Phatr_bicluster_0129 Residual: 0.31
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_0129 0.31 Phaeodactylum tricornutum
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Displaying 1 - 28 of 28
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PHATRDRAFT_10925 ubiquitin-like protein 5 (UBQ superfamily)

PHATRDRAFT_10925 - ubiquitin-like protein 5 (UBQ superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10925
PHATRDRAFT_16067 protein kinase domain containing protein (S_TKc)

PHATRDRAFT_16067 - protein kinase domain containing protein (S_TKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16067
PHATRDRAFT_16509 complex 1lyr family (Complex1_LYR_1)

PHATRDRAFT_16509 - complex 1lyr family (Complex1_LYR_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16509
PHATRDRAFT_21970 biopterin transport-related protein bt1 (BT1)

PHATRDRAFT_21970 - biopterin transport-related protein bt1 (BT1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21970
PHATRDRAFT_23988 cytosolic glucose-6-phosphate isomerase (PLN02649)

PHATRDRAFT_23988 - cytosolic glucose-6-phosphate isomerase (PLN02649)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23988
PHATRDRAFT_29551 (MPP_superfamily superfamily)

PHATRDRAFT_29551 - (MPP_superfamily superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29551
PHATRDRAFT_35478

PHATRDRAFT_35478 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35478
PHATRDRAFT_36358 (NYN_YacP superfamily)

PHATRDRAFT_36358 - (NYN_YacP superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36358
PHATRDRAFT_36534 dtw domain (DTW superfamily)

PHATRDRAFT_36534 - dtw domain (DTW superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36534
PHATRDRAFT_37399

PHATRDRAFT_37399 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37399
PHATRDRAFT_38494

PHATRDRAFT_38494 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38494
PHATRDRAFT_40369 pdz domain protein (PDZ_signaling)

PHATRDRAFT_39961 - pdz domain protein (PDZ_signaling)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39961
PHATRDRAFT_40489 (Smr)

PHATRDRAFT_40369 - (Smr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40369
PHATRDRAFT_41298

PHATRDRAFT_40489 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40489
PHATRDRAFT_42563

PHATRDRAFT_41298 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41298
PHATRDRAFT_43163 pentatricopeptiderepeat-containing protein

PHATRDRAFT_42563 - pentatricopeptiderepeat-containing protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42563
PHATRDRAFT_43907 chromosome 20 open reading frame 67 (PCIF1_WW superfamily)

PHATRDRAFT_43163 - chromosome 20 open reading frame 67 (PCIF1_WW superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43163
PHATRDRAFT_45587

PHATRDRAFT_43907 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43907
PHATRDRAFT_46192

PHATRDRAFT_45587 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45587
PHATRDRAFT_46348 choline o-acetyltransferase(choline acetylase) (ANK)

PHATRDRAFT_46192 - choline o-acetyltransferase(choline acetylase) (ANK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46192
PHATRDRAFT_46398 (2OG-FeII_Oxy_5 superfamily)

PHATRDRAFT_46348 - (2OG-FeII_Oxy_5 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46348
PHATRDRAFT_46465

PHATRDRAFT_46398 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46398
PHATRDRAFT_48450 ring zinc finger protein (RING)

PHATRDRAFT_46465 - ring zinc finger protein (RING)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46465
PHATRDRAFT_50535

PHATRDRAFT_48450 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48450
PHATRDRAFT_50618 (DUF1279 superfamily)

PHATRDRAFT_50535 - (DUF1279 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50535
PHATRDRAFT_54088 cell surface flocculin

PHATRDRAFT_50618 - cell surface flocculin

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50618
PHATRDRAFT_55187

PHATRDRAFT_54088 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54088

PHATRDRAFT_55187 - sensory transduction histidine kinase (REC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55187
GO ID Go Term p-value q-value Cluster
GO:0006118 electron transport 0.33492 1 Phatr_bicluster_0129
GO:0006094 gluconeogenesis 0.00861852 1 Phatr_bicluster_0129
GO:0006096 glycolysis 0.0590046 1 Phatr_bicluster_0129
GO:0006298 mismatch repair 0.0103346 1 Phatr_bicluster_0129
GO:0006468 protein amino acid phosphorylation 0.262204 1 Phatr_bicluster_0129
GO:0006464 protein modification 0.104035 1 Phatr_bicluster_0129
GO:0016567 protein ubiquitination 0.118111 1 Phatr_bicluster_0129
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