Thaps_bicluster_0240 Residual: 0.25
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_0240 0.25 Thalassiosira pseudonana
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Displaying 1 - 19 of 19
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1011 DSPc superfamily

1011 - DSPc superfamily

GO Terms:

GO:0006470, GO:0008138, GO:0004721

CD Domains:

Go To Gene Page:

1011
1417 GpcrRhopsn4 superfamily

1417 - GpcrRhopsn4 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

1417
1456 (IDH1) IDH superfamily

1456 - (IDH1) IDH superfamily

GO Terms:

GO:0004450, GO:0006099

CD Domains:

Go To Gene Page:

1456
2211 hypothetical protein

2211 - hypothetical protein

GO Terms:

GO:0005515

CD Domains:

Go To Gene Page:

2211
22766 PRK05218

22766 - PRK05218

GO Terms:

GO:0006457, GO:0051082, GO:0005524, GO:0003763

CD Domains:

Go To Gene Page:

22766
22860 hypothetical protein

22860 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22860
23616 Peptidase_A22B superfamily

23616 - Peptidase_A22B superfamily

GO Terms:

GO:0006508, GO:0008233, GO:0016021, GO:0008717

CD Domains:

Go To Gene Page:

23616
24797 VHS_ENTH_ANTH superfamily

24797 - VHS_ENTH_ANTH superfamily

GO Terms:

GO:0004402

CD Domains:

Go To Gene Page:

24797
24862 hypothetical protein

24862 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

24862
25116 (PGK5) Phosphoglycerate_kinase

25116 - (PGK5) Phosphoglycerate_kinase

GO Terms:

GO:0004618, GO:0006096

CD Domains:

Go To Gene Page:

25116
260789 MMT1

260789 - MMT1

GO Terms:

GO:0006812, GO:0008324, GO:0016020

CD Domains:

Go To Gene Page:

260789
267987 (CYS2) CBS_like

267987 - (CYS2) CBS_like

GO Terms:

GO:0003824, GO:0008152, GO:0004124, GO:0006535

CD Domains:

Go To Gene Page:

267987
28334 (GAPD4) PTZ00023

28334 - (GAPD4) PTZ00023

GO Terms:

GO:0004365, GO:0006096, GO:0051287, GO:0006006, GO:0008943

CD Domains:

Go To Gene Page:

28334
3154 (Tp_HSF_1b) HSF_DNA-bind

3154 - (Tp_HSF_1b) HSF_DNA-bind

GO Terms:

GO:0003700, GO:0005634, GO:0006355, GO:0003677

CD Domains:

Go To Gene Page:

3154
4399 Methyltransf_22 superfamily

4399 - Methyltransf_22 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

4399
5638 hypothetical protein

5638 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

5638
5675 hypothetical protein

5675 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

5675
9459 Thioredoxin_like superfamily

9459 - Thioredoxin_like superfamily

GO Terms:

GO:0005489, GO:0006118

CD Domains:

Go To Gene Page:

9459
9947 hypothetical protein

9947 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

9947
GO ID Go Term p-value q-value Cluster
GO:0006096 glycolysis 0.00421191 1 Thaps_bicluster_0240
GO:0006535 cysteine biosynthesis from serine 0.0107105 1 Thaps_bicluster_0240
GO:0006099 tricarboxylic acid cycle 0.0265779 1 Thaps_bicluster_0240
GO:0006006 glucose metabolism 0.0265779 1 Thaps_bicluster_0240
GO:0006470 protein amino acid dephosphorylation 0.0677496 1 Thaps_bicluster_0240
GO:0006812 cation transport 0.109729 1 Thaps_bicluster_0240
GO:0006457 protein folding 0.298558 1 Thaps_bicluster_0240
GO:0008152 metabolism 0.300056 1 Thaps_bicluster_0240
GO:0006118 electron transport 0.521096 1 Thaps_bicluster_0240
GO:0006508 proteolysis and peptidolysis 0.550247 1 Thaps_bicluster_0240
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