Phatr_bicluster_0202 Residual: 0.37
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_0202 0.37 Phaeodactylum tricornutum
Displaying 1 - 32 of 32
PHATRDRAFT_14067 trna-pseudouridine synthase (PseudoU_synth superfamily)

PHATRDRAFT_14067 - trna-pseudouridine synthase (PseudoU_synth superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14067
PHATRDRAFT_16261 disease resistance protein

PHATRDRAFT_16261 - disease resistance protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16261
PHATRDRAFT_33313 ankyrin-repeat protein ank-1 (ANK)

PHATRDRAFT_33313 - ankyrin-repeat protein ank-1 (ANK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33313
PHATRDRAFT_38427 2og-feoxygenase family (2OG-FeII_Oxy_3)

PHATRDRAFT_38427 - 2og-feoxygenase family (2OG-FeII_Oxy_3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38427
PHATRDRAFT_38622

PHATRDRAFT_38622 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38622
PHATRDRAFT_38709

PHATRDRAFT_38709 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38709
PHATRDRAFT_39469

PHATRDRAFT_39469 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39469
PHATRDRAFT_40219

PHATRDRAFT_40219 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40219
PHATRDRAFT_40676

PHATRDRAFT_40676 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40676
PHATRDRAFT_41473

PHATRDRAFT_41473 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41473
PHATRDRAFT_41618

PHATRDRAFT_41618 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41618
PHATRDRAFT_43818

PHATRDRAFT_43818 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43818
PHATRDRAFT_43903 conserved hypothetical membrane protein

PHATRDRAFT_43903 - conserved hypothetical membrane protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43903
PHATRDRAFT_44111 mopfamily transporter (MATE_like superfamily)

PHATRDRAFT_44111 - mopfamily transporter (MATE_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44111
PHATRDRAFT_45264

PHATRDRAFT_45264 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45264
PHATRDRAFT_46264 mgc68579 protein (HATPase_c)

PHATRDRAFT_46264 - mgc68579 protein (HATPase_c)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46264
PHATRDRAFT_47257

PHATRDRAFT_47257 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47257
PHATRDRAFT_47497

PHATRDRAFT_47497 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47497
PHATRDRAFT_47715

PHATRDRAFT_47715 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47715
PHATRDRAFT_47739

PHATRDRAFT_47739 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47739
PHATRDRAFT_48447

PHATRDRAFT_48447 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48447
PHATRDRAFT_48609

PHATRDRAFT_48609 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48609
PHATRDRAFT_48642

PHATRDRAFT_48642 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48642
PHATRDRAFT_49136 heat shock transcription factor hsf1 (HSF_DNA-bind)

PHATRDRAFT_49136 - heat shock transcription factor hsf1 (HSF_DNA-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49136
PHATRDRAFT_49312 (SPS1)

PHATRDRAFT_49312 - (SPS1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49312
PHATRDRAFT_50253 apg4-d protein (Peptidase_C54 superfamily)

PHATRDRAFT_50253 - apg4-d protein (Peptidase_C54 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50253
PHATRDRAFT_50315

PHATRDRAFT_50315 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50315
PHATRDRAFT_50468 (Sulfotransfer_2 superfamily)

PHATRDRAFT_50468 - (Sulfotransfer_2 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50468
PHATRDRAFT_50508 conserved hypothetical membrane protein (DUF4395)

PHATRDRAFT_50508 - conserved hypothetical membrane protein (DUF4395)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50508
PHATRDRAFT_55091 cryptochrome dash (crypto_DASH)

PHATRDRAFT_55091 - cryptochrome dash (crypto_DASH)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55091
PHATRDRAFT_6914 peptide deformylase (Pep_deformylase)

PHATRDRAFT_6914 - peptide deformylase (Pep_deformylase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6914
PHATRDRAFT_9478 phytochelatin synthase (Phytochelatin)

PHATRDRAFT_9478 - phytochelatin synthase (Phytochelatin)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9478
GO ID Go Term p-value q-value Cluster
GO:0019538 protein metabolism 0.0522062 1 Phatr_bicluster_0202
GO:0006396 RNA processing 0.0802144 1 Phatr_bicluster_0202
GO:0006412 protein biosynthesis 0.216202 1 Phatr_bicluster_0202
GO:0006468 protein amino acid phosphorylation 0.229422 1 Phatr_bicluster_0202
GO:0006355 regulation of transcription, DNA-dependent 0.283834 1 Phatr_bicluster_0202
GO:0006118 electron transport 0.294987 1 Phatr_bicluster_0202
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