Phatr_bicluster_0196 Residual: 0.27
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_0196 0.27 Phaeodactylum tricornutum
Displaying 1 - 24 of 24
PHATRDRAFT_1341 hypothetical alcohol dehydrogenase (PRK02106)

PHATRDRAFT_1341 - hypothetical alcohol dehydrogenase (PRK02106)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_1341
PHATRDRAFT_13877 light-harvesting protein (Chloroa_b-bind)

PHATRDRAFT_13877 - light-harvesting protein (Chloroa_b-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13877
PHATRDRAFT_14386 chloroplast light harvesting complex protein (Chloroa_b-bind superfamily)

PHATRDRAFT_14386 - chloroplast light harvesting complex protein (Chloroa_b-bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14386
PHATRDRAFT_16302 fucoxanthin chlorophyll a c binding protein (Chloroa_b-bind superfamily)

PHATRDRAFT_16302 - fucoxanthin chlorophyll a c binding protein (Chloroa_b-bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16302
PHATRDRAFT_20779 fructose-6-phosphate aldolase (Aldolase_Class_I superfamily)

PHATRDRAFT_20779 - fructose-6-phosphate aldolase (Aldolase_Class_I superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20779
PHATRDRAFT_22395 fucoxanthin chlorophyll protein 3 (PLN00120)

PHATRDRAFT_22395 - fucoxanthin chlorophyll protein 3 (PLN00120)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22395
PHATRDRAFT_26921 succinate-ligase (adp-forming) (PLN00124)

PHATRDRAFT_26921 - succinate-ligase (adp-forming) (PLN00124)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_26921
PHATRDRAFT_3369 galactokinase 1 (PRK05101)

PHATRDRAFT_3369 - galactokinase 1 (PRK05101)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3369
PHATRDRAFT_34932

PHATRDRAFT_34932 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34932
PHATRDRAFT_36080

PHATRDRAFT_36080 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36080
PHATRDRAFT_36666

PHATRDRAFT_36666 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36666
PHATRDRAFT_36932 (Condensation superfamily)

PHATRDRAFT_36932 - (Condensation superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36932
PHATRDRAFT_3969 acetylglutamate kinase (AAK_NAGK-like)

PHATRDRAFT_3969 - acetylglutamate kinase (AAK_NAGK-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3969
PHATRDRAFT_42787

PHATRDRAFT_42787 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42787
PHATRDRAFT_44050 h+v1 subunit g2 (V-ATPase_G superfamily)

PHATRDRAFT_44050 - h+v1 subunit g2 (V-ATPase_G superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44050
PHATRDRAFT_48476

PHATRDRAFT_48476 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48476
PHATRDRAFT_48784 exopolysaccharide polymerization protein (PS_pyruv_trans superfamily)

PHATRDRAFT_48784 - exopolysaccharide polymerization protein (PS_pyruv_trans superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48784
PHATRDRAFT_48901

PHATRDRAFT_48901 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48901
PHATRDRAFT_49248

PHATRDRAFT_49248 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49248
PHATRDRAFT_49764 mitochondrial carrier protein (Mito_carr)

PHATRDRAFT_49764 - mitochondrial carrier protein (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49764
PHATRDRAFT_53933 (ABC_ATPase superfamily)

PHATRDRAFT_53933 - (ABC_ATPase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_53933
PHATRDRAFT_54168 mgdg synthase type a (PLN02605)

PHATRDRAFT_54168 - mgdg synthase type a (PLN02605)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54168
PHATRDRAFT_54534 tba2_pelfatubulin alpha-2 chain (PLN00221)

PHATRDRAFT_54534 - tba2_pelfatubulin alpha-2 chain (PLN00221)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54534
PHATRDRAFT_55057 photosystem ii reaction center m protein precursor (PsbM superfamily)

PHATRDRAFT_55057 - photosystem ii reaction center m protein precursor (PsbM superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55057
GO ID Go Term p-value q-value Cluster
GO:0009765 photosynthesis light harvesting 0.0000123 0.0285008 Phatr_bicluster_0196
GO:0046835 carbohydrate phosphorylation 0.00395159 1 Phatr_bicluster_0196
GO:0006561 proline biosynthesis 0.019612 1 Phatr_bicluster_0196
GO:0006012 galactose metabolism 0.019612 1 Phatr_bicluster_0196
GO:0006526 arginine biosynthesis 0.0273554 1 Phatr_bicluster_0196
GO:0008652 amino acid biosynthesis 0.0273554 1 Phatr_bicluster_0196
GO:0016310 phosphorylation 0.0540081 1 Phatr_bicluster_0196
GO:0005975 carbohydrate metabolism 0.222271 1 Phatr_bicluster_0196
GO:0008152 metabolism 0.325688 1 Phatr_bicluster_0196
GO:0006457 protein folding 0.375018 1 Phatr_bicluster_0196
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