Thaps_bicluster_0272 Residual: 0.25
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_0272 0.25 Thalassiosira pseudonana
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Displaying 1 - 17 of 17
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20788 Diphthine_synthase

20788 - Diphthine_synthase

GO Terms:

GO:0008152, GO:0008168, GO:0004164, GO:0017183

CD Domains:

Go To Gene Page:

20788
22204 hypothetical protein

22204 - hypothetical protein

GO Terms:

GO:0031177

CD Domains:

Go To Gene Page:

22204
22672 hypothetical protein

22672 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22672
22901 hypothetical protein

22901 - hypothetical protein

GO Terms:

GO:0004519

CD Domains:

Go To Gene Page:

22901
24590 DUF663

24590 - DUF663

GO Terms:

NA

CD Domains:

Go To Gene Page:

24590
25869 Nrap superfamily

25869 - Nrap superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

25869
261109 NBD_sugar-kinase_HSP70_actin superfamily

261109 - NBD_sugar-kinase_HSP70_actin superfamily

GO Terms:

GO:0005524

CD Domains:

Go To Gene Page:

261109
261462 hypothetical protein

261462 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

261462
262091 eukaryotic translation initiation factor 3, subunit 10

262091 - eukaryotic translation initiation factor 3, subunit 10

GO Terms:

NA

CD Domains:

Go To Gene Page:

262091
262326 ran binding protein 4-like protein

262326 - ran binding protein 4-like protein

GO Terms:

GO:0000059, GO:0005634, GO:0005643, GO:0005737, GO:0008565, GO:0004429, GO:0015072, GO:0015073, GO:0016303

CD Domains:

Go To Gene Page:

262326
264345 SpoU

264345 - SpoU

GO Terms:

GO:0003723, GO:0006396, GO:0008173

CD Domains:

Go To Gene Page:

264345
268678 (Tp_Myb2R3) ZUO1

268678 - (Tp_Myb2R3) ZUO1

GO Terms:

GO:0003677, GO:0005634, GO:0006457, GO:0031072, GO:0051082

CD Domains:

Go To Gene Page:

268678
269434 COG1092

269434 - COG1092

GO Terms:

GO:0008757

CD Domains:

Go To Gene Page:

269434
270145 (LASPO) NadB

270145 - (LASPO) NadB

GO Terms:

GO:0006118, GO:0016491, GO:0008734, GO:0015922

CD Domains:

Go To Gene Page:

270145
3583 PRK13796

3583 - PRK13796

GO Terms:

NA

CD Domains:

Go To Gene Page:

3583
36609 PRK00142

36609 - PRK00142

GO Terms:

GO:0003676

CD Domains:

Go To Gene Page:

36609
37965 S1_like superfamily

37965 - S1_like superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

37965
GO ID Go Term p-value q-value Cluster
GO:0017183 peptidyl-diphthamide biosynthesis from peptidyl-histidine 0.00124044 1 Thaps_bicluster_0272
GO:0000059 protein-nucleus import, docking 0.00618938 1 Thaps_bicluster_0272
GO:0006396 RNA processing 0.0698579 1 Thaps_bicluster_0272
GO:0006457 protein folding 0.150875 1 Thaps_bicluster_0272
GO:0006118 electron transport 0.287914 1 Thaps_bicluster_0272
GO:0008152 metabolism 0.410014 1 Thaps_bicluster_0272
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