Thaps_bicluster_0168 Residual: 0.24
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_0168 0.24 Thalassiosira pseudonana
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Displaying 1 - 15 of 15
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10647 hypothetical protein

10647 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

10647
11789 hypothetical protein

11789 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

11789
1754 Gst

1754 - Gst

GO Terms:

GO:0004364

CD Domains:

Go To Gene Page:

1754
2036 hypothetical protein

2036 - hypothetical protein

GO Terms:

GO:0008168

CD Domains:

Go To Gene Page:

2036
21042 hypothetical protein

21042 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

21042
21300 NADB_Rossmann superfamily

21300 - NADB_Rossmann superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

21300
2356 hypothetical protein

2356 - hypothetical protein

GO Terms:

GO:0005215, GO:0006810, GO:0016020

CD Domains:

Go To Gene Page:

2356
23918 hypothetical protein

23918 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23918
24512 hypothetical protein

24512 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

24512
268713 hypothetical protein

268713 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

268713
3853 DUF3493

3853 - DUF3493

GO Terms:

NA

CD Domains:

Go To Gene Page:

3853
3878 (PPI2) cyclophilin_ABH_like

3878 - (PPI2) cyclophilin_ABH_like

GO Terms:

GO:0006457, GO:0003755, GO:0004600, GO:0030051, GO:0042027

CD Domains:

Go To Gene Page:

3878
38924 PLN02627

38924 - PLN02627

GO Terms:

GO:0000049, GO:0004812, GO:0016876

CD Domains:

Go To Gene Page:

38924
6802 hypothetical protein

6802 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

6802
GO ID Go Term p-value q-value Cluster
GO:0006366 transcription from RNA polymerase II promoter 0.0010337 1 Thaps_bicluster_0168
GO:0006350 transcription 0.0306412 1 Thaps_bicluster_0168
GO:0006457 protein folding 0.127399 1 Thaps_bicluster_0168
GO:0006810 transport 0.176337 1 Thaps_bicluster_0168
GO:0006118 electron transport 0.24643 1 Thaps_bicluster_0168
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