Thaps_bicluster_0196 Residual: 0.36
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_0196 0.36 Thalassiosira pseudonana
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Displaying 1 - 20 of 20
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16947 DEXDc superfamily

16947 - DEXDc superfamily

GO Terms:

GO:0003676, GO:0005524, GO:0008026, GO:0004386, GO:0000810, GO:0004787, GO:0008722, GO:0008758, GO:0008796, GO:0008828, GO:0016462, GO:0016818, GO:0019176, GO:0019177

CD Domains:

Go To Gene Page:

16947
20932 EEP superfamily

20932 - EEP superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

20932
23331 RAP

23331 - RAP

GO Terms:

GO:0031177

CD Domains:

Go To Gene Page:

23331
23650 hypothetical protein

23650 - hypothetical protein

GO Terms:

GO:0003684, GO:0005524, GO:0006298

CD Domains:

Go To Gene Page:

23650
25247 Nudix_Hydrolase superfamily

25247 - Nudix_Hydrolase superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

25247
25722 Beach superfamily

25722 - Beach superfamily

GO Terms:

GO:0003676

CD Domains:

Go To Gene Page:

25722
261769 GDA1_CD39 superfamily

261769 - GDA1_CD39 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

261769
261777 MIF4G

261777 - MIF4G

GO Terms:

GO:0005179, GO:0005576, GO:0003723

CD Domains:

Go To Gene Page:

261777
263669 UvrD

263669 - UvrD

GO Terms:

GO:0000810, GO:0004787, GO:0008722, GO:0008758, GO:0008796, GO:0008828, GO:0016462, GO:0016818, GO:0019176, GO:0019177

CD Domains:

Go To Gene Page:

263669
263987 hypothetical protein

263987 - hypothetical protein

GO Terms:

GO:0005489, GO:0006118

CD Domains:

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263987
30980 EngA2

30980 - EngA2

GO Terms:

GO:0005525

CD Domains:

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30980
31259 HA

31259 - HA

GO Terms:

NA

CD Domains:

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31259
31764 DUF21

31764 - DUF21

GO Terms:

NA

CD Domains:

Go To Gene Page:

31764
33670 RNRR2

33670 - RNRR2

GO Terms:

GO:0004748, GO:0009186

CD Domains:

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33670
33775 MetAP1

33775 - MetAP1

GO Terms:

GO:0006508, GO:0008235, GO:0004239

CD Domains:

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33775
37156 PLN02369

37156 - PLN02369

GO Terms:

GO:0009116, GO:0004749, GO:0009165

CD Domains:

Go To Gene Page:

37156
42194 PTZ00184

42194 - PTZ00184

GO Terms:

GO:0005509

CD Domains:

Go To Gene Page:

42194
4940 MiaA superfamily

4940 - MiaA superfamily

GO Terms:

GO:0004811, GO:0005524, GO:0008033

CD Domains:

Go To Gene Page:

4940
6606 obgE

6606 - obgE

GO Terms:

GO:0005525

CD Domains:

Go To Gene Page:

6606
GO ID Go Term p-value q-value Cluster
GO:0009186 deoxyribonucleoside diphosphate metabolism 0.00495457 1 Thaps_bicluster_0196
GO:0006118 electron transport 0.364179 1 Thaps_bicluster_0196
GO:0006298 mismatch repair 0.0261771 1 Thaps_bicluster_0196
GO:0009116 nucleoside metabolism 0.00988766 1 Thaps_bicluster_0196
GO:0009165 nucleotide biosynthesis 0.00660132 1 Thaps_bicluster_0196
GO:0015031 protein transport 0.068993 1 Thaps_bicluster_0196
GO:0006508 proteolysis and peptidolysis 0.38827 1 Thaps_bicluster_0196
GO:0008033 tRNA processing 0.0294066 1 Thaps_bicluster_0196
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