Thaps_bicluster_0192 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_0192 0.36 Thalassiosira pseudonana
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Displaying 1 - 19 of 19
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20583 hypothetical protein

20583 - hypothetical protein

GO Terms:

GO:0003676, GO:0005622

CD Domains:

Go To Gene Page:

20583
20731 Mito_carr

20731 - Mito_carr

GO Terms:

GO:0005488, GO:0006810, GO:0016020, GO:0005215, GO:0005743

CD Domains:

Go To Gene Page:

20731
22200 hypothetical protein

22200 - hypothetical protein

GO Terms:

GO:0006457, GO:0031072, GO:0051082

CD Domains:

Go To Gene Page:

22200
23718 hypothetical protein

23718 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23718
24977 TRAUB superfamily

24977 - TRAUB superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

24977
25582 hypothetical protein

25582 - hypothetical protein

GO Terms:

GO:0003676, GO:0003755, GO:0004600, GO:0030051, GO:0042027

CD Domains:

Go To Gene Page:

25582
26022 Pam16 superfamily

26022 - Pam16 superfamily

GO Terms:

GO:0005554

CD Domains:

Go To Gene Page:

26022
262862 rimM

262862 - rimM

GO Terms:

GO:0006364, GO:0007046

CD Domains:

Go To Gene Page:

262862
26366 Mito_carr

26366 - Mito_carr

GO Terms:

GO:0005488, GO:0006810, GO:0016020, GO:0005743, GO:0005215

CD Domains:

Go To Gene Page:

26366
26941 (NIR_1) PRK14989

26941 - (NIR_1) PRK14989

GO Terms:

GO:0006118, GO:0015036, GO:0016491, GO:0016656

CD Domains:

Go To Gene Page:

26941
32066 Mito_carr

32066 - Mito_carr

GO Terms:

GO:0005488, GO:0006810, GO:0016020, GO:0005743, GO:0005215

CD Domains:

Go To Gene Page:

32066
33682 (Tp_sigma70.3a) Sig70-cyanoRpoD

33682 - (Tp_sigma70.3a) Sig70-cyanoRpoD

GO Terms:

GO:0003677, GO:0003700, GO:0006352, GO:0006355, GO:0016987

CD Domains:

Go To Gene Page:

33682
35041 COG1094

35041 - COG1094

GO Terms:

GO:0003676

CD Domains:

Go To Gene Page:

35041
36539 hypothetical protein

36539 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

36539
3919 Nop25

3919 - Nop25

GO Terms:

NA

CD Domains:

Go To Gene Page:

3919
39286 Uup

39286 - Uup

GO Terms:

GO:0005524, GO:0016887, GO:0000166, GO:0017111

CD Domains:

Go To Gene Page:

39286
4408 hypothetical protein

4408 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

4408
5130 COG0790

5130 - COG0790

GO Terms:

NA

CD Domains:

Go To Gene Page:

5130
GO ID Go Term p-value q-value Cluster
GO:0006810 transport 0.00383948 1 Thaps_bicluster_0192
GO:0007046 ribosome biogenesis 0.00742418 1 Thaps_bicluster_0192
GO:0006364 rRNA processing 0.0147993 1 Thaps_bicluster_0192
GO:0006352 transcription initiation 0.0239497 1 Thaps_bicluster_0192
GO:0006457 protein folding 0.217609 1 Thaps_bicluster_0192
GO:0006118 electron transport 0.399203 1 Thaps_bicluster_0192
GO:0006355 regulation of transcription, DNA-dependent 0.446038 1 Thaps_bicluster_0192
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