Thaps_bicluster_0094 Residual: 0.37
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_0094 0.37 Thalassiosira pseudonana
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Displaying 1 - 25 of 25
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11397 hypothetical protein

11397 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

11397
15027 PLN00137

15027 - PLN00137

GO Terms:

NA

CD Domains:

Go To Gene Page:

15027
22579 Sec62 superfamily

22579 - Sec62 superfamily

GO Terms:

GO:0008565, GO:0015031, GO:0016021

CD Domains:

Go To Gene Page:

22579
261636

261636 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

261636
261637 AhpC-TSA_2

261637 - AhpC-TSA_2

GO Terms:

NA

CD Domains:

Go To Gene Page:

261637
262254 Uup

262254 - Uup

GO Terms:

GO:0005524, GO:0016887, GO:0000166, GO:0017111

CD Domains:

Go To Gene Page:

262254
268875 hypothetical protein

268875 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

268875
269759 hypothetical protein

269759 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

269759
270249 (NTT3) hypothetical protein

270249 - (NTT3) hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

270249
270314 hypothetical protein

270314 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

270314
270321 hypothetical protein

270321 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

270321
33046 PLN02265

33046 - PLN02265

GO Terms:

GO:0004826, GO:0005524, GO:0005737, GO:0006432, GO:0009328

CD Domains:

Go To Gene Page:

33046
33937 cyt_b5_reduct_like

33937 - cyt_b5_reduct_like

GO Terms:

GO:0006118, GO:0016491, GO:0004128

CD Domains:

Go To Gene Page:

33937
3461 PRK00927

3461 - PRK00927

GO Terms:

GO:0004812, GO:0005524, GO:0006418, GO:0004830, GO:0006436

CD Domains:

Go To Gene Page:

3461
34864 FkpA

34864 - FkpA

GO Terms:

GO:0006457, GO:0003755, GO:0004600, GO:0030051, GO:0042027

CD Domains:

Go To Gene Page:

34864
38030 ABM superfamily

38030 - ABM superfamily

GO Terms:

GO:0005737, GO:0016491, GO:0017000

CD Domains:

Go To Gene Page:

38030
3932 hypothetical protein

3932 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

3932
39622 NAC

39622 - NAC

GO Terms:

NA

CD Domains:

Go To Gene Page:

39622
6264 PLN02256

6264 - PLN02256

GO Terms:

NA

CD Domains:

Go To Gene Page:

6264
9512 PTZ00168

9512 - PTZ00168

GO Terms:

GO:0005488, GO:0006810, GO:0016020, GO:0005743

CD Domains:

Go To Gene Page:

9512
9830 (CBL1) CGS_like

9830 - (CBL1) CGS_like

GO Terms:

GO:0006520, GO:0003962

CD Domains:

Go To Gene Page:

9830
ThpsCp050 (petG) cytochrome b6/f complex subunit V

ThpsCp050 - (petG) cytochrome b6/f complex subunit V

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp050
ThpsCp055 (ycf12) Ycf12

ThpsCp055 - (ycf12) Ycf12

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp055
ThpsCp070 (ycf39) Ycf39

ThpsCp070 - (ycf39) Ycf39

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp070
ThpsCp140 (psbY) photosystem II protein Y

ThpsCp140 - (psbY) photosystem II protein Y

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp140
GO ID Go Term p-value q-value Cluster
GO:0015031 protein transport 0.0772831 1 Thaps_bicluster_0094
GO:0006418 tRNA aminoacylation for protein translation 0.101273 1 Thaps_bicluster_0094
GO:0006457 protein folding 0.217609 1 Thaps_bicluster_0094
GO:0006810 transport 0.294845 1 Thaps_bicluster_0094
GO:0006118 electron transport 0.399203 1 Thaps_bicluster_0094
GO:0006436 tryptophanyl-tRNA aminoacylation 0.00371824 1 Thaps_bicluster_0094
GO:0006432 phenylalanyl-tRNA aminoacylation 0.00742418 1 Thaps_bicluster_0094
GO:0017000 antibiotic biosynthesis 0.00927255 1 Thaps_bicluster_0094
GO:0006520 amino acid metabolism 0.0384333 1 Thaps_bicluster_0094
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