase superfamily

21050 - Ras_like_GTPase superfamily

GO Terms:

GO:0005525

CD Domains:

Go To Gene Page:

21050
21110 Sun

21110 - Sun

GO Terms:

NA

CD Domains:

Go To Gene Page:

21110
21173 hypothetical protein

21173 - hypothetical protein

GO Terms:

GO:0005509

CD Domains:

Go To Gene Page:

21173
21462 (rpoT) rpot-like RNA polymerase

21462 - (rpoT) rpot-like RNA polymerase

GO Terms:

NA

CD Domains:

Go To Gene Page:

21462
22582 S1

22582 - S1

GO Terms:

GO:0003723, GO:0003755, GO:0004600, GO:0030051, GO:0042027

CD Domains:

Go To Gene Page:

22582
23245 hypothetical protein

23245 - hypothetical protein

GO Terms:

GO:0003723

CD Domains:

Go To Gene Page:

23245
23900 hypothetical protein

23900 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23900
25129 hypothetical protein

25129 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25129
268735 (GPB1) WD40

268735 - (GPB1) WD40

GO Terms:

NA

CD Domains:

Go To Gene Page:

268735
2921 RRM_SF

2921 - RRM_SF

GO Terms:

GO:0003676, GO:0003677

CD Domains:

Go To Gene Page:

2921
32395 RNA_pol

32395 - RNA_pol

GO Terms:

GO:0003677, GO:0003899, GO:0006350, GO:0003900, GO:0003901, GO:0003902

CD Domains:

Go To Gene Page:

32395
35207 YihA_EngB

35207 - YihA_EngB

GO Terms:

GO:0005525

CD Domains:

Go To Gene Page:

35207
GO ID Go Term p-value q-value Cluster
GO:0006350 transcription 0.00620219 1 Thaps_bicluster_0193
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