Phatr_bicluster_0109 Residual: 0.44
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_0109 0.44 Phaeodactylum tricornutum
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Displaying 1 - 27 of 27
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PHATRDRAFT_11720 1-phosphatidylinositol-4-phosphate 5-kinase zinc ion binding (FYVE)

PHATRDRAFT_11720 - 1-phosphatidylinositol-4-phosphate 5-kinase zinc ion binding (FYVE)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11720
PHATRDRAFT_31874

PHATRDRAFT_31571 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31571
PHATRDRAFT_31876

PHATRDRAFT_31874 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31874
PHATRDRAFT_33153

PHATRDRAFT_31876 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31876
PHATRDRAFT_34716

PHATRDRAFT_33153 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33153
PHATRDRAFT_36402 nad-dependent epimerase dehydratase (NADB_Rossmann superfamily)

PHATRDRAFT_34716 - nad-dependent epimerase dehydratase (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34716
PHATRDRAFT_36892

PHATRDRAFT_36402 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36402
PHATRDRAFT_39667 mgc132032 protein (CCL1)

PHATRDRAFT_36892 - mgc132032 protein (CCL1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36892
PHATRDRAFT_40651

PHATRDRAFT_39667 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39667
PHATRDRAFT_41403

PHATRDRAFT_40651 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40651
PHATRDRAFT_42698

PHATRDRAFT_41403 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41403
PHATRDRAFT_42870

PHATRDRAFT_42698 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42698
PHATRDRAFT_43229

PHATRDRAFT_42870 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42870
PHATRDRAFT_43252

PHATRDRAFT_43229 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43229
PHATRDRAFT_44963

PHATRDRAFT_43252 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43252
PHATRDRAFT_45584

PHATRDRAFT_44963 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44963
PHATRDRAFT_45604 mfs family transporter: multidrug efflux (MFS)

PHATRDRAFT_45584 - mfs family transporter: multidrug efflux (MFS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45584
PHATRDRAFT_46308 aspm_bovinabnormal spindle-like microcephaly-associated protein homolog

PHATRDRAFT_45604 - aspm_bovinabnormal spindle-like microcephaly-associated protein homolog

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45604
PHATRDRAFT_46487

PHATRDRAFT_46308 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46308
PHATRDRAFT_46569

PHATRDRAFT_46487 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46487
PHATRDRAFT_46895 pollen coat oleosin-glycine rich protein (PHA03247)

PHATRDRAFT_46569 - pollen coat oleosin-glycine rich protein (PHA03247)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46569
PHATRDRAFT_47974

PHATRDRAFT_46895 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46895
PHATRDRAFT_48498

PHATRDRAFT_47974 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47974
PHATRDRAFT_48621

PHATRDRAFT_48498 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48498
PHATRDRAFT_5808

PHATRDRAFT_48621 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48621

PHATRDRAFT_5808 - ppax_caeelacid phosphatase (Fra10Ac1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5808

PHATRDRAFT_5951 - multi-sensor hybrid histidine kinase (REC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5951
GO ID Go Term p-value q-value Cluster
GO:0009225 nucleotide-sugar metabolism 0.0171733 1 Phatr_bicluster_0109
GO:0000160 two-component signal transduction system (phosphorelay) 0.0624567 1 Phatr_bicluster_0109
GO:0000074 regulation of cell cycle 0.080955 1 Phatr_bicluster_0109
GO:0015986 ATP synthesis coupled proton transport 0.0878067 1 Phatr_bicluster_0109
GO:0006310 DNA recombination 0.0878067 1 Phatr_bicluster_0109
GO:0007165 signal transduction 0.110315 1 Phatr_bicluster_0109
GO:0005975 carbohydrate metabolism 0.14529 1 Phatr_bicluster_0109
GO:0006810 transport 0.38354 1 Phatr_bicluster_0109
GO:0006355 regulation of transcription, DNA-dependent 0.426896 1 Phatr_bicluster_0109
GO:0006508 proteolysis and peptidolysis 0.434343 1 Phatr_bicluster_0109
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