Phatr_bicluster_0094 Residual: 0.29
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_0094 0.29 Phaeodactylum tricornutum
Displaying 1 - 21 of 21
PHATRDRAFT_14467 mitochondrion protein (MPC superfamily)

PHATRDRAFT_14467 - mitochondrion protein (MPC superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14467
PHATRDRAFT_23811 5-methylthioribose kinase family protein (mtnK)

PHATRDRAFT_23811 - 5-methylthioribose kinase family protein (mtnK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23811
PHATRDRAFT_24353 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (PLN02291)

PHATRDRAFT_24353 - 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (PLN02291)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_24353
PHATRDRAFT_32315

PHATRDRAFT_32315 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32315
PHATRDRAFT_33007

PHATRDRAFT_33007 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33007
PHATRDRAFT_34460

PHATRDRAFT_34460 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34460
PHATRDRAFT_34642

PHATRDRAFT_34642 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34642
PHATRDRAFT_42606 (SET)

PHATRDRAFT_42606 - (SET)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42606
PHATRDRAFT_43277 chorismate mutase (PLN02344)

PHATRDRAFT_43277 - chorismate mutase (PLN02344)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43277
PHATRDRAFT_43463 (Lipase_3)

PHATRDRAFT_43463 - (Lipase_3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43463
PHATRDRAFT_43545 (Ric8 superfamily)

PHATRDRAFT_43545 - (Ric8 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43545
PHATRDRAFT_44243

PHATRDRAFT_44243 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44243
PHATRDRAFT_44776 component of oligomeric golgi complex 2 (DUF3510)

PHATRDRAFT_44776 - component of oligomeric golgi complex 2 (DUF3510)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44776
PHATRDRAFT_46100

PHATRDRAFT_46100 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46100
PHATRDRAFT_46439

PHATRDRAFT_46439 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46439
PHATRDRAFT_46734 53-exonuclease n- and i-domain-containing protein (WRN_exo)

PHATRDRAFT_46734 - 53-exonuclease n- and i-domain-containing protein (WRN_exo)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46734
PHATRDRAFT_47265 emb2745 (embryo defective 2745) binding

PHATRDRAFT_47265 - emb2745 (embryo defective 2745) binding

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47265
PHATRDRAFT_47590

PHATRDRAFT_47590 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47590
PHATRDRAFT_51058 mgc79146 protein (ATP-synt_D)

PHATRDRAFT_51058 - mgc79146 protein (ATP-synt_D)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51058
PHATRDRAFT_54331 mlh1 protein (mutl)

PHATRDRAFT_54331 - mlh1 protein (mutl)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54331
PHATRDRAFT_9625 presenilin family protein (Peptidase_A22B superfamily)

PHATRDRAFT_9625 - presenilin family protein (Peptidase_A22B superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9625
GO ID Go Term p-value q-value Cluster
GO:0009073 aromatic amino acid family biosynthesis 0.0000341 0.0786566 Phatr_bicluster_0094
GO:0009086 methionine biosynthesis 0.00788271 1 Phatr_bicluster_0094
GO:0006629 lipid metabolism 0.0350457 1 Phatr_bicluster_0094
GO:0006413 translational initiation 0.0464863 1 Phatr_bicluster_0094
GO:0006281 DNA repair 0.0652904 1 Phatr_bicluster_0094
GO:0015986 ATP synthesis coupled proton transport 0.0708679 1 Phatr_bicluster_0094
GO:0007242 intracellular signaling cascade 0.0800992 1 Phatr_bicluster_0094
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