Phatr_bicluster_0008 Residual: 0.47
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_0008 0.47 Phaeodactylum tricornutum
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Displaying 1 - 28 of 28
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PHATRDRAFT_12510 protein phosphatase 2c (PP2Cc)

PHATRDRAFT_12510 - protein phosphatase 2c (PP2Cc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12510
PHATRDRAFT_16648 ferric reductase-like protein (Got1 superfamily)

PHATRDRAFT_16648 - ferric reductase-like protein (Got1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16648
PHATRDRAFT_18228 triosephosphate isomerase (TIM)

PHATRDRAFT_18228 - triosephosphate isomerase (TIM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18228
PHATRDRAFT_31819

PHATRDRAFT_31819 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31819
PHATRDRAFT_32041

PHATRDRAFT_32041 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32041
PHATRDRAFT_34681 (NADB_Rossmann superfamily)

PHATRDRAFT_34681 - (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34681
PHATRDRAFT_35854

PHATRDRAFT_35854 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35854
PHATRDRAFT_36426

PHATRDRAFT_36426 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36426
PHATRDRAFT_37468

PHATRDRAFT_37468 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37468
PHATRDRAFT_37769

PHATRDRAFT_37769 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37769
PHATRDRAFT_38448 m17 (leucyl aminopeptidase) family (Peptidase_M17 superfamily)

PHATRDRAFT_38448 - m17 (leucyl aminopeptidase) family (Peptidase_M17 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38448
PHATRDRAFT_38498 sbf-domain containing protein (DUF4137)

PHATRDRAFT_38498 - sbf-domain containing protein (DUF4137)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38498
PHATRDRAFT_39448

PHATRDRAFT_39448 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39448
PHATRDRAFT_41116

PHATRDRAFT_41116 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41116
PHATRDRAFT_42603

PHATRDRAFT_42603 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42603
PHATRDRAFT_43987

PHATRDRAFT_43987 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43987
PHATRDRAFT_44327 small-conductance mechanosensitive channel (MS_channel superfamily)

PHATRDRAFT_44327 - small-conductance mechanosensitive channel (MS_channel superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44327
PHATRDRAFT_44814

PHATRDRAFT_44814 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44814
PHATRDRAFT_45057

PHATRDRAFT_45057 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45057
PHATRDRAFT_45608 dtw domain protein (DTW superfamily)

PHATRDRAFT_45608 - dtw domain protein (DTW superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45608
PHATRDRAFT_46353 phosphoglycerate bisphosphoglycerate mutase family protein (HP_PGM_like)

PHATRDRAFT_46353 - phosphoglycerate bisphosphoglycerate mutase family protein (HP_PGM_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46353
PHATRDRAFT_47106 m17 (leucyl aminopeptidase) family (Peptidase_M17 superfamily)

PHATRDRAFT_47106 - m17 (leucyl aminopeptidase) family (Peptidase_M17 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47106
PHATRDRAFT_47217

PHATRDRAFT_47217 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47217
PHATRDRAFT_47293 thiamine monophosphate synthase (HMPP_kinase)

PHATRDRAFT_47293 - thiamine monophosphate synthase (HMPP_kinase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47293
PHATRDRAFT_48726 elicitin-like protein sol8

PHATRDRAFT_48726 - elicitin-like protein sol8

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48726
PHATRDRAFT_49578

PHATRDRAFT_49578 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49578
PHATRDRAFT_49797

PHATRDRAFT_49797 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49797
PHATRDRAFT_7957 general transcription factor (Bromodomain)

PHATRDRAFT_7957 - general transcription factor (Bromodomain)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7957
GO ID Go Term p-value q-value Cluster
GO:0016192 vesicle-mediated transport 0.0191218 1 Phatr_bicluster_0008
GO:0009228 thiamin biosynthesis 0.00444005 1 Phatr_bicluster_0008
GO:0006508 proteolysis and peptidolysis 0.0394266 1 Phatr_bicluster_0008
GO:0006470 protein amino acid dephosphorylation 0.0278439 1 Phatr_bicluster_0008
GO:0008152 metabolism 0.364015 1 Phatr_bicluster_0008
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