Phatr_bicluster_0204 Residual: 0.24
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_0204 0.24 Phaeodactylum tricornutum
Displaying 1 - 20 of 20
PHATRDRAFT_13154 nitrite reductaselarge subunit (PRK14989)

PHATRDRAFT_13154 - nitrite reductaselarge subunit (PRK14989)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13154
PHATRDRAFT_32528

PHATRDRAFT_32528 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32528
PHATRDRAFT_32962

PHATRDRAFT_32962 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32962
PHATRDRAFT_33858

PHATRDRAFT_33858 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33858
PHATRDRAFT_34340

PHATRDRAFT_34340 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34340
PHATRDRAFT_35694

PHATRDRAFT_35694 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35694
PHATRDRAFT_36590

PHATRDRAFT_36590 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36590
PHATRDRAFT_42459 membrane protein (Rhomboid)

PHATRDRAFT_42439 - membrane protein (Rhomboid)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42439
PHATRDRAFT_43352 elicitin-like protein 6 precursor

PHATRDRAFT_42459 - elicitin-like protein 6 precursor

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42459
PHATRDRAFT_45750 alpha beta hydrolase fold (PldB)

PHATRDRAFT_43352 - alpha beta hydrolase fold (PldB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43352
PHATRDRAFT_45978 bnr repeat domain protein

PHATRDRAFT_45750 - bnr repeat domain protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45750
PHATRDRAFT_46018

PHATRDRAFT_45978 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45978
PHATRDRAFT_46249

PHATRDRAFT_46018 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46018
PHATRDRAFT_46673 (Alginate_lyase)

PHATRDRAFT_46249 - (Alginate_lyase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46249
PHATRDRAFT_54396

PHATRDRAFT_46673 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46673
PHATRDRAFT_6839 fasciclin domain protein (Fasciclin)

PHATRDRAFT_54396 - fasciclin domain protein (Fasciclin)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54396
PHATRDRAFT_7718 myb-related protein 1 (SANT)

PHATRDRAFT_6839 - myb-related protein 1 (SANT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6839
PHATRDRAFT_8155 methionine-r-sulfoxide reductase (SelR superfamily)

PHATRDRAFT_7718 - methionine-r-sulfoxide reductase (SelR superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7718
PHATRDRAFT_8538 nitrite reductaselarge subunit (Rieske_NirD)

PHATRDRAFT_8155 - nitrite reductaselarge subunit (Rieske_NirD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8155

PHATRDRAFT_8538 - germination protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8538
GO ID Go Term p-value q-value Cluster
GO:0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system 0.0122939 1 Phatr_bicluster_0204
GO:0006725 aromatic compound metabolism 0.0244666 1 Phatr_bicluster_0204
GO:0006118 electron transport 0.0284292 1 Phatr_bicluster_0204
GO:0006508 proteolysis and peptidolysis 0.247762 1 Phatr_bicluster_0204
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