Phatr_bicluster_0227 Residual: 0.17
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_0227 0.17 Phaeodactylum tricornutum
Displaying 1 - 17 of 17
PHATRDRAFT_11490 dna replication licensing factor (MCM)

PHATRDRAFT_11490 - dna replication licensing factor (MCM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11490
PHATRDRAFT_32118 gins complex subunit 3 (GINS_A_psf3)

PHATRDRAFT_32118 - gins complex subunit 3 (GINS_A_psf3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32118
PHATRDRAFT_32848 mcm10_schpo dna replication licensing factor mcm10 (minichromosome maintenance protein 10) (cdc23 protein)

PHATRDRAFT_32848 - mcm10_schpo dna replication licensing factor mcm10 (minichromosome maintenance protein 10) (cdc23 protein)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32848
PHATRDRAFT_34931

PHATRDRAFT_34931 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34931
PHATRDRAFT_35856

PHATRDRAFT_35856 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35856
PHATRDRAFT_35859

PHATRDRAFT_35859 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35859
PHATRDRAFT_36293 nuclear protein qri2 (Nse4_C superfamily)

PHATRDRAFT_36293 - nuclear protein qri2 (Nse4_C superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36293
PHATRDRAFT_36771

PHATRDRAFT_36771 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36771
PHATRDRAFT_36907

PHATRDRAFT_36907 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36907
PHATRDRAFT_42680

PHATRDRAFT_42680 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42680
PHATRDRAFT_42914 (PRK12323)

PHATRDRAFT_42914 - (PRK12323)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42914
PHATRDRAFT_44469

PHATRDRAFT_44469 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44469
PHATRDRAFT_44850 pp2c1_yeast protein phosphatase 2c homolog 1 (pp2c-1) (PP2Cc)

PHATRDRAFT_44850 - pp2c1_yeast protein phosphatase 2c homolog 1 (pp2c-1) (PP2Cc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44850
PHATRDRAFT_44947 (PKc_like superfamily)

PHATRDRAFT_44947 - (PKc_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44947
PHATRDRAFT_46003

PHATRDRAFT_46003 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46003
PHATRDRAFT_46925

PHATRDRAFT_46925 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46925
PHATRDRAFT_48481

PHATRDRAFT_48481 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48481
GO ID Go Term p-value q-value Cluster
GO:0006468 protein amino acid phosphorylation 0.122131 1 Phatr_bicluster_0227
GO:0006270 DNA replication initiation 0.00444005 1 Phatr_bicluster_0227
GO:0006470 protein amino acid dephosphorylation 0.014015 1 Phatr_bicluster_0227
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