Thaps_bicluster_0171 Residual: 0.35
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_0171 0.35 Thalassiosira pseudonana
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Displaying 1 - 24 of 24
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11826 Zip superfamily

11826 - Zip superfamily

GO Terms:

GO:0016020, GO:0030001, GO:0046873

CD Domains:

Go To Gene Page:

11826
11960 hypothetical protein

11960 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

11960
13021 metallo-dependent_hydrolases superfamily

13021 - metallo-dependent_hydrolases superfamily

GO Terms:

GO:0009168, GO:0019239, GO:0003876

CD Domains:

Go To Gene Page:

13021
16082 Solute_trans_a

16082 - Solute_trans_a

GO Terms:

NA

CD Domains:

Go To Gene Page:

16082
1762 PRA1 superfamily

1762 - PRA1 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

1762
22056 hypothetical protein

22056 - hypothetical protein

GO Terms:

GO:0004003, GO:0004004, GO:0008026, GO:0008094, GO:0008186, GO:0015462, GO:0015616, GO:0016887, GO:0017116, GO:0042623, GO:0042624, GO:0042625, GO:0042626

CD Domains:

Go To Gene Page:

22056
22231 hypothetical protein

22231 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22231
22468 hypothetical protein

22468 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22468
25231 hypothetical protein

25231 - hypothetical protein

GO Terms:

GO:0008080

CD Domains:

Go To Gene Page:

25231
25846 PDI_a_family

25846 - PDI_a_family

GO Terms:

GO:0005489, GO:0006118, GO:0003756

CD Domains:

Go To Gene Page:

25846
261414 2A0109

261414 - 2A0109

GO Terms:

GO:0005215, GO:0006810, GO:0016021

CD Domains:

Go To Gene Page:

261414
262163 hypothetical protein

262163 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

262163
29547 (PNP1) PNP_UDP_1 superfamily

29547 - (PNP1) PNP_UDP_1 superfamily

GO Terms:

GO:0016763, GO:0004731, GO:0006139

CD Domains:

Go To Gene Page:

29547
3167 hypothetical protein

3167 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

3167
3483 hypothetical protein

3483 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

3483
39767 TLP_HIUase

39767 - TLP_HIUase

GO Terms:

GO:0005386, GO:0005496, GO:0006810

CD Domains:

Go To Gene Page:

39767
4569 hypothetical protein

4569 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

4569
4677 PKc_like superfamily

4677 - PKc_like superfamily

GO Terms:

GO:0004672, GO:0005524, GO:0006468, GO:0004713, GO:0004674

CD Domains:

Go To Gene Page:

4677
5225 Nsp1_C superfamily

5225 - Nsp1_C superfamily

GO Terms:

GO:0005643, GO:0017056

CD Domains:

Go To Gene Page:

5225
5315 hypothetical protein

5315 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

5315
7032 DUF2358 superfamily

7032 - DUF2358 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

7032
7081 Peptidase_S9 superfamily

7081 - Peptidase_S9 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

7081
8472 Hydrolase_4

8472 - Hydrolase_4

GO Terms:

GO:0003824, GO:0047372

CD Domains:

Go To Gene Page:

8472
9729 COG0398

9729 - COG0398

GO Terms:

NA

CD Domains:

Go To Gene Page:

9729
GO ID Go Term p-value q-value Cluster
GO:0009168 purine ribonucleoside monophosphate biosynthesis 0.00433615 1 Thaps_bicluster_0171
GO:0030001 metal ion transport 0.0186738 1 Thaps_bicluster_0171
GO:0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolism 0.02152 1 Thaps_bicluster_0171
GO:0006810 transport 0.026643 1 Thaps_bicluster_0171
GO:0006468 protein amino acid phosphorylation 0.270534 1 Thaps_bicluster_0171
GO:0006118 electron transport 0.327122 1 Thaps_bicluster_0171
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