Thaps_bicluster_0179 Residual: 0.28
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_0179 0.28 Thalassiosira pseudonana
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Displaying 1 - 15 of 15
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21709 hypothetical protein

21709 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

21709
22356 PseudoU_synth_ScPUS7

22356 - PseudoU_synth_ScPUS7

GO Terms:

GO:0003676, GO:0004730, GO:0008033, GO:0009982, GO:0042299, GO:0042300

CD Domains:

Go To Gene Page:

22356
23812 TrmA

23812 - TrmA

GO Terms:

NA

CD Domains:

Go To Gene Page:

23812
24015 Urb2 superfamily

24015 - Urb2 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

24015
24038 hypothetical protein

24038 - hypothetical protein

GO Terms:

GO:0000287, GO:0008152, GO:0016462

CD Domains:

Go To Gene Page:

24038
260748 AdoMet_MTases superfamily

260748 - AdoMet_MTases superfamily

GO Terms:

GO:0008757, GO:0003723, GO:0004809, GO:0008033

CD Domains:

Go To Gene Page:

260748
264188 COG1026

264188 - COG1026

GO Terms:

GO:0004222, GO:0006508

CD Domains:

Go To Gene Page:

264188
268412 RluA

268412 - RluA

GO Terms:

GO:0003723, GO:0006396, GO:0009982, GO:0004730, GO:0016439

CD Domains:

Go To Gene Page:

268412
269080 PLN02327

269080 - PLN02327

GO Terms:

GO:0003824, GO:0003883, GO:0006221

CD Domains:

Go To Gene Page:

269080
32668 CRCB

32668 - CRCB

GO Terms:

GO:0016020

CD Domains:

Go To Gene Page:

32668
32882 PRK15440

32882 - PRK15440

GO Terms:

GO:0003824, GO:0008152

CD Domains:

Go To Gene Page:

32882
34596 WD40

34596 - WD40

GO Terms:

GO:0003847

CD Domains:

Go To Gene Page:

34596
5794 hypothetical protein

5794 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

5794
GO ID Go Term p-value q-value Cluster
GO:0008033 tRNA processing 0.000271696 0.742002 Thaps_bicluster_0179
GO:0006221 pyrimidine nucleotide biosynthesis 0.00433615 1 Thaps_bicluster_0179
GO:0006396 RNA processing 0.081025 1 Thaps_bicluster_0179
GO:0008152 metabolism 0.111784 1 Thaps_bicluster_0179
GO:0006508 proteolysis and peptidolysis 0.349482 1 Thaps_bicluster_0179
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