Phatr_bicluster_0112 Residual: 0.35
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_0112 0.35 Phaeodactylum tricornutum
Displaying 1 - 28 of 28
PHATRDRAFT_16401 endoplasmic reticulum nucleotide sugar transporter (UAA)

PHATRDRAFT_16401 - endoplasmic reticulum nucleotide sugar transporter (UAA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16401
PHATRDRAFT_19669 vacuolar protein sorting 28 (VPS28 superfamily)

PHATRDRAFT_19669 - vacuolar protein sorting 28 (VPS28 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19669
PHATRDRAFT_32087 cyclin a homolog (Cyclin_C)

PHATRDRAFT_32087 - cyclin a homolog (Cyclin_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32087
PHATRDRAFT_37181

PHATRDRAFT_37181 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37181
PHATRDRAFT_37509 cytochrome c553 (Cytochrom_C superfamily)

PHATRDRAFT_37509 - cytochrome c553 (Cytochrom_C superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37509
PHATRDRAFT_37918 death-specific protein (EFh)

PHATRDRAFT_37918 - death-specific protein (EFh)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37918
PHATRDRAFT_40068

PHATRDRAFT_40068 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40068
PHATRDRAFT_40147 novel protein (ANK)

PHATRDRAFT_40147 - novel protein (ANK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40147
PHATRDRAFT_40338

PHATRDRAFT_40338 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40338
PHATRDRAFT_40594

PHATRDRAFT_40594 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40594
PHATRDRAFT_43891 cct motif family protein (CCT)

PHATRDRAFT_43891 - cct motif family protein (CCT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43891
PHATRDRAFT_43892

PHATRDRAFT_43892 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43892
PHATRDRAFT_44294

PHATRDRAFT_44294 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44294
PHATRDRAFT_45025

PHATRDRAFT_45025 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45025
PHATRDRAFT_47876

PHATRDRAFT_47876 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47876
PHATRDRAFT_47902

PHATRDRAFT_47902 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47902
PHATRDRAFT_48036

PHATRDRAFT_48036 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48036
PHATRDRAFT_48112 dihydroorotate dehydrogenase (TIM_phosphate_binding superfamily)

PHATRDRAFT_48112 - dihydroorotate dehydrogenase (TIM_phosphate_binding superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48112
PHATRDRAFT_48337 kinesin light chain (TPR_12)

PHATRDRAFT_48337 - kinesin light chain (TPR_12)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48337
PHATRDRAFT_49211

PHATRDRAFT_49211 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49211
PHATRDRAFT_49445

PHATRDRAFT_49445 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49445
PHATRDRAFT_49574

PHATRDRAFT_49574 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49574
PHATRDRAFT_49632 loc507659 protein (UEV superfamily)

PHATRDRAFT_49632 - loc507659 protein (UEV superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49632
PHATRDRAFT_49665 ser thr protein phosphatase family (MPP_superfamily superfamily)

PHATRDRAFT_49665 - ser thr protein phosphatase family (MPP_superfamily superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49665
PHATRDRAFT_49729

PHATRDRAFT_49729 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49729
PHATRDRAFT_50366 viral a-type inclusion

PHATRDRAFT_50366 - viral a-type inclusion

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50366
PHATRDRAFT_50516 probable na+ h+ antiporter (Na_H_Exchanger)

PHATRDRAFT_50516 - probable na+ h+ antiporter (Na_H_Exchanger)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50516
PHATRDRAFT_7736 synaptic vesicle transporter svop and related transporters (major facilitator superfamily) (COG5134 superfamily)

PHATRDRAFT_7736 - synaptic vesicle transporter svop and related transporters (major facilitator superfamily) (COG5134 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7736
GO ID Go Term p-value q-value Cluster
GO:0006207 'de novo' pyrimidine base biosynthesis 0.00493217 1 Phatr_bicluster_0112
GO:0015031 protein transport 0.0377177 1 Phatr_bicluster_0112
GO:0000074 regulation of cell cycle 0.0413065 1 Phatr_bicluster_0112
GO:0006512 ubiquitin cycle 0.0460749 1 Phatr_bicluster_0112
GO:0006464 protein modification 0.0754495 1 Phatr_bicluster_0112
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