Thaps_bicluster_0225 Residual: 0.26
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_0225 0.26 Thalassiosira pseudonana
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Displaying 1 - 21 of 21
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1254 Chalcone superfamily

1254 - Chalcone superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

1254
1738 S14_ClpP_2

1738 - S14_ClpP_2

GO Terms:

GO:0006508, GO:0008462

CD Domains:

Go To Gene Page:

1738
2078 hypothetical protein

2078 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2078
21081 hypothetical protein

21081 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

21081
21821 hypothetical protein

21821 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

21821
2386 hypothetical protein

2386 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2386
24700 hypothetical protein

24700 - hypothetical protein

GO Terms:

GO:0006464, GO:0008113

CD Domains:

Go To Gene Page:

24700
261748 COG0523

261748 - COG0523

GO Terms:

NA

CD Domains:

Go To Gene Page:

261748
262796 (ACP3) acpP

262796 - (ACP3) acpP

GO Terms:

GO:0000036, GO:0006633, GO:0031177, GO:0048037

CD Domains:

Go To Gene Page:

262796
262849 Chromate_transp

262849 - Chromate_transp

GO Terms:

GO:0015109, GO:0015703

CD Domains:

Go To Gene Page:

262849
270242 (PsbM) photosystem II reaction center M protein, plastid precursor

270242 - (PsbM) photosystem II reaction center M protein, plastid precursor

GO Terms:

NA

CD Domains:

Go To Gene Page:

270242
31673 PRK05481

31673 - PRK05481

GO Terms:

GO:0009107, GO:0016992, GO:0003824, GO:0005506

CD Domains:

Go To Gene Page:

31673
32955 QOR2

32955 - QOR2

GO Terms:

GO:0008270, GO:0016491, GO:0003960

CD Domains:

Go To Gene Page:

32955
33000 FTHFS

33000 - FTHFS

GO Terms:

GO:0004329, GO:0005524, GO:0009396

CD Domains:

Go To Gene Page:

33000
3353 FMN_dh

3353 - FMN_dh

GO Terms:

GO:0006118, GO:0016491, GO:0003973, GO:0008891, GO:0009339

CD Domains:

Go To Gene Page:

3353
34030 (MAO1) PLN03129

34030 - (MAO1) PLN03129

GO Terms:

GO:0004470, GO:0006108, GO:0004471

CD Domains:

Go To Gene Page:

34030
34585 PLN02389

34585 - PLN02389

GO Terms:

GO:0004076, GO:0009102, GO:0003824, GO:0005506

CD Domains:

Go To Gene Page:

34585
36462 (TPI3) TIM

36462 - (TPI3) TIM

GO Terms:

GO:0004807, GO:0008152

CD Domains:

Go To Gene Page:

36462
4370 hypothetical protein

4370 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

4370
5576 DUF1499 superfamily

5576 - DUF1499 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

5576
9485 mTERF superfamily

9485 - mTERF superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

9485
GO ID Go Term p-value q-value Cluster
GO:0015703 chromate transport 0.00227414 1 Thaps_bicluster_0225
GO:0009102 biotin biosynthesis 0.00454357 1 Thaps_bicluster_0225
GO:0006108 malate metabolism 0.00680831 1 Thaps_bicluster_0225
GO:0009107 lipoate biosynthesis 0.00906837 1 Thaps_bicluster_0225
GO:0009396 folic acid and derivative biosynthesis 0.0158205 1 Thaps_bicluster_0225
GO:0006633 fatty acid biosynthesis 0.0424129 1 Thaps_bicluster_0225
GO:0006464 protein modification 0.126406 1 Thaps_bicluster_0225
GO:0006412 protein biosynthesis 0.319237 1 Thaps_bicluster_0225
GO:0006118 electron transport 0.463588 1 Thaps_bicluster_0225
GO:0006508 proteolysis and peptidolysis 0.491343 1 Thaps_bicluster_0225
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