Thaps_bicluster_0117 Residual: 0.49
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_0117 0.49 Thalassiosira pseudonana
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Displaying 1 - 24 of 24
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10343 hypothetical protein

10343 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

10343
1088 hypothetical protein

1088 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1088
11503 hypothetical protein

11503 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

11503
12030 PRK05764

12030 - PRK05764

GO Terms:

GO:0009058, GO:0016847, GO:0003824, GO:0016769, GO:0004069

CD Domains:

Go To Gene Page:

12030
1385 DUF4137

1385 - DUF4137

GO Terms:

GO:0006814, GO:0008508, GO:0016020

CD Domains:

Go To Gene Page:

1385
1429 hypothetical protein

1429 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1429
25721 hypothetical protein

25721 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25721
261756 pepN

261756 - pepN

GO Terms:

GO:0004179, GO:0006508, GO:0008237, GO:0008270

CD Domains:

Go To Gene Page:

261756
268911 methyl transferase

268911 - methyl transferase

GO Terms:

GO:0008757, GO:0008168, GO:0005737, GO:0008119, GO:0008152

CD Domains:

Go To Gene Page:

268911
2733 hypothetical protein

2733 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2733
30979 PKCI_related

30979 - PKCI_related

GO Terms:

NA

CD Domains:

Go To Gene Page:

30979
31110 (Tp_CSF2) CSP_CDS

31110 - (Tp_CSF2) CSP_CDS

GO Terms:

GO:0003677, GO:0006355

CD Domains:

Go To Gene Page:

31110
31923 DUF4336

31923 - DUF4336

GO Terms:

NA

CD Domains:

Go To Gene Page:

31923
32209 fer2

32209 - fer2

GO Terms:

GO:0005489, GO:0005506, GO:0006118

CD Domains:

Go To Gene Page:

32209
32285 COG1832

32285 - COG1832

GO Terms:

NA

CD Domains:

Go To Gene Page:

32285
3270 hypothetical protein

3270 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

3270
32745 PDI_a_family

32745 - PDI_a_family

GO Terms:

GO:0005489, GO:0006118, GO:0003756

CD Domains:

Go To Gene Page:

32745
35022 ICL_PEPM

35022 - ICL_PEPM

GO Terms:

GO:0003824, GO:0008152, GO:0008807

CD Domains:

Go To Gene Page:

35022
3524 hypothetical protein

3524 - hypothetical protein

GO Terms:

GO:0005488, GO:0006810, GO:0016020

CD Domains:

Go To Gene Page:

3524
36709 WcaG

36709 - WcaG

GO Terms:

NA

CD Domains:

Go To Gene Page:

36709
38322 Sar1

38322 - Sar1

GO Terms:

GO:0005525, GO:0007264, GO:0006886

CD Domains:

Go To Gene Page:

38322
5830 DUF3054

5830 - DUF3054

GO Terms:

NA

CD Domains:

Go To Gene Page:

5830
7208 Ras_like_GTPase superfamily

7208 - Ras_like_GTPase superfamily

GO Terms:

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

CD Domains:

Go To Gene Page:

7208
7239 hypothetical protein

7239 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

7239
GO ID Go Term p-value q-value Cluster
GO:0007264 small GTPase mediated signal transduction 0.00356404 1 Thaps_bicluster_0117
GO:0006814 sodium ion transport 0.0291995 1 Thaps_bicluster_0117
GO:0015031 protein transport 0.109729 1 Thaps_bicluster_0117
GO:0006886 intracellular protein transport 0.135954 1 Thaps_bicluster_0117
GO:0009058 biosynthesis 0.138303 1 Thaps_bicluster_0117
GO:0006118 electron transport 0.157847 1 Thaps_bicluster_0117
GO:0008152 metabolism 0.300056 1 Thaps_bicluster_0117
GO:0006810 transport 0.396381 1 Thaps_bicluster_0117
GO:0006508 proteolysis and peptidolysis 0.550247 1 Thaps_bicluster_0117
GO:0006355 regulation of transcription, DNA-dependent 0.574096 1 Thaps_bicluster_0117
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