Thaps_bicluster_0091 Residual: 0.31
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_0091 0.31 Thalassiosira pseudonana
Displaying 1 - 20 of 20
1122 hypothetical protein

1122 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1122
1357 FKBP_C

1357 - FKBP_C

GO Terms:

GO:0006457, GO:0003700, GO:0006355, GO:0000287, GO:0008152, GO:0016462, GO:0003755, GO:0004600, GO:0030051, GO:0042027

CD Domains:

Go To Gene Page:

1357
19301 sigpep_I_bact

19301 - sigpep_I_bact

GO Terms:

GO:0006508, GO:0008236, GO:0016020, GO:0008233, GO:0008234

CD Domains:

Go To Gene Page:

19301
20653 PseudoU_synth superfamily

20653 - PseudoU_synth superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

20653
20734 hypothetical protein
21176 FMO-like

21176 - FMO-like

GO Terms:

GO:0004497, GO:0006118, GO:0016491, GO:0015036, GO:0004499

CD Domains:

Go To Gene Page:

21176
22417 Sun

22417 - Sun

GO Terms:

NA

CD Domains:

Go To Gene Page:

22417
22847 hypothetical protein

22847 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22847
23246 hypothetical protein

23246 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23246
25365 hypothetical protein

25365 - hypothetical protein

GO Terms:

GO:0008757, GO:0008168

CD Domains:

Go To Gene Page:

25365
262503 Nudix_Hydrolase superfamily

262503 - Nudix_Hydrolase superfamily

GO Terms:

GO:0004788

CD Domains:

Go To Gene Page:

262503
269034 hypothetical protein

269034 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

269034
269798 hypothetical protein

269798 - hypothetical protein

GO Terms:

GO:0008080

CD Domains:

Go To Gene Page:

269798
31627 RluA

31627 - RluA

GO Terms:

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

CD Domains:

Go To Gene Page:

31627
31819 DUF2419 superfamily

31819 - DUF2419 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

31819
3292 COG2319

3292 - COG2319

GO Terms:

NA

CD Domains:

Go To Gene Page:

3292
35297 AdoMet_MTases superfamily

35297 - AdoMet_MTases superfamily

GO Terms:

GO:0008757

CD Domains:

Go To Gene Page:

35297
36917 TGT superfamily

36917 - TGT superfamily

GO Terms:

GO:0006400, GO:0008479, GO:0008616

CD Domains:

Go To Gene Page:

36917
5241 RNase_P_p30 superfamily

5241 - RNase_P_p30 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

5241
8261 DUF819 superfamily

8261 - DUF819 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

8261
GO ID Go Term p-value q-value Cluster
GO:0008616 queuosine biosynthesis 0.00660132 1 Thaps_bicluster_0091
GO:0006400 tRNA modification 0.00660132 1 Thaps_bicluster_0091
GO:0006396 RNA processing 0.0920603 1 Thaps_bicluster_0091
GO:0006457 protein folding 0.195964 1 Thaps_bicluster_0091
GO:0006118 electron transport 0.364179 1 Thaps_bicluster_0091
GO:0006508 proteolysis and peptidolysis 0.38827 1 Thaps_bicluster_0091
GO:0006355 regulation of transcription, DNA-dependent 0.40843 1 Thaps_bicluster_0091
GO:0008152 metabolism 0.505245 1 Thaps_bicluster_0091
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