Phatr_bicluster_0233 Residual: 0.25
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_0233 0.25 Phaeodactylum tricornutum
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Displaying 1 - 25 of 25
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PHATRDRAFT_11021 branched-chain alpha-keto acid decarboxylase e1 beta subunit (PTZ00182)

PHATRDRAFT_11021 - branched-chain alpha-keto acid decarboxylase e1 beta subunit (PTZ00182)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11021
PHATRDRAFT_1905 ibr domain protein (IBR)

PHATRDRAFT_1905 - ibr domain protein (IBR)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_1905
PHATRDRAFT_20310 acyl-coenzyme ashort branched chain (ACAD superfamily)

PHATRDRAFT_20310 - acyl-coenzyme ashort branched chain (ACAD superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20310
PHATRDRAFT_35818 methylated-dna--protein-cysteine methyltransferase (ATase)

PHATRDRAFT_35818 - methylated-dna--protein-cysteine methyltransferase (ATase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35818
PHATRDRAFT_42604

PHATRDRAFT_42604 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42604
PHATRDRAFT_43085

PHATRDRAFT_43085 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43085
PHATRDRAFT_43181

PHATRDRAFT_43181 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43181
PHATRDRAFT_43188

PHATRDRAFT_43188 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43188
PHATRDRAFT_43304

PHATRDRAFT_43304 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43304
PHATRDRAFT_43862

PHATRDRAFT_43862 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43862
PHATRDRAFT_43899 riken cdna 2810055g22 gene

PHATRDRAFT_43899 - riken cdna 2810055g22 gene

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43899
PHATRDRAFT_44106 amine oxidase (Amino_oxidase)

PHATRDRAFT_44106 - amine oxidase (Amino_oxidase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44106
PHATRDRAFT_44412 riken cdnaisoform cra_b

PHATRDRAFT_44412 - riken cdnaisoform cra_b

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44412
PHATRDRAFT_44732

PHATRDRAFT_44732 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44732
PHATRDRAFT_44934

PHATRDRAFT_44934 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44934
PHATRDRAFT_45054 metallo-beta-lactamase family protein (GloB)

PHATRDRAFT_45054 - metallo-beta-lactamase family protein (GloB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45054
PHATRDRAFT_45160 (ANK)

PHATRDRAFT_45160 - (ANK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45160
PHATRDRAFT_45612 cog4371: membrane protein (DUF1517 superfamily)

PHATRDRAFT_45612 - cog4371: membrane protein (DUF1517 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45612
PHATRDRAFT_46423 tumor differentially expressed 2-like (Serinc superfamily)

PHATRDRAFT_46423 - tumor differentially expressed 2-like (Serinc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46423
PHATRDRAFT_46602

PHATRDRAFT_46602 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46602
PHATRDRAFT_46752 (CHD)

PHATRDRAFT_46752 - (CHD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46752
PHATRDRAFT_46805

PHATRDRAFT_46805 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46805
PHATRDRAFT_47817 wd domain containingexpressed

PHATRDRAFT_47817 - wd domain containingexpressed

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47817
PHATRDRAFT_50213

PHATRDRAFT_50213 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50213
PHATRDRAFT_54219 mgc85493 protein (PLN02528)

PHATRDRAFT_54219 - mgc85493 protein (PLN02528)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54219
GO ID Go Term p-value q-value Cluster
GO:0051341 regulation of oxidoreductase activity 0.0312056 1 Phatr_bicluster_0233
GO:0009190 cyclic nucleotide biosynthesis 0.0331273 1 Phatr_bicluster_0233
GO:0006281 DNA repair 0.0652904 1 Phatr_bicluster_0233
GO:0007242 intracellular signaling cascade 0.0800992 1 Phatr_bicluster_0233
GO:0016567 protein ubiquitination 0.13382 1 Phatr_bicluster_0233
GO:0006118 electron transport 0.00808825 1 Phatr_bicluster_0233
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