Thaps_bicluster_0241 Residual: 0.29
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_0241 0.29 Thalassiosira pseudonana
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Displaying 1 - 19 of 19
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10156 Tcp10_C superfamily

10156 - Tcp10_C superfamily

GO Terms:

GO:0003910

CD Domains:

Go To Gene Page:

10156
10437 hypothetical protein

10437 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

10437
15138 MFS

15138 - MFS

GO Terms:

NA

CD Domains:

Go To Gene Page:

15138
15226 PLN02407

15226 - PLN02407

GO Terms:

GO:0004163, GO:0008299, GO:0005524, GO:0016301, GO:0016310

CD Domains:

Go To Gene Page:

15226
1622 AE_Prim_S

1622 - AE_Prim_S

GO Terms:

GO:0003896, GO:0006269

CD Domains:

Go To Gene Page:

1622
20903 CAF1A

20903 - CAF1A

GO Terms:

GO:0003910

CD Domains:

Go To Gene Page:

20903
22374 hypothetical protein

22374 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22374
23064 hypothetical protein

23064 - hypothetical protein

GO Terms:

GO:0004339

CD Domains:

Go To Gene Page:

23064
260808

260808 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

260808
263366 Pkinase

263366 - Pkinase

GO Terms:

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

CD Domains:

Go To Gene Page:

263366
268247 SLBP_RNA_bind

268247 - SLBP_RNA_bind

GO Terms:

NA

CD Domains:

Go To Gene Page:

268247
269422 wd-40 repeat-containing protein

269422 - wd-40 repeat-containing protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

269422
33513 CYCLIN

33513 - CYCLIN

GO Terms:

GO:0000074

CD Domains:

Go To Gene Page:

33513
34379 NIF

34379 - NIF

GO Terms:

GO:0000158, GO:0004721, GO:0004723, GO:0004724, GO:0005963, GO:0008420, GO:0008597, GO:0015071, GO:0017018, GO:0017020, GO:0017023, GO:0030357

CD Domains:

Go To Gene Page:

34379
35387 (cdc2) PKc_like superfamily

35387 - (cdc2) PKc_like superfamily

GO Terms:

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

CD Domains:

Go To Gene Page:

35387
4159 hypothetical protein

4159 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

4159
6356 hypothetical protein

6356 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

6356
7091 hypothetical protein

7091 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

7091
GO ID Go Term p-value q-value Cluster
GO:0006275 regulation of DNA replication 0.00144718 1 Thaps_bicluster_0241
GO:0006269 DNA replication, synthesis of RNA primer 0.00433615 1 Thaps_bicluster_0241
GO:0008299 isoprenoid biosynthesis 0.0158205 1 Thaps_bicluster_0241
GO:0016310 phosphorylation 0.0186738 1 Thaps_bicluster_0241
GO:0006468 protein amino acid phosphorylation 0.0350131 1 Thaps_bicluster_0241
GO:0000074 regulation of cell cycle 0.0837154 1 Thaps_bicluster_0241
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