Thaps_bicluster_0174 Residual: 0.29
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_0174 0.29 Thalassiosira pseudonana
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Displaying 1 - 19 of 19
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11460 hypothetical protein

11460 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

11460
1875 hypothetical protein

1875 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1875
2039 hypothetical protein

2039 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2039
23593 hypothetical protein

23593 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23593
261242 (PSBP) PsbP superfamily

261242 - (PSBP) PsbP superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

261242
261284 Aldo_ket_red

261284 - Aldo_ket_red

GO Terms:

GO:0016491, GO:0050236

CD Domains:

Go To Gene Page:

261284
261935 thioredoxin

261935 - thioredoxin

GO Terms:

GO:0005489, GO:0006118

CD Domains:

Go To Gene Page:

261935
263116 rubredoxin

263116 - rubredoxin

GO Terms:

GO:0006118, GO:0046872

CD Domains:

Go To Gene Page:

263116
263902 PT_UbiA_HPT1

263902 - PT_UbiA_HPT1

GO Terms:

GO:0004659, GO:0016021

CD Domains:

Go To Gene Page:

263902
268669 hypothetical protein

268669 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

268669
2770 hypothetical protein

2770 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2770
31294 DUF1230 superfamily

31294 - DUF1230 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

31294
37599 hypothetical protein

37599 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

37599
3845 hypothetical protein

3845 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

3845
38769 PLN00033

38769 - PLN00033

GO Terms:

NA

CD Domains:

Go To Gene Page:

38769
40966 (Tp_sigma70.6) Sig70-cyanoRpoD

40966 - (Tp_sigma70.6) Sig70-cyanoRpoD

GO Terms:

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

CD Domains:

Go To Gene Page:

40966
5928 hypothetical protein

5928 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

5928
7583 DUF1995 superfamily

7583 - DUF1995 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

7583
8293 hypothetical protein

8293 - hypothetical protein

GO Terms:

GO:0005515

CD Domains:

Go To Gene Page:

8293
GO ID Go Term p-value q-value Cluster
GO:0006352 transcription initiation 0.0133715 1 Thaps_bicluster_0174
GO:0006118 electron transport 0.0269761 1 Thaps_bicluster_0174
GO:0015031 protein transport 0.0436835 1 Thaps_bicluster_0174
GO:0006355 regulation of transcription, DNA-dependent 0.27964 1 Thaps_bicluster_0174
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