Thaps_bicluster_0231 Residual: 0.32
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_0231 0.32 Thalassiosira pseudonana
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Displaying 1 - 21 of 21
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10302 hypothetical protein

10302 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

10302
11738 hypothetical protein

11738 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

11738
11831 hypothetical protein

11831 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

11831
22963 WD40 superfamily

22963 - WD40 superfamily

GO Terms:

GO:0004806

CD Domains:

Go To Gene Page:

22963
23341 hypothetical protein

23341 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23341
2462 hypothetical protein

2462 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2462
25886 DUF1824 superfamily

25886 - DUF1824 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

25886
263200 PLN02605

263200 - PLN02605

GO Terms:

GO:0009058, GO:0046509

CD Domains:

Go To Gene Page:

263200
264925 Flavodoxin_1

264925 - Flavodoxin_1

GO Terms:

GO:0005489, GO:0006118, GO:0010181, GO:0016491

CD Domains:

Go To Gene Page:

264925
268844 hypothetical protein

268844 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

268844
2950 (UroS) HemD

2950 - (UroS) HemD

GO Terms:

GO:0004852, GO:0006779, GO:0006783

CD Domains:

Go To Gene Page:

2950
32874 SodA

32874 - SodA

GO Terms:

GO:0004784, GO:0006801, GO:0046872, GO:0004785, GO:0008382, GO:0008383, GO:0016954

CD Domains:

Go To Gene Page:

32874
37838 M32_Taq

37838 - M32_Taq

GO Terms:

GO:0004181, GO:0006508

CD Domains:

Go To Gene Page:

37838
40655 PRK06349

40655 - PRK06349

GO Terms:

GO:0004412, GO:0008652, GO:0008152, GO:0016597

CD Domains:

Go To Gene Page:

40655
4160 PMT_2 superfamily

4160 - PMT_2 superfamily

GO Terms:

GO:0004576, GO:0006486, GO:0016020, GO:0004579

CD Domains:

Go To Gene Page:

4160
4225 hypothetical protein

4225 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

4225
6942 DUF89

6942 - DUF89

GO Terms:

NA

CD Domains:

Go To Gene Page:

6942
7160 hypothetical protein

7160 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

7160
8872 hypothetical protein

8872 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

8872
9166 hypothetical protein

9166 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

9166
9776 hypothetical protein

9776 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

9776
GO ID Go Term p-value q-value Cluster
GO:0006486 protein amino acid glycosylation 0.00557274 1 Thaps_bicluster_0231
GO:0006801 superoxide metabolism 0.00742418 1 Thaps_bicluster_0231
GO:0006783 heme biosynthesis 0.00742418 1 Thaps_bicluster_0231
GO:0008652 amino acid biosynthesis 0.0202987 1 Thaps_bicluster_0231
GO:0006779 porphyrin biosynthesis 0.0202987 1 Thaps_bicluster_0231
GO:0009058 biosynthesis 0.0978804 1 Thaps_bicluster_0231
GO:0006118 electron transport 0.399203 1 Thaps_bicluster_0231
GO:0006508 proteolysis and peptidolysis 0.424754 1 Thaps_bicluster_0231
GO:0008152 metabolism 0.546944 1 Thaps_bicluster_0231
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