Thaps_bicluster_0278 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_0278 0.24 Thalassiosira pseudonana
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Displaying 1 - 13 of 13
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11949 Nop14

11949 - Nop14

GO Terms:

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

CD Domains:

Go To Gene Page:

11949
18557 HrpA

18557 - HrpA

GO Terms:

GO:0005524, GO:0008026, GO:0003676, GO:0004386

CD Domains:

Go To Gene Page:

18557
21368 hypothetical protein

21368 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

21368
21375 hypothetical protein

21375 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

21375
21805 hypothetical protein

21805 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

21805
23079 zf-LYAR

23079 - zf-LYAR

GO Terms:

NA

CD Domains:

Go To Gene Page:

23079
25436 hypothetical protein

25436 - hypothetical protein

GO Terms:

GO:0004308

CD Domains:

Go To Gene Page:

25436
268746 SXM1

268746 - SXM1

GO Terms:

GO:0000059, GO:0005634, GO:0005643, GO:0005737, GO:0008565, GO:0006508, GO:0008237, GO:0008270

CD Domains:

Go To Gene Page:

268746
34661 COG4581
34881 Pescadillo_N superfamily

34881 - Pescadillo_N superfamily

GO Terms:

GO:0005622, GO:0005730, GO:0008283

CD Domains:

Go To Gene Page:

34881
36798 S_TKc

36798 - S_TKc

GO Terms:

GO:0004672, GO:0005524, GO:0006468, GO:0006397, GO:0016891

CD Domains:

Go To Gene Page:

36798
40529 COG2319

40529 - COG2319

GO Terms:

GO:0008567

CD Domains:

Go To Gene Page:

40529
8336 hypothetical protein

8336 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

8336
GO ID Go Term p-value q-value Cluster
GO:0008283 cell proliferation 0.00206654 1 Thaps_bicluster_0278
GO:0000059 protein-nucleus import, docking 0.00515995 1 Thaps_bicluster_0278
GO:0006397 mRNA processing 0.0225447 1 Thaps_bicluster_0278
GO:0006468 protein amino acid phosphorylation 0.201698 1 Thaps_bicluster_0278
GO:0006508 proteolysis and peptidolysis 0.264399 1 Thaps_bicluster_0278
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