Thaps_bicluster_0129 Residual: 0.19
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_0129 0.19 Thalassiosira pseudonana
" class="views-fluidgrid-wrapper clear-block">
Displaying 1 - 11 of 11
" class="views-fluidgrid-wrapper clear-block">
1049 MviM

1049 - MviM

GO Terms:

GO:0006118, GO:0008152, GO:0016491, GO:0050112

CD Domains:

Go To Gene Page:

1049
11924 hypothetical protein

11924 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

11924
20335 Rotamase

20335 - Rotamase

GO Terms:

GO:0016853

CD Domains:

Go To Gene Page:

20335
26548 MviM

26548 - MviM

GO Terms:

GO:0006118, GO:0008152, GO:0016491, GO:0050112

CD Domains:

Go To Gene Page:

26548
270092 Chloroa_b-bind superfamily

270092 - Chloroa_b-bind superfamily

GO Terms:

GO:0009765, GO:0016020

CD Domains:

Go To Gene Page:

270092
31983 Chloroa_b-bind superfamily

31983 - Chloroa_b-bind superfamily

GO Terms:

GO:0009765, GO:0016020

CD Domains:

Go To Gene Page:

31983
32431 Fe_bilin_red superfamily

32431 - Fe_bilin_red superfamily

GO Terms:

GO:0010024, GO:0016636, GO:0050897, GO:0050619

CD Domains:

Go To Gene Page:

32431
37294 AarF

37294 - AarF

GO Terms:

NA

CD Domains:

Go To Gene Page:

37294
3815 (Lhca6) Chloroa_b-bind

3815 - (Lhca6) Chloroa_b-bind

GO Terms:

GO:0009765, GO:0016020

CD Domains:

Go To Gene Page:

3815
38715 PLN00120

38715 - PLN00120

GO Terms:

GO:0009765, GO:0016020

CD Domains:

Go To Gene Page:

38715
7916 (FCP_2) Chloroa_b-bind superfamily

7916 - (FCP_2) Chloroa_b-bind superfamily

GO Terms:

GO:0009765, GO:0016020

CD Domains:

Go To Gene Page:

7916
GO ID Go Term p-value q-value Cluster
GO:0009765 photosynthesis light harvesting 0.00000000731 0.0000202 Thaps_bicluster_0129
GO:0010024 phytochromobilin biosynthesis 0.00413095 1 Thaps_bicluster_0129
GO:0006118 electron transport 0.101293 1 Thaps_bicluster_0129
GO:0008152 metabolism 0.203212 1 Thaps_bicluster_0129
Log in to post comments