Phatr_bicluster_0250 Residual: 0.22
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_0250 0.22 Phaeodactylum tricornutum
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Displaying 1 - 20 of 20
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PHATRDRAFT_11795 proteasome beta 2 subunit (Ntn_hydrolase superfamily)

PHATRDRAFT_11795 - proteasome beta 2 subunit (Ntn_hydrolase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11795
PHATRDRAFT_12095 iron inhibited abc transporter 2 (Uup)

PHATRDRAFT_12095 - iron inhibited abc transporter 2 (Uup)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12095
PHATRDRAFT_12588 heme oxygenase1 (HemeO)

PHATRDRAFT_12588 - heme oxygenase1 (HemeO)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12588
PHATRDRAFT_21354 cytochrome c oxidase subunit 15homolog isoform 1 precursor (COX15-CtaA)

PHATRDRAFT_21354 - cytochrome c oxidase subunit 15homolog isoform 1 precursor (COX15-CtaA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21354
PHATRDRAFT_34217 (HP_PGM_like)

PHATRDRAFT_34217 - (HP_PGM_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34217
PHATRDRAFT_35594 thns2_ponpythreonine synthase-like 2 (Trp-synth-beta_II superfamily)

PHATRDRAFT_35594 - thns2_ponpythreonine synthase-like 2 (Trp-synth-beta_II superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35594
PHATRDRAFT_36629

PHATRDRAFT_36629 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36629
PHATRDRAFT_3843 protein phosphatase (PP2Cc)

PHATRDRAFT_3843 - protein phosphatase (PP2Cc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3843
PHATRDRAFT_41928 ubiquitin carboxyl-terminal esterase l3 (Peptidase_C12_UCH_L1_L3)

PHATRDRAFT_41928 - ubiquitin carboxyl-terminal esterase l3 (Peptidase_C12_UCH_L1_L3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41928
PHATRDRAFT_42896

PHATRDRAFT_42896 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42896
PHATRDRAFT_44253 (NADB_Rossmann superfamily)

PHATRDRAFT_44253 - (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44253
PHATRDRAFT_44966 dna helicase

PHATRDRAFT_44966 - dna helicase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44966
PHATRDRAFT_45185 (NADB_Rossmann superfamily)

PHATRDRAFT_45185 - (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45185
PHATRDRAFT_45614

PHATRDRAFT_45614 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45614
PHATRDRAFT_45815

PHATRDRAFT_45815 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45815
PHATRDRAFT_49245

PHATRDRAFT_47079 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47079
PHATRDRAFT_54326 prmt7 protein

PHATRDRAFT_49245 - prmt7 protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49245
PHATRDRAFT_54552 ssl1 cg11115-pa (SSL1)

PHATRDRAFT_54326 - ssl1 cg11115-pa (SSL1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54326
PHATRDRAFT_9529

PHATRDRAFT_54552 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54552

PHATRDRAFT_9529 - atp-dependent dna helicase (DEXDc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9529
GO ID Go Term p-value q-value Cluster
GO:0006511 ubiquitin-dependent protein catabolism 0.00324149 1 Phatr_bicluster_0250
GO:0006788 heme oxidation 0.00591714 1 Phatr_bicluster_0250
GO:0009088 threonine biosynthesis 0.00591714 1 Phatr_bicluster_0250
GO:0006461 protein complex assembly 0.00788271 1 Phatr_bicluster_0250
GO:0006259 DNA metabolism 0.0234852 1 Phatr_bicluster_0250
GO:0006470 protein amino acid dephosphorylation 0.0369608 1 Phatr_bicluster_0250
GO:0008152 metabolism 0.453158 1 Phatr_bicluster_0250
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