Phatr_bicluster_0121 Residual: 0.14
Phaeodactylum tricornutum

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
Phatr_bicluster_0121 0.14 Phaeodactylum tricornutum
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Displaying 1 - 16 of 16
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PHATRDRAFT_34754

PHATRDRAFT_34754 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34754
PHATRDRAFT_39347

PHATRDRAFT_39347 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39347
PHATRDRAFT_43221

PHATRDRAFT_43221 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43221
PHATRDRAFT_44270 (SET)

PHATRDRAFT_44270 - (SET)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44270
PHATRDRAFT_44511

PHATRDRAFT_44511 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44511
PHATRDRAFT_44577

PHATRDRAFT_44577 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44577
PHATRDRAFT_45556

PHATRDRAFT_45556 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45556
PHATRDRAFT_45765 cell wall surface anchor family protein

PHATRDRAFT_45765 - cell wall surface anchor family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45765
PHATRDRAFT_46198

PHATRDRAFT_46198 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46198
PHATRDRAFT_47045 viral a-type inclusion

PHATRDRAFT_47045 - viral a-type inclusion

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47045
PHATRDRAFT_47140

PHATRDRAFT_47140 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47140
PHATRDRAFT_48125

PHATRDRAFT_48125 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48125
PHATRDRAFT_48736

PHATRDRAFT_48736 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48736
PHATRDRAFT_50277

PHATRDRAFT_50277 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50277
PHATRDRAFT_50592

PHATRDRAFT_50592 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50592
PHATRDRAFT_54395 beta-ig-h3 fasciclin (COG2335)

PHATRDRAFT_54395 - beta-ig-h3 fasciclin (COG2335)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54395
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