Thaps_bicluster_0201 Residual: 0.23
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_0201 0.23 Thalassiosira pseudonana
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Displaying 1 - 16 of 16
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10879 (Tpt4) hypothetical protein

10879 - (Tpt4) hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

10879
2341 (Lhcr12) fucoxanthin chlorophyll a/c protein

2341 - (Lhcr12) fucoxanthin chlorophyll a/c protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2341
258111 hypothetical protein

258111 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

258111
270210 (PsbO) oxygen-evolving enhancer protein 1 precursor

270210 - (PsbO) oxygen-evolving enhancer protein 1 precursor

GO Terms:

NA

CD Domains:

Go To Gene Page:

270210
270230 (Trx-f) thioredoxin f

270230 - (Trx-f) thioredoxin f

GO Terms:

NA

CD Domains:

Go To Gene Page:

270230
270304 hypothetical protein

270304 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

270304
270306 hypothetical protein

270306 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

270306
270308 hypothetical protein

270308 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

270308
270323 hypothetical protein

270323 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

270323
270336 hypothetical protein

270336 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

270336
270340 hypothetical protein

270340 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

270340
270348 hypothetical protein

270348 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

270348
35712 Phosphoglycerate_kinase

35712 - Phosphoglycerate_kinase

GO Terms:

GO:0004618, GO:0006096

CD Domains:

Go To Gene Page:

35712
4748 hypothetical protein

4748 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

4748
547 PRK11856

547 - PRK11856

GO Terms:

GO:0008152, GO:0008415, GO:0005515, GO:0004742, GO:0009351, GO:0030523

CD Domains:

Go To Gene Page:

547
6290 (NDK2) NDPk_I

6290 - (NDK2) NDPk_I

GO Terms:

GO:0004550, GO:0005524, GO:0006183, GO:0006228, GO:0006241

CD Domains:

Go To Gene Page:

6290
GO ID Go Term p-value q-value Cluster
GO:0006241 CTP biosynthesis 0.00721795 1 Thaps_bicluster_0201
GO:0006183 GTP biosynthesis 0.00721795 1 Thaps_bicluster_0201
GO:0006228 UTP biosynthesis 0.00721795 1 Thaps_bicluster_0201
GO:0006096 glycolysis 0.0376815 1 Thaps_bicluster_0201
GO:0008152 metabolism 0.355748 1 Thaps_bicluster_0201
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