Thaps_bicluster_0123 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_0123 0.31 Thalassiosira pseudonana
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Displaying 1 - 25 of 25
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10185 hypothetical protein

10185 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

10185
11331 GcvR

11331 - GcvR

GO Terms:

GO:0008152, GO:0016597

CD Domains:

Go To Gene Page:

11331
17362 Kua-UEV1_localn superfamily

17362 - Kua-UEV1_localn superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

17362
1899 hypothetical protein

1899 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1899
20846 LPLAT_MGAT-like

20846 - LPLAT_MGAT-like

GO Terms:

NA

CD Domains:

Go To Gene Page:

20846
2270 hypothetical protein

2270 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2270
23492 hypothetical protein

23492 - hypothetical protein

GO Terms:

GO:0003700, GO:0006355, GO:0006464, GO:0008113

CD Domains:

Go To Gene Page:

23492
25167 hypothetical protein

25167 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25167
2578 hypothetical protein

2578 - hypothetical protein

GO Terms:

GO:0008152, GO:0016491

CD Domains:

Go To Gene Page:

2578
2597 hypothetical protein

2597 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2597
260832 sigpep_I_bact

260832 - sigpep_I_bact

GO Terms:

GO:0006508, GO:0008236, GO:0016020

CD Domains:

Go To Gene Page:

260832
26769 ERG4_ERG24 superfamily

26769 - ERG4_ERG24 superfamily

GO Terms:

GO:0016020, GO:0000246

CD Domains:

Go To Gene Page:

26769
30986 SCO

30986 - SCO

GO Terms:

GO:0006118

CD Domains:

Go To Gene Page:

30986
33024 cysteine_hydrolases superfamily

33024 - cysteine_hydrolases superfamily

GO Terms:

GO:0003824, GO:0008152

CD Domains:

Go To Gene Page:

33024
33829 Ycf34 superfamily

33829 - Ycf34 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

33829
36928 Lin0512_fam superfamily

36928 - Lin0512_fam superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

36928
37793 hypothetical protein

37793 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

37793
38602 Ndh

38602 - Ndh

GO Terms:

GO:0006118, GO:0016491, GO:0015036, GO:0003954

CD Domains:

Go To Gene Page:

38602
4171 hypothetical protein

4171 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

4171
4571 P4Hc

4571 - P4Hc

GO Terms:

GO:0016706, GO:0019538, GO:0004656, GO:0016222

CD Domains:

Go To Gene Page:

4571
5198 ClpS

5198 - ClpS

GO Terms:

NA

CD Domains:

Go To Gene Page:

5198
5958 hypothetical protein

5958 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

5958
5967 hypothetical protein

5967 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

5967
9087 Mito_carr

9087 - Mito_carr

GO Terms:

GO:0005488, GO:0006810, GO:0016020, GO:0005743

CD Domains:

Go To Gene Page:

9087
937 Methyltransf_21 superfamily

937 - Methyltransf_21 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

937
GO ID Go Term p-value q-value Cluster
GO:0008152 metabolism 0.0454147 1 Thaps_bicluster_0123
GO:0019538 protein metabolism 0.0912132 1 Thaps_bicluster_0123
GO:0006118 electron transport 0.101293 1 Thaps_bicluster_0123
GO:0006464 protein modification 0.115596 1 Thaps_bicluster_0123
GO:0006810 transport 0.321719 1 Thaps_bicluster_0123
GO:0006508 proteolysis and peptidolysis 0.459068 1 Thaps_bicluster_0123
GO:0006355 regulation of transcription, DNA-dependent 0.481263 1 Thaps_bicluster_0123
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