Thaps_bicluster_0116 Residual: 0.38
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_0116 0.38 Thalassiosira pseudonana
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Displaying 1 - 28 of 28
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10068 hypothetical protein

10068 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

10068
10567 (GFA_2) PTZ00295

10567 - (GFA_2) PTZ00295

GO Terms:

GO:0008152, GO:0005529, GO:0005975, GO:0004360

CD Domains:

Go To Gene Page:

10567
10802 MPP_PhoD

10802 - MPP_PhoD

GO Terms:

NA

CD Domains:

Go To Gene Page:

10802
11734 hypothetical protein

11734 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

11734
2287 AAA_17 superfamily

2287 - AAA_17 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

2287
23556 hypothetical protein

23556 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23556
23726 hypothetical protein

23726 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23726
24882 hypothetical protein

24882 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

24882
24950 hypothetical protein

24950 - hypothetical protein

GO Terms:

GO:0000074

CD Domains:

Go To Gene Page:

24950
24953 hypothetical protein

24953 - hypothetical protein

GO Terms:

GO:0000074

CD Domains:

Go To Gene Page:

24953
25062 PA superfamily

25062 - PA superfamily

GO Terms:

GO:0006508, GO:0008233

CD Domains:

Go To Gene Page:

25062
25387 hypothetical protein

25387 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25387
2595 RNase_HI_like

2595 - RNase_HI_like

GO Terms:

GO:0003676, GO:0004523

CD Domains:

Go To Gene Page:

2595
26136 MRS6 superfamily

26136 - MRS6 superfamily

GO Terms:

GO:0005093, GO:0015031, GO:0043087

CD Domains:

Go To Gene Page:

26136
261711 Sulfotransfer_1 superfamily

261711 - Sulfotransfer_1 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

261711
261744 PTZ00088

261744 - PTZ00088

GO Terms:

GO:0005524, GO:0006139, GO:0019201, GO:0004017

CD Domains:

Go To Gene Page:

261744
268228 2A0106

268228 - 2A0106

GO Terms:

GO:0005215, GO:0006810, GO:0016021

CD Domains:

Go To Gene Page:

268228
269456 CBS_pair superfamily

269456 - CBS_pair superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

269456
2973 hypothetical protein

2973 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2973
33096 UNC-50

33096 - UNC-50

GO Terms:

NA

CD Domains:

Go To Gene Page:

33096
34187 (ACAS2) PRK00174

34187 - (ACAS2) PRK00174

GO Terms:

GO:0003824, GO:0008152, GO:0003987

CD Domains:

Go To Gene Page:

34187
39696 PTZ00295

39696 - PTZ00295

GO Terms:

GO:0008152, GO:0005529, GO:0005975, GO:0004360

CD Domains:

Go To Gene Page:

39696
5584 P4Hc

5584 - P4Hc

GO Terms:

GO:0016706, GO:0019538, GO:0000907, GO:0018602, GO:0019798, GO:0045432, GO:0045442

CD Domains:

Go To Gene Page:

5584
6480 P4Hc

6480 - P4Hc

GO Terms:

GO:0016706, GO:0019538

CD Domains:

Go To Gene Page:

6480
6963 hypothetical protein

6963 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

6963
7617 hypothetical protein

7617 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

7617
7878 hypothetical protein

7878 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

7878
8497 (Tp_bZIP9) regulator [Rayko]

8497 - (Tp_bZIP9) regulator [Rayko]

GO Terms:

GO:0003677, GO:0005634, GO:0006355

CD Domains:

Go To Gene Page:

8497
GO ID Go Term p-value q-value Cluster
GO:0019538 protein metabolism 0.00858751 1 Thaps_bicluster_0116
GO:0000074 regulation of cell cycle 0.014323 1 Thaps_bicluster_0116
GO:0005975 carbohydrate metabolism 0.0218621 1 Thaps_bicluster_0116
GO:0043087 regulation of GTPase activity 0.0306099 1 Thaps_bicluster_0116
GO:0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolism 0.0455847 1 Thaps_bicluster_0116
GO:0015031 protein transport 0.125531 1 Thaps_bicluster_0116
GO:0008152 metabolism 0.126308 1 Thaps_bicluster_0116
GO:0006810 transport 0.441554 1 Thaps_bicluster_0116
GO:0006508 proteolysis and peptidolysis 0.602351 1 Thaps_bicluster_0116
GO:0006355 regulation of transcription, DNA-dependent 0.626585 1 Thaps_bicluster_0116
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