Phatr_bicluster_0078 Residual: 0.34
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_0078 0.34 Phaeodactylum tricornutum
Displaying 1 - 19 of 19
PHATRDRAFT_16798 synaptobrevin 8-1 (Synaptobrevin)

PHATRDRAFT_16798 - synaptobrevin 8-1 (Synaptobrevin)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16798
PHATRDRAFT_27067 abc transporter like protein (AarF)

PHATRDRAFT_27067 - abc transporter like protein (AarF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27067
PHATRDRAFT_30461 sterol delta7 reductase (ERG4_ERG24 superfamily)

PHATRDRAFT_30461 - sterol delta7 reductase (ERG4_ERG24 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30461
PHATRDRAFT_34919

PHATRDRAFT_34919 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34919
PHATRDRAFT_4074 atnadk-3 nadk3 (nadkinase 3) nad+ kinase nadh kinase (PLN02929)

PHATRDRAFT_4074 - atnadk-3 nadk3 (nadkinase 3) nad+ kinase nadh kinase (PLN02929)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_4074
PHATRDRAFT_42741 tpr repeat protein (Sulfotransfer_1 superfamily)

PHATRDRAFT_42741 - tpr repeat protein (Sulfotransfer_1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42741
PHATRDRAFT_44044 npl4 family protein (MPN_NPL4)

PHATRDRAFT_44044 - npl4 family protein (MPN_NPL4)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44044
PHATRDRAFT_44089 arp1 actin-related protein 1 homologcentractin alpha (ACTIN)

PHATRDRAFT_44089 - arp1 actin-related protein 1 homologcentractin alpha (ACTIN)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44089
PHATRDRAFT_44716 proteinmembrane associated tyrosine threonine 1 (PKc)

PHATRDRAFT_44716 - proteinmembrane associated tyrosine threonine 1 (PKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44716
PHATRDRAFT_45928 phytanoyl-dioxygenase (PhyH superfamily)

PHATRDRAFT_45928 - phytanoyl-dioxygenase (PhyH superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45928
PHATRDRAFT_47187 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy--benzoquinol methylase-like protein

PHATRDRAFT_47187 - 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy--benzoquinol methylase-like protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47187
PHATRDRAFT_48012 casein kinasedelta isoform 1 (Pkinase)

PHATRDRAFT_48012 - casein kinasedelta isoform 1 (Pkinase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48012
PHATRDRAFT_48385

PHATRDRAFT_48385 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48385
PHATRDRAFT_49335 duf647 family protein (DUF647)

PHATRDRAFT_49335 - duf647 family protein (DUF647)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49335
PHATRDRAFT_49466

PHATRDRAFT_49466 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49466
PHATRDRAFT_49501 deacetylase sulfotransferase

PHATRDRAFT_49501 - deacetylase sulfotransferase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49501
PHATRDRAFT_49942

PHATRDRAFT_49942 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49942
PHATRDRAFT_50237

PHATRDRAFT_50237 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50237
PHATRDRAFT_50431

PHATRDRAFT_50431 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50431
GO ID Go Term p-value q-value Cluster
GO:0006468 protein amino acid phosphorylation 0.000707349 1 Phatr_bicluster_0078
GO:0016192 vesicle-mediated transport 0.0159584 1 Phatr_bicluster_0078
GO:0006810 transport 0.21473 1 Phatr_bicluster_0078
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