Thaps_bicluster_0178 Residual: 0.28
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_0178 0.28 Thalassiosira pseudonana
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Displaying 1 - 16 of 16
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12189 hypothetical protein

12189 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

12189
17214 PLN02512

17214 - PLN02512

GO Terms:

GO:0008652, GO:0004349, GO:0006561, GO:0003991, GO:0005737, GO:0006526

CD Domains:

Go To Gene Page:

17214
1788 hypothetical protein

1788 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1788
24754 hypothetical protein

24754 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

24754
2553 MDR1

2553 - MDR1

GO Terms:

GO:0008270, GO:0016491, GO:0003960

CD Domains:

Go To Gene Page:

2553
262455 COG1272

262455 - COG1272

GO Terms:

GO:0016021

CD Domains:

Go To Gene Page:

262455
2678 Rotamase

2678 - Rotamase

GO Terms:

GO:0016853

CD Domains:

Go To Gene Page:

2678
268343 NA

268343 - NA

GO Terms:

NA

CD Domains:

Go To Gene Page:

268343
269395 hypothetical protein

269395 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

269395
30659 GloB

30659 - GloB

GO Terms:

GO:0004416

CD Domains:

Go To Gene Page:

30659
36037 Trypsin_2

36037 - Trypsin_2

GO Terms:

GO:0004295, GO:0006508, GO:0005515, GO:0004252, GO:0004289, GO:0008132, GO:0008243, GO:0008991, GO:0016808

CD Domains:

Go To Gene Page:

36037
38121 (clpA) ClpB_D2-small

38121 - (clpA) ClpB_D2-small

GO Terms:

GO:0005524, GO:0000166, GO:0017111

CD Domains:

Go To Gene Page:

38121
42577 (PGK3) Phosphoglycerate_kinase

42577 - (PGK3) Phosphoglycerate_kinase

GO Terms:

GO:0004618, GO:0006096

CD Domains:

Go To Gene Page:

42577
7597 2A0111

7597 - 2A0111

GO Terms:

NA

CD Domains:

Go To Gene Page:

7597
9130 hypothetical protein

9130 - hypothetical protein

GO Terms:

GO:0016491

CD Domains:

Go To Gene Page:

9130
9855 hypothetical protein

9855 - hypothetical protein

GO Terms:

GO:0008757, GO:0008168

CD Domains:

Go To Gene Page:

9855
GO ID Go Term p-value q-value Cluster
GO:0006561 proline biosynthesis 0.00412967 1 Thaps_bicluster_0178
GO:0006526 arginine biosynthesis 0.00927255 1 Thaps_bicluster_0178
GO:0008652 amino acid biosynthesis 0.0113237 1 Thaps_bicluster_0178
GO:0006096 glycolysis 0.0376815 1 Thaps_bicluster_0178
GO:0006508 proteolysis and peptidolysis 0.264399 1 Thaps_bicluster_0178
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