Thaps_bicluster_0188 Residual: 0.22
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_0188 0.22 Thalassiosira pseudonana
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Displaying 1 - 19 of 19
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10278 YihA_EngB

10278 - YihA_EngB

GO Terms:

NA

CD Domains:

Go To Gene Page:

10278
14890 Cupin_8 superfamily

14890 - Cupin_8 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

14890
16287 Pkinase

16287 - Pkinase

GO Terms:

GO:0004672, GO:0005524, GO:0006468, GO:0004713, GO:0004674

CD Domains:

Go To Gene Page:

16287
21959 hypothetical protein

21959 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

21959
22448 hypothetical protein

22448 - hypothetical protein

GO Terms:

GO:0003723, GO:0016071

CD Domains:

Go To Gene Page:

22448
22685 COG2520

22685 - COG2520

GO Terms:

GO:0008757

CD Domains:

Go To Gene Page:

22685
23061 hypothetical protein

23061 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23061
24332 hypothetical protein

24332 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

24332
24709 (NTT6) TLC superfamily

24709 - (NTT6) TLC superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

24709
24893 hypothetical protein

24893 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

24893
25473 SpoU_methylase

25473 - SpoU_methylase

GO Terms:

GO:0003723, GO:0006396, GO:0008173

CD Domains:

Go To Gene Page:

25473
262699 YgdL_like

262699 - YgdL_like

GO Terms:

GO:0003824, GO:0004842

CD Domains:

Go To Gene Page:

262699
264090 AAA_12

264090 - AAA_12

GO Terms:

NA

CD Domains:

Go To Gene Page:

264090
264632 COG0826

264632 - COG0826

GO Terms:

GO:0006508, GO:0008233

CD Domains:

Go To Gene Page:

264632
269925 AAA_12 superfamily

269925 - AAA_12 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

269925
36597 trmE

36597 - trmE

GO Terms:

GO:0005525

CD Domains:

Go To Gene Page:

36597
3858 PTZ00141

3858 - PTZ00141

GO Terms:

GO:0005525, GO:0006412, GO:0003746, GO:0005737, GO:0006414, GO:0003924, GO:0008547

CD Domains:

Go To Gene Page:

3858
5666 Las1 superfamily

5666 - Las1 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

5666
8541 PRK00142

8541 - PRK00142

GO Terms:

GO:0003676, GO:0003917

CD Domains:

Go To Gene Page:

8541
GO ID Go Term p-value q-value Cluster
GO:0016071 mRNA metabolism 0.0111179 1 Thaps_bicluster_0188
GO:0006414 translational elongation 0.0148008 1 Thaps_bicluster_0188
GO:0006396 RNA processing 0.0698579 1 Thaps_bicluster_0188
GO:0006412 protein biosynthesis 0.189123 1 Thaps_bicluster_0188
GO:0006468 protein amino acid phosphorylation 0.236888 1 Thaps_bicluster_0188
GO:0006508 proteolysis and peptidolysis 0.308243 1 Thaps_bicluster_0188
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