Thaps_bicluster_0069 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_0069 0.35 Thalassiosira pseudonana
Displaying 1 - 22 of 22
20712 hypothetical protein

20712 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

20712
20859 SIR2 superfamily

20859 - SIR2 superfamily

GO Terms:

GO:0003677, GO:0005677, GO:0006342, GO:0006355, GO:0008939

CD Domains:

Go To Gene Page:

20859
22163 hypothetical protein

22163 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22163
22296 hypothetical protein

22296 - hypothetical protein

GO Terms:

GO:0003676, GO:0004308

CD Domains:

Go To Gene Page:

22296
23232 hypothetical protein

23232 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23232
2350 hypothetical protein

2350 - hypothetical protein

GO Terms:

GO:0006508, GO:0008236

CD Domains:

Go To Gene Page:

2350
23599 Cyto_heme_lyase superfamily

23599 - Cyto_heme_lyase superfamily

GO Terms:

GO:0004408, GO:0005739

CD Domains:

Go To Gene Page:

23599
25475 hypothetical protein

25475 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25475
263641 InfB

263641 - InfB

GO Terms:

GO:0003743, GO:0005525, GO:0006413, GO:0006412, GO:0003924, GO:0008547

CD Domains:

Go To Gene Page:

263641
26492 PRK05385

26492 - PRK05385

GO Terms:

GO:0004637, GO:0009113, GO:0003824, GO:0009058, GO:0016742, GO:0004644, GO:0006189, GO:0004641, GO:0005737

CD Domains:

Go To Gene Page:

26492
268048 MFS

268048 - MFS

GO Terms:

GO:0005215, GO:0006810, GO:0016021

CD Domains:

Go To Gene Page:

268048
26926 DEXDc superfamily
32108 hypothetical protein

32108 - hypothetical protein

GO Terms:

GO:0005489, GO:0005506, GO:0006118

CD Domains:

Go To Gene Page:

32108
34994 (vhl1) Prefoldin

34994 - (vhl1) Prefoldin

GO Terms:

GO:0005515, GO:0006457, GO:0016272

CD Domains:

Go To Gene Page:

34994
35911 COG1092

35911 - COG1092

GO Terms:

GO:0008757

CD Domains:

Go To Gene Page:

35911
40044 (MAP1) PLN03158

40044 - (MAP1) PLN03158

GO Terms:

GO:0006508, GO:0008235, GO:0004239

CD Domains:

Go To Gene Page:

40044
4543 hypothetical protein

4543 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

4543
5421 hypothetical protein

5421 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

5421
5484 DUF914

5484 - DUF914

GO Terms:

NA

CD Domains:

Go To Gene Page:

5484
8270 ANK

8270 - ANK

GO Terms:

NA

CD Domains:

Go To Gene Page:

8270
9598 hypothetical protein

9598 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

9598
GO ID Go Term p-value q-value Cluster
GO:0009113 purine base biosynthesis 0.00495611 1 Thaps_bicluster_0069
GO:0006189 'de novo' IMP biosynthesis 0.0123481 1 Thaps_bicluster_0069
GO:0006342 chromatin silencing 0.0221257 1 Thaps_bicluster_0069
GO:0006413 translational initiation 0.058007 1 Thaps_bicluster_0069
GO:0009058 biosynthesis 0.128367 1 Thaps_bicluster_0069
GO:0006508 proteolysis and peptidolysis 0.157438 1 Thaps_bicluster_0069
GO:0006457 protein folding 0.279136 1 Thaps_bicluster_0069
GO:0006412 protein biosynthesis 0.342653 1 Thaps_bicluster_0069
GO:0006810 transport 0.372449 1 Thaps_bicluster_0069
GO:0006118 electron transport 0.493154 1 Thaps_bicluster_0069
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