Thaps_bicluster_0126 Residual: 0.34
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_0126 0.34 Thalassiosira pseudonana
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Displaying 1 - 25 of 25
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1218 Aa_trans superfamily

1218 - Aa_trans superfamily

GO Terms:

GO:0005279, GO:0006865, GO:0016020, GO:0006508, GO:0008237, GO:0008270

CD Domains:

Go To Gene Page:

1218
1275 hypothetical protein

1275 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1275
1741 hypothetical protein

1741 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1741
20633 Aa_trans superfamily

20633 - Aa_trans superfamily

GO Terms:

GO:0005279, GO:0006865, GO:0016020

CD Domains:

Go To Gene Page:

20633
20854 hypothetical protein

20854 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

20854
21238 (ALD3) ALDH_F3-13-14_CALDH-like

21238 - (ALD3) ALDH_F3-13-14_CALDH-like

GO Terms:

GO:0008152, GO:0016491, GO:0004029

CD Domains:

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21238
21712 APG9 superfamily

21712 - APG9 superfamily

GO Terms:

GO:0000285

CD Domains:

Go To Gene Page:

21712
22823 Maf1 superfamily

22823 - Maf1 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

22823
22902 hypothetical protein

22902 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22902
23990 hypothetical protein

23990 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23990
268867 Peptidase_S28 superfamily

268867 - Peptidase_S28 superfamily

GO Terms:

GO:0005509, GO:0005576, GO:0006508, GO:0008236, GO:0008233, GO:0008234

CD Domains:

Go To Gene Page:

268867
269328 (PCB1) COG4799

269328 - (PCB1) COG4799

GO Terms:

GO:0016874, GO:0004485

CD Domains:

Go To Gene Page:

269328
269513 PTZ00461

269513 - PTZ00461

GO Terms:

GO:0003995, GO:0006118, GO:0016491, GO:0016937, GO:0017099, GO:0019109

CD Domains:

Go To Gene Page:

269513
2906 hypothetical protein

2906 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2906
31777 (OCT1) CoA_trans superfamily

31777 - (OCT1) CoA_trans superfamily

GO Terms:

GO:0008152, GO:0008410, GO:0008260

CD Domains:

Go To Gene Page:

31777
3260 hypothetical protein

3260 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

3260
3456 Peptidase_S41_CPP

3456 - Peptidase_S41_CPP

GO Terms:

GO:0005515, GO:0006508, GO:0008236, GO:0019132

CD Domains:

Go To Gene Page:

3456
3493 hypothetical protein

3493 - hypothetical protein

GO Terms:

GO:0005622

CD Domains:

Go To Gene Page:

3493
4100 hypothetical protein

4100 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

4100
4322 PLN00113

4322 - PLN00113

GO Terms:

NA

CD Domains:

Go To Gene Page:

4322
5340 hypothetical protein

5340 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

5340
6047 TLD superfamily

6047 - TLD superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

6047
6568 PLPDE_IV superfamily

6568 - PLPDE_IV superfamily

GO Terms:

GO:0003824, GO:0008152

CD Domains:

Go To Gene Page:

6568
885 DUF544 superfamily

885 - DUF544 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

885
9861 DUF563

9861 - DUF563

GO Terms:

NA

CD Domains:

Go To Gene Page:

9861
GO ID Go Term p-value q-value Cluster
GO:0006865 amino acid transport 0.0012175 1 Thaps_bicluster_0126
GO:0006508 proteolysis and peptidolysis 0.0134124 1 Thaps_bicluster_0126
GO:0008152 metabolism 0.0338556 1 Thaps_bicluster_0126
GO:0006118 electron transport 0.399203 1 Thaps_bicluster_0126
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