Thaps_bicluster_0269 Residual: 0.41
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_0269 0.41 Thalassiosira pseudonana
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Displaying 1 - 24 of 24
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10624 hypothetical protein

10624 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

10624
10810 HP superfamily

10810 - HP superfamily

GO Terms:

GO:0008152, GO:0016491

CD Domains:

Go To Gene Page:

10810
21239 Cyt_b561_FRRS1_like

21239 - Cyt_b561_FRRS1_like

GO Terms:

NA

CD Domains:

Go To Gene Page:

21239
21948 DUF179

21948 - DUF179

GO Terms:

NA

CD Domains:

Go To Gene Page:

21948
22349 hypothetical protein

22349 - hypothetical protein

GO Terms:

GO:0004365, GO:0006096, GO:0051287, GO:0006508, GO:0008237, GO:0008270

CD Domains:

Go To Gene Page:

22349
23170 hypothetical protein

23170 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23170
23618 RING

23618 - RING

GO Terms:

GO:0000151, GO:0004842, GO:0008270, GO:0016567

CD Domains:

Go To Gene Page:

23618
261381 Rab5_related

261381 - Rab5_related

GO Terms:

GO:0005525, GO:0007264, GO:0006886, GO:0015031, GO:0003924, GO:0003925

CD Domains:

Go To Gene Page:

261381
261827 PDI_a_family

261827 - PDI_a_family

GO Terms:

GO:0005489, GO:0006118, GO:0003756

CD Domains:

Go To Gene Page:

261827
263742 Synaptobrevin

263742 - Synaptobrevin

GO Terms:

GO:0016021, GO:0016192

CD Domains:

Go To Gene Page:

263742
27352 PLN00158

27352 - PLN00158

GO Terms:

GO:0000786, GO:0003677, GO:0005634, GO:0006334, GO:0007001

CD Domains:

Go To Gene Page:

27352
27377 Peptidase_S9

27377 - Peptidase_S9

GO Terms:

GO:0003824, GO:0006508, GO:0008236, GO:0004254

CD Domains:

Go To Gene Page:

27377
32945 (SDH1) sdhB

32945 - (SDH1) sdhB

GO Terms:

GO:0005489, GO:0005506, GO:0006118, GO:0006099, GO:0016491, GO:0008177

CD Domains:

Go To Gene Page:

32945
3359 hypothetical protein

3359 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

3359
3426 zf-DNL superfamily

3426 - zf-DNL superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

3426
34738 AAA_12 superfamily

34738 - AAA_12 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

34738
35407 PLN00157

35407 - PLN00157

GO Terms:

GO:0000786, GO:0003677, GO:0005634, GO:0006334, GO:0007001

CD Domains:

Go To Gene Page:

35407
36076 HDAC_classIV

36076 - HDAC_classIV

GO Terms:

NA

CD Domains:

Go To Gene Page:

36076
36764 PRK05279

36764 - PRK05279

GO Terms:

GO:0008080, GO:0004042, GO:0005737, GO:0006526

CD Domains:

Go To Gene Page:

36764
39847 (APM2) AP-2_Mu2_Cterm

39847 - (APM2) AP-2_Mu2_Cterm

GO Terms:

GO:0006886, GO:0030125

CD Domains:

Go To Gene Page:

39847
40586 (GMD1) PLN02653

40586 - (GMD1) PLN02653

GO Terms:

GO:0008152, GO:0016491, GO:0008446, GO:0009058

CD Domains:

Go To Gene Page:

40586
4774 hypothetical protein

4774 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

4774
7012 hypothetical protein

7012 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

7012
8058 hypothetical protein

8058 - hypothetical protein

GO Terms:

GO:0005509

CD Domains:

Go To Gene Page:

8058
GO ID Go Term p-value q-value Cluster
GO:0007001 chromosome organization and biogenesis (sensu Eukaryota) 0.00616834 1 Thaps_bicluster_0269
GO:0006334 nucleosome assembly 0.00702986 1 Thaps_bicluster_0269
GO:0006886 intracellular protein transport 0.0204396 1 Thaps_bicluster_0269
GO:0006526 arginine biosynthesis 0.0366334 1 Thaps_bicluster_0269
GO:0006099 tricarboxylic acid cycle 0.0406241 1 Thaps_bicluster_0269
GO:0016192 vesicle-mediated transport 0.0642408 1 Thaps_bicluster_0269
GO:0007264 small GTPase mediated signal transduction 0.131822 1 Thaps_bicluster_0269
GO:0006096 glycolysis 0.142624 1 Thaps_bicluster_0269
GO:0015031 protein transport 0.163848 1 Thaps_bicluster_0269
GO:0009058 biosynthesis 0.204806 1 Thaps_bicluster_0269
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