Thaps_bicluster_0268 Residual: 0.24
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_0268 0.24 Thalassiosira pseudonana
Displaying 1 - 15 of 15
15992 COG0820

15992 - COG0820

GO Terms:

GO:0005554, GO:0003824, GO:0005506

CD Domains:

Go To Gene Page:

15992
17654 REX4_like

17654 - REX4_like

GO Terms:

GO:0004527, GO:0005622, GO:0008859

CD Domains:

Go To Gene Page:

17654
20742 hypothetical protein

20742 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

20742
21966 SLX9

21966 - SLX9

GO Terms:

NA

CD Domains:

Go To Gene Page:

21966
22334 hypothetical protein

22334 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22334
22498 DEXDc superfamily

22498 - DEXDc superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

22498
23202 RsuA

23202 - RsuA

GO Terms:

GO:0003723, GO:0006396, GO:0009982

CD Domains:

Go To Gene Page:

23202
23277 EEP superfamily

23277 - EEP superfamily

GO Terms:

GO:0004518, GO:0016788, GO:0042578

CD Domains:

Go To Gene Page:

23277
261270

261270 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

261270
261746 PRK00142

261746 - PRK00142

GO Terms:

GO:0003723, GO:0006396, GO:0009982, GO:0004730, GO:0016439

CD Domains:

Go To Gene Page:

261746
34729 NGP_1

34729 - NGP_1

GO Terms:

GO:0005525

CD Domains:

Go To Gene Page:

34729
39075 PRK09246

39075 - PRK09246

GO Terms:

GO:0008152, GO:0009116, GO:0016740, GO:0004044, GO:0009113

CD Domains:

Go To Gene Page:

39075
5294 hypothetical protein

5294 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

5294
GO ID Go Term p-value q-value Cluster
GO:0006396 RNA processing 0.00205534 1 Thaps_bicluster_0268
GO:0009113 purine base biosynthesis 0.00247959 1 Thaps_bicluster_0268
GO:0009116 nucleoside metabolism 0.00742341 1 Thaps_bicluster_0268
GO:0006118 electron transport 0.287914 1 Thaps_bicluster_0268
GO:0008152 metabolism 0.410014 1 Thaps_bicluster_0268
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