Thaps_bicluster_0166 Residual: 0.18
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_0166 0.18 Thalassiosira pseudonana
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Displaying 1 - 14 of 14
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23862 Syo1_like superfamily

23862 - Syo1_like superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

23862
25689 hypothetical protein

25689 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25689
262722 DEXDc superfamily

262722 - DEXDc superfamily

GO Terms:

GO:0005524, GO:0008026, GO:0003676, GO:0004386, GO:0000810, GO:0004787, GO:0008722, GO:0008758, GO:0008796, GO:0008828, GO:0016462, GO:0016818, GO:0019176, GO:0019177

CD Domains:

Go To Gene Page:

262722
268130 hypothetical protein

268130 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

268130
268252 Utp21 superfamily

268252 - Utp21 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

268252
2772 Utp14

2772 - Utp14

GO Terms:

GO:0003910

CD Domains:

Go To Gene Page:

2772
29018 NMD3

29018 - NMD3

GO Terms:

NA

CD Domains:

Go To Gene Page:

29018
33425 BMS1

33425 - BMS1

GO Terms:

GO:0005524

CD Domains:

Go To Gene Page:

33425
36434 DUF1253

36434 - DUF1253

GO Terms:

NA

CD Domains:

Go To Gene Page:

36434
38143 WD40 superfamily

38143 - WD40 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

38143
40871 COG1444

40871 - COG1444

GO Terms:

GO:0008152, GO:0016491

CD Domains:

Go To Gene Page:

40871
GO ID Go Term p-value q-value Cluster
GO:0006508 proteolysis and peptidolysis 0.115549 1 Thaps_bicluster_0166
GO:0008152 metabolism 0.161222 1 Thaps_bicluster_0166
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