Thaps_bicluster_0125 Residual: 0.41
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_0125 0.41 Thalassiosira pseudonana
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Displaying 1 - 28 of 28
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1020 ADP_ribosyl_GH

1020 - ADP_ribosyl_GH

GO Terms:

NA

CD Domains:

Go To Gene Page:

1020
11164 hypothetical protein

11164 - hypothetical protein

GO Terms:

GO:0006457, GO:0031072, GO:0051082

CD Domains:

Go To Gene Page:

11164
11656 hypothetical protein

11656 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

11656
1936 hypothetical protein

1936 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1936
1954 hypothetical protein

1954 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1954
1972 Lipase superfamily

1972 - Lipase superfamily

GO Terms:

GO:0004806, GO:0006629

CD Domains:

Go To Gene Page:

1972
20923 DUF1279 superfamily

20923 - DUF1279 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

20923
20940 hypothetical protein

20940 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

20940
23519 SIN3

23519 - SIN3

GO Terms:

GO:0005634, GO:0006355, GO:0004402

CD Domains:

Go To Gene Page:

23519
24023 HA

24023 - HA

GO Terms:

NA

CD Domains:

Go To Gene Page:

24023
25140 zf-CXXC

25140 - zf-CXXC

GO Terms:

GO:0003677, GO:0006355, GO:0008270, GO:0004339

CD Domains:

Go To Gene Page:

25140
25681 hypothetical protein

25681 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25681
262078 Trp_Tyr_perm superfamily

262078 - Trp_Tyr_perm superfamily

GO Terms:

GO:0005279, GO:0006865, GO:0016020

CD Domains:

Go To Gene Page:

262078
263566 ribokinase_pfkB_like superfamily

263566 - ribokinase_pfkB_like superfamily

GO Terms:

GO:0008865

CD Domains:

Go To Gene Page:

263566
268301 PRK13566

268301 - PRK13566

GO Terms:

GO:0003824, GO:0000156, GO:0000160, GO:0003677, GO:0006355, GO:0009058, GO:0004049, GO:0008152, GO:0016833, GO:0000162

CD Domains:

Go To Gene Page:

268301
29314 Peptidase_M17

29314 - Peptidase_M17

GO Terms:

GO:0004177, GO:0005622, GO:0006508, GO:0004178

CD Domains:

Go To Gene Page:

29314
3174 MDR superfamily

3174 - MDR superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

3174
31930 (ftsH) FtsH_fam
34698 Transcrip_reg

34698 - Transcrip_reg

GO Terms:

NA

CD Domains:

Go To Gene Page:

34698
4277 PGAP1 superfamily

4277 - PGAP1 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

4277
5865 FUN14

5865 - FUN14

GO Terms:

GO:0005509

CD Domains:

Go To Gene Page:

5865
6505 hypothetical protein

6505 - hypothetical protein

GO Terms:

GO:0003824

CD Domains:

Go To Gene Page:

6505
6765 (Tp_HSF_1.3g) HSF_DNA-bind superfamily

6765 - (Tp_HSF_1.3g) HSF_DNA-bind superfamily

GO Terms:

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

CD Domains:

Go To Gene Page:

6765
6787 hypothetical protein

6787 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

6787
7093 Lipase_3

7093 - Lipase_3

GO Terms:

GO:0004806, GO:0006629, GO:0003824

CD Domains:

Go To Gene Page:

7093
7475 hypothetical protein

7475 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

7475
8749 hypothetical protein

8749 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

8749
8877 hypothetical protein

8877 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

8877
GO ID Go Term p-value q-value Cluster
GO:0000162 tryptophan biosynthesis 0.0031011 1 Thaps_bicluster_0125
GO:0006629 lipid metabolism 0.00347268 1 Thaps_bicluster_0125
GO:0006355 regulation of transcription, DNA-dependent 0.0124234 1 Thaps_bicluster_0125
GO:0030163 protein catabolism 0.0396209 1 Thaps_bicluster_0125
GO:0000160 two-component signal transduction system (phosphorelay) 0.080648 1 Thaps_bicluster_0125
GO:0006865 amino acid transport 0.0863737 1 Thaps_bicluster_0125
GO:0009058 biosynthesis 0.157842 1 Thaps_bicluster_0125
GO:0006508 proteolysis and peptidolysis 0.223555 1 Thaps_bicluster_0125
GO:0006457 protein folding 0.335858 1 Thaps_bicluster_0125
GO:0008152 metabolism 0.732978 1 Thaps_bicluster_0125
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