Thaps_bicluster_0136 Residual: 0.28
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_0136 0.28 Thalassiosira pseudonana
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Displaying 1 - 21 of 21
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10353 hypothetical protein

10353 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

10353
1038 SPRYD7

1038 - SPRYD7

GO Terms:

NA

CD Domains:

Go To Gene Page:

1038
13117 GTPBP1

13117 - GTPBP1

GO Terms:

GO:0005525, GO:0006412, GO:0003924, GO:0008547

CD Domains:

Go To Gene Page:

13117
1850 PKc_like superfamily

1850 - PKc_like superfamily

GO Terms:

GO:0004672, GO:0005524, GO:0006468, GO:0004713, GO:0004674

CD Domains:

Go To Gene Page:

1850
2086 zf-UBP

2086 - zf-UBP

GO Terms:

NA

CD Domains:

Go To Gene Page:

2086
2319 hypothetical protein

2319 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2319
263219 MFS_1

263219 - MFS_1

GO Terms:

NA

CD Domains:

Go To Gene Page:

263219
263558 Menin superfamily

263558 - Menin superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

263558
263810 PTZ00430

263810 - PTZ00430

GO Terms:

GO:0004347, GO:0006094, GO:0006096

CD Domains:

Go To Gene Page:

263810
264157 CBS_pair superfamily

264157 - CBS_pair superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

264157
2702 Pro_isomerase

2702 - Pro_isomerase

GO Terms:

GO:0006457

CD Domains:

Go To Gene Page:

2702
28148 (NIT2) nit

28148 - (NIT2) nit

GO Terms:

GO:0006807, GO:0016810

CD Domains:

Go To Gene Page:

28148
35956 SIR2 superfamily

35956 - SIR2 superfamily

GO Terms:

GO:0003677, GO:0005677, GO:0006342, GO:0006355, GO:0008939

CD Domains:

Go To Gene Page:

35956
3837 UshA

3837 - UshA

GO Terms:

GO:0016787, GO:0009166, GO:0008253, GO:0017175

CD Domains:

Go To Gene Page:

3837
4456 Abhydrolase_6

4456 - Abhydrolase_6

GO Terms:

GO:0003824

CD Domains:

Go To Gene Page:

4456
5038 DUF179

5038 - DUF179

GO Terms:

NA

CD Domains:

Go To Gene Page:

5038
5335 Cyt_b561 superfamily

5335 - Cyt_b561 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

5335
6140 hypothetical protein

6140 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

6140
7516 Aldo_ket_red

7516 - Aldo_ket_red

GO Terms:

GO:0016491, GO:0004032

CD Domains:

Go To Gene Page:

7516
GO ID Go Term p-value q-value Cluster
GO:0009166 nucleotide catabolism 0.00454357 1 Thaps_bicluster_0136
GO:0006342 chromatin silencing 0.0202987 1 Thaps_bicluster_0136
GO:0006094 gluconeogenesis 0.0202987 1 Thaps_bicluster_0136
GO:0006807 nitrogen compound metabolism 0.0247583 1 Thaps_bicluster_0136
GO:0006334 nucleosome assembly 0.0683505 1 Thaps_bicluster_0136
GO:0006096 glycolysis 0.0810783 1 Thaps_bicluster_0136
GO:0006457 protein folding 0.25918 1 Thaps_bicluster_0136
GO:0006412 protein biosynthesis 0.319237 1 Thaps_bicluster_0136
GO:0006468 protein amino acid phosphorylation 0.39098 1 Thaps_bicluster_0136
GO:0006118 electron transport 0.463588 1 Thaps_bicluster_0136
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