Phatr_bicluster_0014 Residual: 0.30
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_0014 0.30 Phaeodactylum tricornutum
Displaying 1 - 25 of 25
PHATRDRAFT_10988 permease

PHATRDRAFT_10988 - permease

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10988
PHATRDRAFT_12043 at4g20760 f21c20_110 (carb_red_sniffer_like_SDR_c)

PHATRDRAFT_12043 - at4g20760 f21c20_110 (carb_red_sniffer_like_SDR_c)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12043
PHATRDRAFT_12577 protein phosphatase (PP2Cc)

PHATRDRAFT_12577 - protein phosphatase (PP2Cc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12577
PHATRDRAFT_15060 (PTZ00341)

PHATRDRAFT_15060 - (PTZ00341)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15060
PHATRDRAFT_20547 dihydroxy-acid dehydratase (PRK00911)

PHATRDRAFT_20547 - dihydroxy-acid dehydratase (PRK00911)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20547
PHATRDRAFT_31906 aldh_linusprobable aldehyde dehydrogenase (flax-inducible sequence 1) (ALDH-SF superfamily)

PHATRDRAFT_31906 - aldh_linusprobable aldehyde dehydrogenase (flax-inducible sequence 1) (ALDH-SF superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31906
PHATRDRAFT_31997 (RING superfamily)

PHATRDRAFT_31997 - (RING superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31997
PHATRDRAFT_32775

PHATRDRAFT_32775 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32775
PHATRDRAFT_33783

PHATRDRAFT_33783 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33783
PHATRDRAFT_35332 notch homolog scalloped wings

PHATRDRAFT_35332 - notch homolog scalloped wings

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35332
PHATRDRAFT_35579 glutathione s-transferase (Gst)

PHATRDRAFT_35579 - glutathione s-transferase (Gst)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35579
PHATRDRAFT_36289 glycosyltransferase aer61 (DUF563)

PHATRDRAFT_36289 - glycosyltransferase aer61 (DUF563)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36289
PHATRDRAFT_42807 ran-specific gtpase-activating protein (RanBD_family)

PHATRDRAFT_42712 - ran-specific gtpase-activating protein (RanBD_family)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42712
PHATRDRAFT_43024 chromosome 7 open reading frame 30 (Oligomerization)

PHATRDRAFT_42807 - chromosome 7 open reading frame 30 (Oligomerization)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42807
PHATRDRAFT_43588 tetratricopeptide tpr_2 (TPR_12)

PHATRDRAFT_43024 - tetratricopeptide tpr_2 (TPR_12)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43024
PHATRDRAFT_44297

PHATRDRAFT_43588 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43588
PHATRDRAFT_44551 (CP12 superfamily)

PHATRDRAFT_44297 - (CP12 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44297
PHATRDRAFT_45080 (Chorein_N)

PHATRDRAFT_44551 - (Chorein_N)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44551
PHATRDRAFT_45834

PHATRDRAFT_45080 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45080
PHATRDRAFT_45921 asp (abnormal spindle)-microcephaly associated

PHATRDRAFT_45834 - asp (abnormal spindle)-microcephaly associated

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45834
PHATRDRAFT_46825 nucleoredoxin 1 (Thioredoxin_like superfamily)

PHATRDRAFT_45921 - nucleoredoxin 1 (Thioredoxin_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45921
PHATRDRAFT_46898

PHATRDRAFT_46825 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46825
PHATRDRAFT_51761

PHATRDRAFT_46898 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46898
PHATRDRAFT_9323 germination protein

PHATRDRAFT_51761 - germination protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51761

PHATRDRAFT_9323 - chloroplast polyprotein of elongation factor ts precursor (S1_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9323
GO ID Go Term p-value q-value Cluster
GO:0009082 branched chain family amino acid biosynthesis 0.00394818 1 Phatr_bicluster_0014
GO:0006118 electron transport 0.3726 1 Phatr_bicluster_0014
GO:0006096 glycolysis 0.0671528 1 Phatr_bicluster_0014
GO:0008152 metabolism 0.0161272 1 Phatr_bicluster_0014
GO:0006470 protein amino acid dephosphorylation 0.0369608 1 Phatr_bicluster_0014
GO:0051341 regulation of oxidoreductase activity 0.0312056 1 Phatr_bicluster_0014
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