Phatr_bicluster_0240 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_0240 0.31 Phaeodactylum tricornutum
Displaying 1 - 25 of 25
PHATRDRAFT_18911 aspartate--ammonia ligase (class_II_aaRS-like_core superfamily)

PHATRDRAFT_18911 - aspartate--ammonia ligase (class_II_aaRS-like_core superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18911
PHATRDRAFT_32218

PHATRDRAFT_32218 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32218
PHATRDRAFT_33006 (Methyltransf_16 superfamily)

PHATRDRAFT_33006 - (Methyltransf_16 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33006
PHATRDRAFT_34528

PHATRDRAFT_34528 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34528
PHATRDRAFT_34746

PHATRDRAFT_34746 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34746
PHATRDRAFT_34848

PHATRDRAFT_34848 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34848
PHATRDRAFT_35739 (DUF202)

PHATRDRAFT_35739 - (DUF202)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35739
PHATRDRAFT_42479 temporarily assigned gene name family member (tag-148) (Zip)

PHATRDRAFT_42479 - temporarily assigned gene name family member (tag-148) (Zip)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42479
PHATRDRAFT_43109 oxygenase-like protein

PHATRDRAFT_43109 - oxygenase-like protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43109
PHATRDRAFT_43402 (APG6)

PHATRDRAFT_43402 - (APG6)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43402
PHATRDRAFT_43423

PHATRDRAFT_43423 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43423
PHATRDRAFT_43684 aldehyde reductase (Aldo_ket_red)

PHATRDRAFT_43684 - aldehyde reductase (Aldo_ket_red)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43684
PHATRDRAFT_44363 (DnaQ_like_exo superfamily)

PHATRDRAFT_44363 - (DnaQ_like_exo superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44363
PHATRDRAFT_44428

PHATRDRAFT_44428 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44428
PHATRDRAFT_44445 eukaryotic translation initiation factor 2-alpha kinase 3 (Luminal_IRE1_like)

PHATRDRAFT_44445 - eukaryotic translation initiation factor 2-alpha kinase 3 (Luminal_IRE1_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44445
PHATRDRAFT_44727

PHATRDRAFT_44727 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44727
PHATRDRAFT_45225

PHATRDRAFT_45225 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45225
PHATRDRAFT_45419 myosinisoform cra_a

PHATRDRAFT_45419 - myosinisoform cra_a

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45419
PHATRDRAFT_45632

PHATRDRAFT_45632 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45632
PHATRDRAFT_46175 nitric oxide synthase interacting protein

PHATRDRAFT_46175 - nitric oxide synthase interacting protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46175
PHATRDRAFT_46556 channelhemolysin iii family (HlyIII)

PHATRDRAFT_46556 - channelhemolysin iii family (HlyIII)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46556
PHATRDRAFT_47174 conserved hypothetical (Methyltransf_24)

PHATRDRAFT_47174 - conserved hypothetical (Methyltransf_24)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47174
PHATRDRAFT_47535 (DUF1294)

PHATRDRAFT_47535 - (DUF1294)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47535
PHATRDRAFT_49095

PHATRDRAFT_49095 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49095
PHATRDRAFT_54602 tpr repeat (TPR_12)

PHATRDRAFT_54602 - tpr repeat (TPR_12)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54602
GO ID Go Term p-value q-value Cluster
GO:0006529 asparagine biosynthesis 0.0039472 1 Phatr_bicluster_0240
GO:0030001 metal ion transport 0.0157187 1 Phatr_bicluster_0240
GO:0006418 tRNA aminoacylation for protein translation 0.0504079 1 Phatr_bicluster_0240
GO:0006468 protein amino acid phosphorylation 0.15945 1 Phatr_bicluster_0240
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