Thaps_bicluster_0271 Residual: 0.35
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_0271 0.35 Thalassiosira pseudonana
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Displaying 1 - 25 of 25
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1196 hypothetical protein

1196 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1196
13647 (TMS1) PTZ00164

13647 - (TMS1) PTZ00164

GO Terms:

GO:0004799, GO:0006231, GO:0004146, GO:0006545, GO:0009165

CD Domains:

Go To Gene Page:

13647
20931 hypothetical protein

20931 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

20931
20977 COG0398

20977 - COG0398

GO Terms:

GO:0005554, GO:0016020

CD Domains:

Go To Gene Page:

20977
21916 hypothetical protein

21916 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

21916
2463 hypothetical protein

2463 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2463
24710 hypothetical protein

24710 - hypothetical protein

GO Terms:

GO:0000285

CD Domains:

Go To Gene Page:

24710
24711 hypothetical protein

24711 - hypothetical protein

GO Terms:

GO:0000786, GO:0003677, GO:0005634, GO:0007001, GO:0007283

CD Domains:

Go To Gene Page:

24711
25733 TRAM_LAG1_CLN8

25733 - TRAM_LAG1_CLN8

GO Terms:

GO:0016021, GO:0050291

CD Domains:

Go To Gene Page:

25733
262564 VATPase_H superfamily

262564 - VATPase_H superfamily

GO Terms:

GO:0003936, GO:0046933, GO:0046961

CD Domains:

Go To Gene Page:

262564
268857 Peptidase_C14

268857 - Peptidase_C14

GO Terms:

GO:0006508, GO:0030693

CD Domains:

Go To Gene Page:

268857
29053 V-ATPase_C superfamily

29053 - V-ATPase_C superfamily

GO Terms:

GO:0005524, GO:0015986, GO:0016469, GO:0016820, GO:0003936, GO:0046933, GO:0046961

CD Domains:

Go To Gene Page:

29053
29117 vATP-synt_E

29117 - vATP-synt_E

GO Terms:

GO:0015986, GO:0016469, GO:0046933, GO:0046961, GO:0003936

CD Domains:

Go To Gene Page:

29117
37509 (VAT3) vATP-synt_AC39 superfamily

37509 - (VAT3) vATP-synt_AC39 superfamily

GO Terms:

GO:0015986, GO:0016469, GO:0046933, GO:0046961, GO:0003936

CD Domains:

Go To Gene Page:

37509
37665 ATP-synt_F superfamily

37665 - ATP-synt_F superfamily

GO Terms:

GO:0015986, GO:0016469, GO:0046933, GO:0046961, GO:0003936

CD Domains:

Go To Gene Page:

37665
3952 hypothetical protein

3952 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

3952
40522 (VAT1) V-ATPase_V1_B

40522 - (VAT1) V-ATPase_V1_B

GO Terms:

GO:0005524, GO:0015986, GO:0016469, GO:0046933, GO:0046961, GO:0006754, GO:0005737, GO:0008553, GO:0015988, GO:0003936

CD Domains:

Go To Gene Page:

40522
4179 hypothetical protein

4179 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

4179
6105 hypothetical protein

6105 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

6105
6130 hypothetical protein

6130 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

6130
789 S_TKc

789 - S_TKc

GO Terms:

GO:0004672, GO:0005524, GO:0006468, GO:0004713, GO:0005509, GO:0004674

CD Domains:

Go To Gene Page:

789
8038 hypothetical protein

8038 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

8038
8041 hypothetical protein

8041 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

8041
8301 hypothetical protein

8301 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

8301
9849 SQR_TypeC_SdhC

9849 - SQR_TypeC_SdhC

GO Terms:

GO:0000104, GO:0006099, GO:0006118, GO:0016020, GO:0008177

CD Domains:

Go To Gene Page:

9849
GO ID Go Term p-value q-value Cluster
GO:0015986 ATP synthesis coupled proton transport 0.000000252 0.000695662 Thaps_bicluster_0271
GO:0006099 tricarboxylic acid cycle 0.0326202 1 Thaps_bicluster_0271
GO:0007001 chromosome organization and biogenesis (sensu Eukaryota) 0.0918683 1 Thaps_bicluster_0271
GO:0006468 protein amino acid phosphorylation 0.514074 1 Thaps_bicluster_0271
GO:0006118 electron transport 0.596044 1 Thaps_bicluster_0271
GO:0006508 proteolysis and peptidolysis 0.626101 1 Thaps_bicluster_0271
GO:0006231 dTMP biosynthesis 0.00330783 1 Thaps_bicluster_0271
GO:0015988 energy coupled proton transport, against electrochemical gradient 0.00330783 1 Thaps_bicluster_0271
GO:0006545 glycine biosynthesis 0.00660541 1 Thaps_bicluster_0271
GO:0007283 spermatogenesis 0.00660541 1 Thaps_bicluster_0271
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