Phatr_bicluster_0166 Residual: 0.21
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_0166 0.21 Phaeodactylum tricornutum
Displaying 1 - 23 of 23
PHATRDRAFT_32851 fructose-6-phosphate 2-kinase fructose--biphosphatase (AAA_17 superfamily)

PHATRDRAFT_17495 - fructose-6-phosphate 2-kinase fructose--biphosphatase (AAA_17 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17495
PHATRDRAFT_34059 glycine oxidase (NAD_binding_8 superfamily)

PHATRDRAFT_31544 - glycine oxidase (NAD_binding_8 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31544
PHATRDRAFT_35895 c1galt1-specific chaperone 1

PHATRDRAFT_32851 - c1galt1-specific chaperone 1

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32851
PHATRDRAFT_38045

PHATRDRAFT_34059 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34059
PHATRDRAFT_42891

PHATRDRAFT_35895 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35895
PHATRDRAFT_43271

PHATRDRAFT_38045 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38045
PHATRDRAFT_43649

PHATRDRAFT_42891 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42891
PHATRDRAFT_44272 mgc114783 protein

PHATRDRAFT_43271 - mgc114783 protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43271
PHATRDRAFT_45125 nadph-dependent fmn fad containing (FNR_like superfamily)

PHATRDRAFT_43649 - nadph-dependent fmn fad containing (FNR_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43649
PHATRDRAFT_45267 deacetylase sulfotransferase

PHATRDRAFT_44272 - deacetylase sulfotransferase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44272
PHATRDRAFT_45348 4-hydroxybenzoate octaprenyltransferase (PT_UbiA superfamily)

PHATRDRAFT_45125 - 4-hydroxybenzoate octaprenyltransferase (PT_UbiA superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45125
PHATRDRAFT_45577

PHATRDRAFT_45267 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45267
PHATRDRAFT_45629 cupin 4 (Cupin_8 superfamily)

PHATRDRAFT_45348 - cupin 4 (Cupin_8 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45348
PHATRDRAFT_45684

PHATRDRAFT_45577 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45577
PHATRDRAFT_45891

PHATRDRAFT_45629 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45629
PHATRDRAFT_45910 ferredoxin (bacterial type ferredoxin family) (Fer4_15)

PHATRDRAFT_45684 - ferredoxin (bacterial type ferredoxin family) (Fer4_15)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45684
PHATRDRAFT_46664

PHATRDRAFT_45891 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45891
PHATRDRAFT_46720

PHATRDRAFT_45910 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45910
PHATRDRAFT_46742 d-lactate dehydrogenase (PRK11183)

PHATRDRAFT_46664 - d-lactate dehydrogenase (PRK11183)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46664
PHATRDRAFT_47186 transcriptional repressor (NADB_Rossmann superfamily)

PHATRDRAFT_46720 - transcriptional repressor (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46720
PHATRDRAFT_8970 mc family transporter

PHATRDRAFT_46742 - mc family transporter

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46742

PHATRDRAFT_47186 - dna repair protein (RecN)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47186

PHATRDRAFT_8970 - probable sensor response regulator hybrid (REC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8970
GO ID Go Term p-value q-value Cluster
GO:0006118 electron transport 0.00159697 1 Phatr_bicluster_0166
GO:0007218 neuropeptide signaling pathway 0.00246975 1 Phatr_bicluster_0166
GO:0006003 fructose 2,6-bisphosphate metabolism 0.004934 1 Phatr_bicluster_0166
GO:0000160 two-component signal transduction system (phosphorelay) 0.0624567 1 Phatr_bicluster_0166
GO:0006810 transport 0.38354 1 Phatr_bicluster_0166
GO:0006355 regulation of transcription, DNA-dependent 0.426896 1 Phatr_bicluster_0166
GO:0008152 metabolism 0.529843 1 Phatr_bicluster_0166
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