Thaps_bicluster_0218 Residual: 0.15
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_0218 0.15 Thalassiosira pseudonana
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Displaying 1 - 14 of 14
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20603 hypothetical protein

20603 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

20603
24099 hypothetical protein

24099 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

24099
24769 hypothetical protein

24769 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

24769
2601 (Lhca2) Chloroa_b-bind

2601 - (Lhca2) Chloroa_b-bind

GO Terms:

GO:0009765, GO:0016020

CD Domains:

Go To Gene Page:

2601
268127 (Lhcf9) PLN00120

268127 - (Lhcf9) PLN00120

GO Terms:

GO:0009765, GO:0016020

CD Domains:

Go To Gene Page:

268127
268304 hypothetical protein

268304 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

268304
2848 PsbU

2848 - PsbU

GO Terms:

GO:0009654, GO:0019898, GO:0042549

CD Domains:

Go To Gene Page:

2848
29842 Rieske_2

29842 - Rieske_2

GO Terms:

GO:0006118, GO:0016491

CD Domains:

Go To Gene Page:

29842
30385 (Lhcx6_1) Chloroa_b-bind superfamily

30385 - (Lhcx6_1) Chloroa_b-bind superfamily

GO Terms:

GO:0009765, GO:0016020

CD Domains:

Go To Gene Page:

30385
3141 hypothetical protein

3141 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

3141
34830 MSP superfamily

34830 - MSP superfamily

GO Terms:

GO:0005509, GO:0009654, GO:0015979, GO:0019898, GO:0042549

CD Domains:

Go To Gene Page:

34830
38583 (Lhcf1) PLN00120

38583 - (Lhcf1) PLN00120

GO Terms:

GO:0009765, GO:0016020

CD Domains:

Go To Gene Page:

38583
42962 (Lhcf5) PLN00120

42962 - (Lhcf5) PLN00120

GO Terms:

GO:0009765, GO:0016020

CD Domains:

Go To Gene Page:

42962
5174 (Lhcf8) PLN00120

5174 - (Lhcf8) PLN00120

GO Terms:

GO:0009765, GO:0016020

CD Domains:

Go To Gene Page:

5174
GO ID Go Term p-value q-value Cluster
GO:0009765 photosynthesis, light harvesting 0.00454357 1 Thaps_bicluster_0218
GO:0042549 photosystem II stabilization 0.0000281 0.0774835 Thaps_bicluster_0218
GO:0015979 photosynthesis 0.0291995 1 Thaps_bicluster_0218
GO:0006118 electron transport 0.463588 1 Thaps_bicluster_0218
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