Thaps_bicluster_0288 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_0288 0.28 Thalassiosira pseudonana
Displaying 1 - 18 of 18
12152 PRK07967

12152 - PRK07967

GO Terms:

GO:0004197, GO:0006508, GO:0003824, GO:0006633, GO:0004315

CD Domains:

Go To Gene Page:

12152
1584 cyclophilin

1584 - cyclophilin

GO Terms:

GO:0006457

CD Domains:

Go To Gene Page:

1584
1637 hypothetical protein

1637 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1637
20194 hypothetical protein

20194 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

20194
21175 (TKT2) PLN02790

21175 - (TKT2) PLN02790

GO Terms:

GO:0004802

CD Domains:

Go To Gene Page:

21175
21261 hypothetical protein

21261 - hypothetical protein

GO Terms:

GO:0006118, GO:0046872

CD Domains:

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21261
22214 hypothetical protein

22214 - hypothetical protein

GO Terms:

NA

CD Domains:

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22214
2343 hypothetical protein

2343 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2343
261226 thylakoid lumenal 17.4 kDa protein, chloroplast precursor

261226 - thylakoid lumenal 17.4 kDa protein, chloroplast precursor

GO Terms:

NA

CD Domains:

Go To Gene Page:

261226
26131 PRK13474

26131 - PRK13474

GO Terms:

GO:0006118, GO:0008121, GO:0016020, GO:0045285, GO:0016491, GO:0009496

CD Domains:

Go To Gene Page:

26131
30976 FKBP_C

30976 - FKBP_C

GO Terms:

GO:0006457

CD Domains:

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30976
32332 RPI_A

32332 - RPI_A

GO Terms:

GO:0004751, GO:0009052

CD Domains:

Go To Gene Page:

32332
32924 RPE

32924 - RPE

GO Terms:

GO:0004750, GO:0005975

CD Domains:

Go To Gene Page:

32924
33701 DUF4079

33701 - DUF4079

GO Terms:

NA

CD Domains:

Go To Gene Page:

33701
37198 (Tp_aureochrome2) PAS_9

37198 - (Tp_aureochrome2) PAS_9

GO Terms:

GO:0004871, GO:0007165, GO:0000155, GO:0000160

CD Domains:

Go To Gene Page:

37198
3883 hypothetical protein

3883 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

3883
4439 hypothetical protein

4439 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

4439
8713 hypothetical protein

8713 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

8713
GO ID Go Term p-value q-value Cluster
GO:0009052 pentose-phosphate shunt, non-oxidative branch 0.00413095 1 Thaps_bicluster_0288
GO:0006457 protein folding 0.0280077 1 Thaps_bicluster_0288
GO:0006633 fatty acid biosynthesis 0.0386288 1 Thaps_bicluster_0288
GO:0000160 two-component signal transduction system (phosphorelay) 0.0544877 1 Thaps_bicluster_0288
GO:0007165 signal transduction 0.0797569 1 Thaps_bicluster_0288
GO:0006118 electron transport 0.101293 1 Thaps_bicluster_0288
GO:0005975 carbohydrate metabolism 0.144797 1 Thaps_bicluster_0288
GO:0006508 proteolysis and peptidolysis 0.459068 1 Thaps_bicluster_0288
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