Phatr_bicluster_0236 Residual: 0.25
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_0236 0.25 Phaeodactylum tricornutum
Displaying 1 - 17 of 17
PHATRDRAFT_27246 dna2l protein (AAA_12)

PHATRDRAFT_27246 - dna2l protein (AAA_12)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27246
PHATRDRAFT_35545

PHATRDRAFT_35545 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35545
PHATRDRAFT_39117 two component regulator three y domain protein

PHATRDRAFT_39117 - two component regulator three y domain protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39117
PHATRDRAFT_42868

PHATRDRAFT_42868 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42868
PHATRDRAFT_43317 (DUF2088 superfamily)

PHATRDRAFT_43317 - (DUF2088 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43317
PHATRDRAFT_44199

PHATRDRAFT_44199 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44199
PHATRDRAFT_44222 enhanced disease susceptibility 5 (MATE_like superfamily)

PHATRDRAFT_44222 - enhanced disease susceptibility 5 (MATE_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44222
PHATRDRAFT_44868 leucine aminopeptidase (PRK00913)

PHATRDRAFT_44868 - leucine aminopeptidase (PRK00913)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44868
PHATRDRAFT_47791 (Ecm29 superfamily)

PHATRDRAFT_47791 - (Ecm29 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47791
PHATRDRAFT_47881 af225976_1 flavoredoxin (Flavin_Reduct)

PHATRDRAFT_47881 - af225976_1 flavoredoxin (Flavin_Reduct)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47881
PHATRDRAFT_48187 protein familywith a coiled coil-4 domain (Methyltransf_22)

PHATRDRAFT_48187 - protein familywith a coiled coil-4 domain (Methyltransf_22)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48187
PHATRDRAFT_48825

PHATRDRAFT_48825 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48825
PHATRDRAFT_49321

PHATRDRAFT_49321 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49321
PHATRDRAFT_49951 trans-golgi p230

PHATRDRAFT_49951 - trans-golgi p230

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49951
PHATRDRAFT_50146 amino acid transporter (Aa_trans superfamily)

PHATRDRAFT_50146 - amino acid transporter (Aa_trans superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50146
PHATRDRAFT_50470 (zf-MYND)

PHATRDRAFT_50470 - (zf-MYND)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50470
PHATRDRAFT_52678 (POLBc_epsilon)

PHATRDRAFT_52678 - (POLBc_epsilon)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52678
GO ID Go Term p-value q-value Cluster
GO:0006865 amino acid transport 0.0206078 1 Phatr_bicluster_0236
GO:0019538 protein metabolism 0.0264433 1 Phatr_bicluster_0236
GO:0006508 proteolysis and peptidolysis 0.156991 1 Phatr_bicluster_0236
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