Phatr_bicluster_0116 Residual: 0.40
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_0116 0.40 Phaeodactylum tricornutum
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Displaying 1 - 27 of 27
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PHATRDRAFT_16870 hmdh2_dicdi3-hydroxy-3-methylglutaryl-coenzyme a reductase 2 (hmg-reductase 2) (HMG-CoA_reductase_classI)

PHATRDRAFT_16870 - hmdh2_dicdi3-hydroxy-3-methylglutaryl-coenzyme a reductase 2 (hmg-reductase 2) (HMG-CoA_reductase_classI)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16870
PHATRDRAFT_22166 zinc transporter (Zip superfamily)

PHATRDRAFT_22166 - zinc transporter (Zip superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22166
PHATRDRAFT_33568 cytochrome p450 (p450 superfamily)

PHATRDRAFT_33568 - cytochrome p450 (p450 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33568
PHATRDRAFT_36211

PHATRDRAFT_36211 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36211
PHATRDRAFT_37703

PHATRDRAFT_37703 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37703
PHATRDRAFT_38294 (HSF)

PHATRDRAFT_38294 - (HSF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38294
PHATRDRAFT_39366

PHATRDRAFT_39366 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39366
PHATRDRAFT_39949 lpp3 (lipid phosphate phosphatase 3) (PAP2_like superfamily)

PHATRDRAFT_39949 - lpp3 (lipid phosphate phosphatase 3) (PAP2_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39949
PHATRDRAFT_43594 pdz dhr glgf (DUF399 superfamily)

PHATRDRAFT_43594 - pdz dhr glgf (DUF399 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43594
PHATRDRAFT_43878 ion transport protein (Ion_trans)

PHATRDRAFT_43878 - ion transport protein (Ion_trans)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43878
PHATRDRAFT_43957

PHATRDRAFT_43957 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43957
PHATRDRAFT_44085

PHATRDRAFT_44085 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44085
PHATRDRAFT_44097

PHATRDRAFT_44097 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44097
PHATRDRAFT_47930 histidine kinase response regulator hybrid protein (REC)

PHATRDRAFT_47930 - histidine kinase response regulator hybrid protein (REC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47930
PHATRDRAFT_48148

PHATRDRAFT_48148 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48148
PHATRDRAFT_48179 myb-like dna-binding domain containing protein

PHATRDRAFT_48179 - myb-like dna-binding domain containing protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48179
PHATRDRAFT_48210

PHATRDRAFT_48210 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48210
PHATRDRAFT_48357

PHATRDRAFT_48357 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48357
PHATRDRAFT_48597 helicase domain protein (HA)

PHATRDRAFT_48597 - helicase domain protein (HA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48597
PHATRDRAFT_48696

PHATRDRAFT_48696 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48696
PHATRDRAFT_48747 (JmjC)

PHATRDRAFT_48747 - (JmjC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48747
PHATRDRAFT_49190

PHATRDRAFT_49190 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49190
PHATRDRAFT_50059 cj022_human uncharacterized protein c10orf22 (DUF1637 superfamily)

PHATRDRAFT_50059 - cj022_human uncharacterized protein c10orf22 (DUF1637 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50059
PHATRDRAFT_50497 adenylate cyclase (CHD)

PHATRDRAFT_50497 - adenylate cyclase (CHD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50497
PHATRDRAFT_50607 methyltransferase protein (Methyltransf_21)

PHATRDRAFT_50607 - methyltransferase protein (Methyltransf_21)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50607
PHATRDRAFT_52551 n-acetylglucosaminyl transferase component (Gpi1 superfamily)

PHATRDRAFT_52551 - n-acetylglucosaminyl transferase component (Gpi1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52551
PHATRDRAFT_55209 (Carboxyl_trans)

PHATRDRAFT_55209 - (Carboxyl_trans)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55209
GO ID Go Term p-value q-value Cluster
GO:0006412 protein biosynthesis 0.456487 1 Phatr_bicluster_0116
GO:0006468 protein amino acid phosphorylation 0.479142 1 Phatr_bicluster_0116
GO:0007165 signal transduction 0.0125788 1 Phatr_bicluster_0116
GO:0006811 ion transport 0.0400529 1 Phatr_bicluster_0116
GO:0030001 metal ion transport 0.0577592 1 Phatr_bicluster_0116
GO:0009190 cyclic nucleotide biosynthesis 0.0612637 1 Phatr_bicluster_0116
GO:0006629 lipid metabolism 0.064756 1 Phatr_bicluster_0116
GO:0000160 two-component signal transduction system (phosphorelay) 0.0922612 1 Phatr_bicluster_0116
GO:0006812 cation transport 0.0956458 1 Phatr_bicluster_0116
GO:0000074 regulation of cell cycle 0.11901 1 Phatr_bicluster_0116
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