Thaps_bicluster_0110 Residual: 0.24
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_0110 0.24 Thalassiosira pseudonana
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Displaying 1 - 14 of 14
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13224 (pabA) PABP-1234

13224 - (pabA) PABP-1234

GO Terms:

GO:0003676, GO:0003723

CD Domains:

Go To Gene Page:

13224
21397 Nop52 superfamily

21397 - Nop52 superfamily

GO Terms:

GO:0006364, GO:0030688

CD Domains:

Go To Gene Page:

21397
22467 AdoMet_MTases superfamily

22467 - AdoMet_MTases superfamily

GO Terms:

GO:0005554, GO:0003677, GO:0006306, GO:0008170, GO:0005351, GO:0009401

CD Domains:

Go To Gene Page:

22467
23887 hypothetical protein

23887 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23887
24358 RAP

24358 - RAP

GO Terms:

NA

CD Domains:

Go To Gene Page:

24358
268688 hypothetical protein

268688 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

268688
37327 tRNA_Me_trans

37327 - tRNA_Me_trans

GO Terms:

GO:0004808, GO:0005737, GO:0008033

CD Domains:

Go To Gene Page:

37327
38073 NAP

38073 - NAP

GO Terms:

GO:0005634, GO:0006334

CD Domains:

Go To Gene Page:

38073
38776 BOP1NT

38776 - BOP1NT

GO Terms:

NA

CD Domains:

Go To Gene Page:

38776
39540 Alpha_ANH_like_II

39540 - Alpha_ANH_like_II

GO Terms:

NA

CD Domains:

Go To Gene Page:

39540
6250 reductase

6250 - reductase

GO Terms:

GO:0008152, GO:0016491

CD Domains:

Go To Gene Page:

6250
7788 (Tp_CCHH23) regulator [Rayko]

7788 - (Tp_CCHH23) regulator [Rayko]

GO Terms:

GO:0003676, GO:0005634, GO:0008270

CD Domains:

Go To Gene Page:

7788
GO ID Go Term p-value q-value Cluster
GO:0006364 rRNA processing 0.00988766 1 Thaps_bicluster_0110
GO:0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system 0.0221325 1 Thaps_bicluster_0110
GO:0008033 tRNA processing 0.0221325 1 Thaps_bicluster_0110
GO:0006306 DNA methylation 0.0354559 1 Thaps_bicluster_0110
GO:0006334 nucleosome assembly 0.037862 1 Thaps_bicluster_0110
GO:0008152 metabolism 0.410014 1 Thaps_bicluster_0110
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