Thaps_bicluster_0142 Residual: 0.24
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_0142 0.24 Thalassiosira pseudonana
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Displaying 1 - 14 of 14
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22076 violaxanthin de-epoxidase-like 1

22076 - violaxanthin de-epoxidase-like 1

GO Terms:

NA

CD Domains:

Go To Gene Page:

22076
22546 hypothetical protein

22546 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22546
22608 hypothetical protein

22608 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22608
25787 hypothetical protein

25787 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25787
264039 (CYP2) p450 superfamily
268592 VDE superfamily

268592 - VDE superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

268592
270281 hypothetical protein

270281 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

270281
31636 Aldose_epim superfamily

31636 - Aldose_epim superfamily

GO Terms:

GO:0004034, GO:0006012

CD Domains:

Go To Gene Page:

31636
32053 PRK08661

32053 - PRK08661

GO Terms:

GO:0004812, GO:0005524, GO:0006418, GO:0006412, GO:0004827, GO:0005737

CD Domains:

Go To Gene Page:

32053
36078 PRX5_like

36078 - PRX5_like

GO Terms:

NA

CD Domains:

Go To Gene Page:

36078
38022 PLN02873

38022 - PLN02873

GO Terms:

GO:0004109, GO:0006779

CD Domains:

Go To Gene Page:

38022
38608 SDR_a5

38608 - SDR_a5

GO Terms:

NA

CD Domains:

Go To Gene Page:

38608
575 PRK00062

575 - PRK00062

GO Terms:

GO:0005737, GO:0006779, GO:0042286, GO:0008483, GO:0030170

CD Domains:

Go To Gene Page:

575
6988 PTZ00401

6988 - PTZ00401

GO Terms:

GO:0004815, GO:0005524, GO:0006422, GO:0004812, GO:0005737, GO:0006418, GO:0003676

CD Domains:

Go To Gene Page:

6988
GO ID Go Term p-value q-value Cluster
GO:0006779 porphyrin biosynthesis 0.000130693 0.358099 Thaps_bicluster_0142
GO:0006418 tRNA aminoacylation for protein translation 0.00365058 1 Thaps_bicluster_0142
GO:0006422 aspartyl-tRNA aminoacylation 0.00824568 1 Thaps_bicluster_0142
GO:0006012 galactose metabolism 0.00988766 1 Thaps_bicluster_0142
GO:0006412 protein biosynthesis 0.243897 1 Thaps_bicluster_0142
GO:0006118 electron transport 0.364179 1 Thaps_bicluster_0142
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