Phatr_bicluster_0225 Residual: 0.20
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_0225 0.20 Phaeodactylum tricornutum
Displaying 1 - 24 of 24
PHATRDRAFT_13243 mini-chromosome maintenance 7 (MCM)

PHATRDRAFT_13243 - mini-chromosome maintenance 7 (MCM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13243
PHATRDRAFT_1769 novel protein (zgc:112282) (metallo-dependent_hydrolases superfamily)

PHATRDRAFT_1769 - novel protein (zgc:112282) (metallo-dependent_hydrolases superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_1769
PHATRDRAFT_19708 sjchgc09380 protein (PLN00133)

PHATRDRAFT_19708 - sjchgc09380 protein (PLN00133)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19708
PHATRDRAFT_20424 urea high-affinity symporter (SLC5sbd_DUR3)

PHATRDRAFT_20424 - urea high-affinity symporter (SLC5sbd_DUR3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20424
PHATRDRAFT_20445 betaine aldehyde dehydrogenase-like (ALDH-SF superfamily)

PHATRDRAFT_20445 - betaine aldehyde dehydrogenase-like (ALDH-SF superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20445
PHATRDRAFT_27923 vacuolar type atpase subunit a (V-ATPase_V1_A)

PHATRDRAFT_27923 - vacuolar type atpase subunit a (V-ATPase_V1_A)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27923
PHATRDRAFT_27976 phosphoenolpyruvate carboxylase (PEPcase superfamily)

PHATRDRAFT_27976 - phosphoenolpyruvate carboxylase (PEPcase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27976
PHATRDRAFT_33955 (DUF1295 superfamily)

PHATRDRAFT_33955 - (DUF1295 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33955
PHATRDRAFT_35036

PHATRDRAFT_35036 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35036
PHATRDRAFT_35680 (dna directed) polypeptide g-like (PTZ00162)

PHATRDRAFT_35680 - (dna directed) polypeptide g-like (PTZ00162)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35680
PHATRDRAFT_37543 (DUF633 superfamily)

PHATRDRAFT_37543 - (DUF633 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37543
PHATRDRAFT_42015 succinyl-ligase alpha subunit (PTZ00187)

PHATRDRAFT_42015 - succinyl-ligase alpha subunit (PTZ00187)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42015
PHATRDRAFT_43473 tetratricopeptide repeat protein (Transglut_core2)

PHATRDRAFT_43473 - tetratricopeptide repeat protein (Transglut_core2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43473
PHATRDRAFT_43544 large ala glu-rich protein

PHATRDRAFT_43544 - large ala glu-rich protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43544
PHATRDRAFT_44288

PHATRDRAFT_44288 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44288
PHATRDRAFT_44626

PHATRDRAFT_44626 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44626
PHATRDRAFT_44724

PHATRDRAFT_44724 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44724
PHATRDRAFT_45385

PHATRDRAFT_45385 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45385
PHATRDRAFT_45630 integral membrane protein (RhaT)

PHATRDRAFT_45630 - integral membrane protein (RhaT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45630
PHATRDRAFT_45997 pyruvate kinase (PLN02461)

PHATRDRAFT_45997 - pyruvate kinase (PLN02461)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45997
PHATRDRAFT_46001 pyruvate kinase (PLN02461)

PHATRDRAFT_46001 - pyruvate kinase (PLN02461)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46001
PHATRDRAFT_47178 signal-transduction protein with cbs domains (CBS_pair_10)

PHATRDRAFT_47178 - signal-transduction protein with cbs domains (CBS_pair_10)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47178
PHATRDRAFT_47650

PHATRDRAFT_47650 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47650
PHATRDRAFT_54028

PHATRDRAFT_54028 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54028
GO ID Go Term p-value q-value Cluster
GO:0006091 generation of precursor metabolites and energy 0.00345764 1 Phatr_bicluster_0225
GO:0006096 glycolysis 0.00618972 1 Phatr_bicluster_0225
GO:0006754 ATP biosynthesis 0.0103397 1 Phatr_bicluster_0225
GO:0006270 DNA replication initiation 0.02058 1 Phatr_bicluster_0225
GO:0006099 tricarboxylic acid cycle 0.0273521 1 Phatr_bicluster_0225
GO:0007186 G-protein coupled receptor protein signaling pathway 0.0440926 1 Phatr_bicluster_0225
GO:0006629 lipid metabolism 0.0605653 1 Phatr_bicluster_0225
GO:0006350 transcription 0.0703219 1 Phatr_bicluster_0225
GO:0015986 ATP synthesis coupled proton transport 0.120788 1 Phatr_bicluster_0225
GO:0006310 DNA recombination 0.120788 1 Phatr_bicluster_0225
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