Thaps_bicluster_0189 Residual: 0.32
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_0189 0.32 Thalassiosira pseudonana
Displaying 1 - 22 of 22
10796 hypothetical protein

10796 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

10796
11148 (Tp_HSF_3.8a) HSF_DNA-bind

11148 - (Tp_HSF_3.8a) HSF_DNA-bind

GO Terms:

GO:0003700, GO:0005634, GO:0006355, GO:0003677

CD Domains:

Go To Gene Page:

11148
21076 hypothetical protein

21076 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

21076
21602 NUC173 superfamily

21602 - NUC173 superfamily

GO Terms:

GO:0004308

CD Domains:

Go To Gene Page:

21602
21951 Sterol-sensing superfamily

21951 - Sterol-sensing superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

21951
22345 (PYK2) PLN02461

22345 - (PYK2) PLN02461

GO Terms:

GO:0004743, GO:0006096

CD Domains:

Go To Gene Page:

22345
22721 hypothetical protein

22721 - hypothetical protein

GO Terms:

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

CD Domains:

Go To Gene Page:

22721
24704 COG3899

24704 - COG3899

GO Terms:

NA

CD Domains:

Go To Gene Page:

24704
25161 hypothetical protein

25161 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25161
25417 hypothetical protein

25417 - hypothetical protein

GO Terms:

GO:0003676, GO:0005634, GO:0008270

CD Domains:

Go To Gene Page:

25417
25909 hypothetical protein

25909 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25909
260975 (nhe3) Na_H_Exchanger

260975 - (nhe3) Na_H_Exchanger

GO Terms:

NA

CD Domains:

Go To Gene Page:

260975
261601 PA14

261601 - PA14

GO Terms:

NA

CD Domains:

Go To Gene Page:

261601
262433 Pumilio superfamily

262433 - Pumilio superfamily

GO Terms:

GO:0003723, GO:0016071

CD Domains:

Go To Gene Page:

262433
269238 (Tp_HSF_1.3e) HSF_DNA-bind superfamily

269238 - (Tp_HSF_1.3e) HSF_DNA-bind superfamily

GO Terms:

GO:0003700, GO:0005634, GO:0006355, GO:0003677

CD Domains:

Go To Gene Page:

269238
269900 (glsF) gltB

269900 - (glsF) gltB

GO Terms:

GO:0008152, GO:0016491, GO:0006537, GO:0015930, GO:0006807, GO:0016041

CD Domains:

Go To Gene Page:

269900
28239 PLN02272

28239 - PLN02272

GO Terms:

GO:0004365, GO:0006096, GO:0051287, GO:0004807, GO:0008152, GO:0006006, GO:0008943

CD Domains:

Go To Gene Page:

28239
3398 hypothetical protein

3398 - hypothetical protein

GO Terms:

GO:0008270, GO:0016787

CD Domains:

Go To Gene Page:

3398
3478 hypothetical protein

3478 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

3478
40393 (PYK1) PLN02461

40393 - (PYK1) PLN02461

GO Terms:

GO:0004743, GO:0006096

CD Domains:

Go To Gene Page:

40393
4972 hypothetical protein

4972 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

4972
9604 hypothetical protein

9604 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

9604
GO ID Go Term p-value q-value Cluster
GO:0006096 glycolysis 0.0000865 0.237367 Thaps_bicluster_0189
GO:0006537 glutamate biosynthesis 0.00988969 1 Thaps_bicluster_0189
GO:0016071 mRNA metabolism 0.0221257 1 Thaps_bicluster_0189
GO:0006006 glucose metabolism 0.0245562 1 Thaps_bicluster_0189
GO:0006807 nitrogen compound metabolism 0.0269812 1 Thaps_bicluster_0189
GO:0015986 ATP synthesis coupled proton transport 0.108453 1 Thaps_bicluster_0189
GO:0006355 regulation of transcription, DNA-dependent 0.174355 1 Thaps_bicluster_0189
GO:0008152 metabolism 0.267706 1 Thaps_bicluster_0189
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