Thaps_bicluster_0120 Residual: 0.39
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_0120 0.39 Thalassiosira pseudonana
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Displaying 1 - 22 of 22
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21155 hypothetical protein

21155 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

21155
22822 NTF2

22822 - NTF2

GO Terms:

GO:0005622, GO:0005634, GO:0006606, GO:0008565

CD Domains:

Go To Gene Page:

22822
25662 hypothetical protein

25662 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25662
261766 PGP_euk

261766 - PGP_euk

GO Terms:

GO:0003824, GO:0008152, GO:0016787

CD Domains:

Go To Gene Page:

261766
263770 hypothetical protein

263770 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

263770
268187 (ycf19_1) COG0762

268187 - (ycf19_1) COG0762

GO Terms:

GO:0016020

CD Domains:

Go To Gene Page:

268187
268668 HAD_like

268668 - HAD_like

GO Terms:

GO:0000105, GO:0004401

CD Domains:

Go To Gene Page:

268668
31402 DUF3007 superfamily

31402 - DUF3007 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

31402
31951 MMT1

31951 - MMT1

GO Terms:

GO:0006812, GO:0008324, GO:0016020

CD Domains:

Go To Gene Page:

31951
3341 hypothetical protein

3341 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

3341
33780 UBQ superfamily

33780 - UBQ superfamily

GO Terms:

GO:0006464

CD Domains:

Go To Gene Page:

33780
36879 BolA

36879 - BolA

GO Terms:

GO:0004496

CD Domains:

Go To Gene Page:

36879
40788 NADB_Rossmann superfamily

40788 - NADB_Rossmann superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

40788
4331 Aldolase_Class_I superfamily

4331 - Aldolase_Class_I superfamily

GO Terms:

GO:0005975, GO:0004801

CD Domains:

Go To Gene Page:

4331
5601 hypothetical protein

5601 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

5601
6173 hypothetical protein

6173 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

6173
6383 PTZ00162

6383 - PTZ00162

GO Terms:

GO:0003899, GO:0006350, GO:0003900, GO:0003901, GO:0003902

CD Domains:

Go To Gene Page:

6383
7611 hypothetical protein

7611 - hypothetical protein

GO Terms:

GO:0003676

CD Domains:

Go To Gene Page:

7611
8954 hypothetical protein

8954 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

8954
9490 hypothetical protein

9490 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

9490
968 RimI

968 - RimI

GO Terms:

GO:0008080

CD Domains:

Go To Gene Page:

968
GO ID Go Term p-value q-value Cluster
GO:0006606 protein-nucleus import 0.00557274 1 Thaps_bicluster_0120
GO:0000105 histidine biosynthesis 0.0147993 1 Thaps_bicluster_0120
GO:0006636 fatty acid desaturation 0.0221257 1 Thaps_bicluster_0120
GO:0006350 transcription 0.0544987 1 Thaps_bicluster_0120
GO:0006812 cation transport 0.0772831 1 Thaps_bicluster_0120
GO:0006464 protein modification 0.104655 1 Thaps_bicluster_0120
GO:0005975 carbohydrate metabolism 0.131302 1 Thaps_bicluster_0120
GO:0006508 proteolysis and peptidolysis 0.424754 1 Thaps_bicluster_0120
GO:0008152 metabolism 0.546944 1 Thaps_bicluster_0120
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