Thaps_bicluster_0119 Residual: 0.42
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_0119 0.42 Thalassiosira pseudonana
Displaying 1 - 38 of 38
10547 Init_tRNA_PT superfamily

10547 - Init_tRNA_PT superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

10547
13308 PLN02948

13308 - PLN02948

GO Terms:

GO:0004638, GO:0006189, GO:0009320

CD Domains:

Go To Gene Page:

13308
1628 PRK01415

1628 - PRK01415

GO Terms:

NA

CD Domains:

Go To Gene Page:

1628
1905 hypothetical protein

1905 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1905
1907 hypothetical protein

1907 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1907
21665 hypothetical protein

21665 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

21665
22741 hypothetical protein

22741 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22741
23081 NADB_Rossmann superfamily

23081 - NADB_Rossmann superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

23081
2332 PTZ00340

2332 - PTZ00340

GO Terms:

GO:0006508, GO:0008450

CD Domains:

Go To Gene Page:

2332
23404 Lipase superfamily

23404 - Lipase superfamily

GO Terms:

GO:0003824, GO:0004806, GO:0006629

CD Domains:

Go To Gene Page:

23404
24125 hypothetical protein

24125 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

24125
24733 COG3899

24733 - COG3899

GO Terms:

NA

CD Domains:

Go To Gene Page:

24733
25507 hypothetical protein

25507 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25507
260786 PTZ00345

260786 - PTZ00345

GO Terms:

GO:0005975, GO:0016614, GO:0004367, GO:0006072, GO:0009331, GO:0005737, GO:0016616, GO:0046168, GO:0051287

CD Domains:

Go To Gene Page:

260786
261719 AdoMet_MTases superfamily

261719 - AdoMet_MTases superfamily

GO Terms:

GO:0016206

CD Domains:

Go To Gene Page:

261719
262965

262965 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

262965
263495 PRK11824

263495 - PRK11824

GO Terms:

GO:0000175, GO:0003723, GO:0006396, GO:0003676, GO:0004654

CD Domains:

Go To Gene Page:

263495
268010 (RPC2) PRK08565

268010 - (RPC2) PRK08565

GO Terms:

GO:0003677, GO:0003899, GO:0006350, GO:0003900, GO:0003901, GO:0003902

CD Domains:

Go To Gene Page:

268010
2737 DadA

2737 - DadA

GO Terms:

GO:0006118, GO:0016491

CD Domains:

Go To Gene Page:

2737
31256 TGT superfamily

31256 - TGT superfamily

GO Terms:

GO:0006400, GO:0008479, GO:0008616

CD Domains:

Go To Gene Page:

31256
31375 DcpS_C

31375 - DcpS_C

GO Terms:

NA

CD Domains:

Go To Gene Page:

31375
31932 hypothetical protein

31932 - hypothetical protein

GO Terms:

GO:0003676, GO:0004386, GO:0005524

CD Domains:

Go To Gene Page:

31932
3250 hypothetical protein

3250 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

3250
3650 hypothetical protein

3650 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

3650
38193 MoaE

38193 - MoaE

GO Terms:

GO:0006777

CD Domains:

Go To Gene Page:

38193
38428 (AOX1_2) AOX

38428 - (AOX1_2) AOX

GO Terms:

GO:0005740, GO:0007585, GO:0016491, GO:0051341

CD Domains:

Go To Gene Page:

38428
40991 E1_enzyme_family superfamily

40991 - E1_enzyme_family superfamily

GO Terms:

GO:0003824, GO:0004842

CD Domains:

Go To Gene Page:

40991
42533 N2227 superfamily

42533 - N2227 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

42533
4347 hypothetical protein

4347 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

4347
4467 hypothetical protein

4467 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

4467
4853 hypothetical protein

4853 - hypothetical protein

GO Terms:

GO:0003723, GO:0006396

CD Domains:

Go To Gene Page:

4853
4921 DUF2779 superfamily

4921 - DUF2779 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

4921
5017 hypothetical protein

5017 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

5017
5992 TPD

5992 - TPD

GO Terms:

NA

CD Domains:

Go To Gene Page:

5992
6642 hypothetical protein

6642 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

6642
6711 hypothetical protein

6711 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

6711
8861 PRK11752

8861 - PRK11752

GO Terms:

GO:0004364

CD Domains:

Go To Gene Page:

8861
9577 Trypsin_2

9577 - Trypsin_2

GO Terms:

NA

CD Domains:

Go To Gene Page:

9577
GO ID Go Term p-value q-value Cluster
GO:0007585 respiratory gaseous exchange 0.00619321 1 Thaps_bicluster_0119
GO:0046168 glycerol-3-phosphate catabolism 0.00927638 1 Thaps_bicluster_0119
GO:0006072 glycerol-3-phosphate metabolism 0.0123506 1 Thaps_bicluster_0119
GO:0008616 queuosine biosynthesis 0.0123506 1 Thaps_bicluster_0119
GO:0006400 tRNA modification 0.0123506 1 Thaps_bicluster_0119
GO:0006396 RNA processing 0.0134241 1 Thaps_bicluster_0119
GO:0006189 'de novo' IMP biosynthesis 0.0154159 1 Thaps_bicluster_0119
GO:0006777 Mo-molybdopterin cofactor biosynthesis 0.0184724 1 Thaps_bicluster_0119
GO:0051341 regulation of oxidoreductase activity 0.0690961 1 Thaps_bicluster_0119
GO:0006629 lipid metabolism 0.0863737 1 Thaps_bicluster_0119
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