Thaps_bicluster_0130 Residual: 0.40
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_0130 0.40 Thalassiosira pseudonana
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Displaying 1 - 25 of 25
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11739 hypothetical protein

11739 - hypothetical protein

GO Terms:

GO:0003824, GO:0008152

CD Domains:

Go To Gene Page:

11739
12662 COG2907

12662 - COG2907

GO Terms:

GO:0008757, GO:0006118, GO:0008610, GO:0008825

CD Domains:

Go To Gene Page:

12662
1512 hypothetical protein

1512 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1512
1626 Acid_PPase superfamily

1626 - Acid_PPase superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

1626
21194 hypothetical protein

21194 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

21194
2262 SNc superfamily

2262 - SNc superfamily

GO Terms:

GO:0003676, GO:0004518

CD Domains:

Go To Gene Page:

2262
23698 DUF4336 superfamily

23698 - DUF4336 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

23698
2441 Thymidylate_kin

2441 - Thymidylate_kin

GO Terms:

GO:0004798, GO:0005524, GO:0006233, GO:0006235

CD Domains:

Go To Gene Page:

2441
25513 Mnd1

25513 - Mnd1

GO Terms:

NA

CD Domains:

Go To Gene Page:

25513
261525 CypX

261525 - CypX

GO Terms:

GO:0004497, GO:0006118

CD Domains:

Go To Gene Page:

261525
261582 PKCI_related

261582 - PKCI_related

GO Terms:

NA

CD Domains:

Go To Gene Page:

261582
26436 Dcp

26436 - Dcp

GO Terms:

GO:0004222, GO:0006508, GO:0008237, GO:0008270, GO:0008944

CD Domains:

Go To Gene Page:

26436
2690 WD40 superfamily

2690 - WD40 superfamily

GO Terms:

GO:0003676

CD Domains:

Go To Gene Page:

2690
269110 hypothetical protein

269110 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

269110
30851 (CLPC2) clpA

30851 - (CLPC2) clpA

GO Terms:

GO:0005524, GO:0004176, GO:0004252, GO:0006508, GO:0000166, GO:0017111, GO:0008462

CD Domains:

Go To Gene Page:

30851
32206 Fer4_15

32206 - Fer4_15

GO Terms:

GO:0005489, GO:0006118, GO:0005506

CD Domains:

Go To Gene Page:

32206
38285 (PMSR1) MsrA

38285 - (PMSR1) MsrA

GO Terms:

GO:0006464, GO:0008113

CD Domains:

Go To Gene Page:

38285
5288 DUF393 superfamily

5288 - DUF393 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

5288
5635 hypothetical protein

5635 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

5635
6122 hypothetical protein

6122 - hypothetical protein

GO Terms:

GO:0008080, GO:0004182, GO:0006508

CD Domains:

Go To Gene Page:

6122
6138 hypothetical protein

6138 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

6138
6176 hypothetical protein

6176 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

6176
7716 (Tp_CCCH27_RING95) regulator [Rayko]

7716 - (Tp_CCCH27_RING95) regulator [Rayko]

GO Terms:

GO:0003676, GO:0000151, GO:0004842, GO:0008270, GO:0016567

CD Domains:

Go To Gene Page:

7716
8065 hypothetical protein

8065 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

8065
9483 CoAse

9483 - CoAse

GO Terms:

NA

CD Domains:

Go To Gene Page:

9483
GO ID Go Term p-value q-value Cluster
GO:0006233 dTDP biosynthesis 0.00248088 1 Thaps_bicluster_0130
GO:0006235 dTTP biosynthesis 0.00248088 1 Thaps_bicluster_0130
GO:0008610 lipid biosynthesis 0.00742571 1 Thaps_bicluster_0130
GO:0006118 electron transport 0.024985 1 Thaps_bicluster_0130
GO:0006508 proteolysis and peptidolysis 0.0307611 1 Thaps_bicluster_0130
GO:0006464 protein modification 0.137086 1 Thaps_bicluster_0130
GO:0016567 protein ubiquitination 0.179494 1 Thaps_bicluster_0130
GO:0008152 metabolism 0.652155 1 Thaps_bicluster_0130
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