Phatr_bicluster_0182 Residual: 0.31
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_0182 0.31 Phaeodactylum tricornutum
Displaying 1 - 21 of 21
PHATRDRAFT_12198 protein kinase familyexpressed (PKc_like superfamily)

PHATRDRAFT_12198 - protein kinase familyexpressed (PKc_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12198
PHATRDRAFT_32629

PHATRDRAFT_32629 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32629
PHATRDRAFT_33028 allergen v5 tpx-1 related (SCP_bacterial)

PHATRDRAFT_33028 - allergen v5 tpx-1 related (SCP_bacterial)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33028
PHATRDRAFT_34488 elongation factor-2 kinase (Alpha_kinase)

PHATRDRAFT_34488 - elongation factor-2 kinase (Alpha_kinase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34488
PHATRDRAFT_36022

PHATRDRAFT_36022 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36022
PHATRDRAFT_42824 af208544_1heat stress transcription factor a3 (HSF_DNA-bind)

PHATRDRAFT_42824 - af208544_1heat stress transcription factor a3 (HSF_DNA-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42824
PHATRDRAFT_43052 na h exchanger family member (nhx-8) (NhaP)

PHATRDRAFT_43052 - na h exchanger family member (nhx-8) (NhaP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43052
PHATRDRAFT_43394 (DUF221)

PHATRDRAFT_43394 - (DUF221)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43394
PHATRDRAFT_44285

PHATRDRAFT_44285 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44285
PHATRDRAFT_44301

PHATRDRAFT_44301 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44301
PHATRDRAFT_44316

PHATRDRAFT_44316 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44316
PHATRDRAFT_44800

PHATRDRAFT_44800 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44800
PHATRDRAFT_44828 proteophosphoglycan ppg4

PHATRDRAFT_44828 - proteophosphoglycan ppg4

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44828
PHATRDRAFT_44889 monovalent cation:proton antiporter-2family (Na_H_Exchanger)

PHATRDRAFT_44889 - monovalent cation:proton antiporter-2family (Na_H_Exchanger)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44889
PHATRDRAFT_45061

PHATRDRAFT_45061 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45061
PHATRDRAFT_45518 patatin-like serine (Pat_PLPL)

PHATRDRAFT_45518 - patatin-like serine (Pat_PLPL)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45518
PHATRDRAFT_45635

PHATRDRAFT_45635 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45635
PHATRDRAFT_46048

PHATRDRAFT_46048 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46048
PHATRDRAFT_46597

PHATRDRAFT_46597 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46597
PHATRDRAFT_49001

PHATRDRAFT_49001 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49001
PHATRDRAFT_55097 cpk19 (calcium-dependent protein kinase 19) calcium- and calmodulin-dependent protein kinase kinase (EFh)

PHATRDRAFT_55097 - cpk19 (calcium-dependent protein kinase 19) calcium- and calmodulin-dependent protein kinase kinase (EFh)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55097
GO ID Go Term p-value q-value Cluster
GO:0006885 regulation of pH 0.00984487 1 Phatr_bicluster_0182
GO:0006814 sodium ion transport 0.0135166 1 Phatr_bicluster_0182
GO:0006468 protein amino acid phosphorylation 0.0164838 1 Phatr_bicluster_0182
GO:0006355 regulation of transcription, DNA-dependent 0.24283 1 Phatr_bicluster_0182
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