Thaps_bicluster_0284 Residual: 0.26
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_0284 0.26 Thalassiosira pseudonana
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Displaying 1 - 18 of 18
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10853 hypothetical protein

10853 - hypothetical protein

GO Terms:

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

CD Domains:

Go To Gene Page:

10853
11824 hypothetical protein

11824 - hypothetical protein

GO Terms:

GO:0008757, GO:0007049

CD Domains:

Go To Gene Page:

11824
13378 PRK13762

13378 - PRK13762

GO Terms:

GO:0003824, GO:0005506, GO:0010181, GO:0016491

CD Domains:

Go To Gene Page:

13378
21781 hypothetical protein

21781 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

21781
22462 FtsJ

22462 - FtsJ

GO Terms:

NA

CD Domains:

Go To Gene Page:

22462
23242 PRK00142

23242 - PRK00142

GO Terms:

NA

CD Domains:

Go To Gene Page:

23242
2392 hypothetical protein

2392 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2392
24180 PhyH

24180 - PhyH

GO Terms:

NA

CD Domains:

Go To Gene Page:

24180
25412 Nitro_FMN_reductase superfamily

25412 - Nitro_FMN_reductase superfamily

GO Terms:

GO:0006118, GO:0016491

CD Domains:

Go To Gene Page:

25412
268027 Met_10

268027 - Met_10

GO Terms:

NA

CD Domains:

Go To Gene Page:

268027
269049 hypothetical protein

269049 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

269049
269559 hypothetical protein

269559 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

269559
30454 Brix

30454 - Brix

GO Terms:

NA

CD Domains:

Go To Gene Page:

30454
30862 PTZ00368

30862 - PTZ00368

GO Terms:

GO:0003676

CD Domains:

Go To Gene Page:

30862
31415 hypothetical protein

31415 - hypothetical protein

GO Terms:

GO:0005554

CD Domains:

Go To Gene Page:

31415
5237 hypothetical protein

5237 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

5237
5532 hypothetical protein

5532 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

5532
6835 DUF947

6835 - DUF947

GO Terms:

NA

CD Domains:

Go To Gene Page:

6835
GO ID Go Term p-value q-value Cluster
GO:0007049 cell cycle 0.00289256 1 Thaps_bicluster_0284
GO:0006118 electron transport 0.106972 1 Thaps_bicluster_0284
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