Thaps_bicluster_0204 Residual: 0.18
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_0204 0.18 Thalassiosira pseudonana
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Displaying 1 - 14 of 14
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12695 Glucan_synthase superfamily

12695 - Glucan_synthase superfamily

GO Terms:

GO:0000148, GO:0003843, GO:0006075, GO:0016020

CD Domains:

Go To Gene Page:

12695
1953 hypothetical protein

1953 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1953
21517 Methyltransf_6 superfamily

21517 - Methyltransf_6 superfamily

GO Terms:

GO:0003677, GO:0006306

CD Domains:

Go To Gene Page:

21517
23283 hypothetical protein

23283 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23283
25892 PLN03116

25892 - PLN03116

GO Terms:

GO:0006118, GO:0016491, GO:0004324, GO:0015039

CD Domains:

Go To Gene Page:

25892
262674 NADB_Rossmann superfamily

262674 - NADB_Rossmann superfamily

GO Terms:

GO:0008152, GO:0016491, GO:0000252, GO:0000253, GO:0004448, GO:0004495, GO:0008875, GO:0016229, GO:0016616, GO:0018451, GO:0018452, GO:0018453, GO:0048258

CD Domains:

Go To Gene Page:

262674
264865 (Tp_CSF4) CSP_CDS

264865 - (Tp_CSF4) CSP_CDS

GO Terms:

GO:0003677, GO:0006355, GO:0003676

CD Domains:

Go To Gene Page:

264865
31383 (GAPD1) GapA

31383 - (GAPD1) GapA

GO Terms:

GO:0004365, GO:0006096, GO:0051287, GO:0006006, GO:0008943, GO:0005737

CD Domains:

Go To Gene Page:

31383
35878 PLN02307

35878 - PLN02307

GO Terms:

GO:0005975, GO:0016868, GO:0004614

CD Domains:

Go To Gene Page:

35878
40156 F1-ATPase_gamma

40156 - F1-ATPase_gamma

GO Terms:

GO:0015986, GO:0016020, GO:0016469, GO:0046933, GO:0046961, GO:0003936

CD Domains:

Go To Gene Page:

40156
42326 PLN02830

42326 - PLN02830

GO Terms:

NA

CD Domains:

Go To Gene Page:

42326
4914 PLN03116

4914 - PLN03116

GO Terms:

GO:0006118, GO:0016491, GO:0004324, GO:0015039

CD Domains:

Go To Gene Page:

4914
5434 hypothetical protein

5434 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

5434
7881 hypothetical protein

7881 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

7881
GO ID Go Term p-value q-value Cluster
GO:0006075 beta-1,3 glucan biosynthesis 0.00268762 1 Thaps_bicluster_0204
GO:0006816 calcium ion transport 0.016026 1 Thaps_bicluster_0204
GO:0006006 glucose metabolism 0.0265779 1 Thaps_bicluster_0204
GO:0006306 DNA methylation 0.075288 1 Thaps_bicluster_0204
GO:0006096 glycolysis 0.0951161 1 Thaps_bicluster_0204
GO:0006812 cation transport 0.109729 1 Thaps_bicluster_0204
GO:0015986 ATP synthesis coupled proton transport 0.116953 1 Thaps_bicluster_0204
GO:0006118 electron transport 0.157847 1 Thaps_bicluster_0204
GO:0005975 carbohydrate metabolism 0.184052 1 Thaps_bicluster_0204
GO:0008152 metabolism 0.300056 1 Thaps_bicluster_0204
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