Phatr_bicluster_0050 Residual: 0.33
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_0050 0.33 Phaeodactylum tricornutum
Displaying 1 - 26 of 26
PHATRDRAFT_14967 serine threonine phosphatase typeexpressed (PP2Cc superfamily)

PHATRDRAFT_14967 - serine threonine phosphatase typeexpressed (PP2Cc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14967
PHATRDRAFT_15239 otuubiquitin aldehyde binding 1 (Peptidase_C65)

PHATRDRAFT_15239 - otuubiquitin aldehyde binding 1 (Peptidase_C65)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15239
PHATRDRAFT_19244 pxphosphoserine phosphatase (Hydrolase)

PHATRDRAFT_19244 - pxphosphoserine phosphatase (Hydrolase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19244
PHATRDRAFT_33189

PHATRDRAFT_33189 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33189
PHATRDRAFT_33351

PHATRDRAFT_33351 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33351
PHATRDRAFT_33427 riboflavin biosynthesis protein (Riboflavin_deaminase-reductase)

PHATRDRAFT_33427 - riboflavin biosynthesis protein (Riboflavin_deaminase-reductase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33427
PHATRDRAFT_40193

PHATRDRAFT_40193 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40193
PHATRDRAFT_40315 (Lin0512_fam superfamily)

PHATRDRAFT_40315 - (Lin0512_fam superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40315
PHATRDRAFT_40979

PHATRDRAFT_40979 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40979
PHATRDRAFT_41351 atp-binding component of abc transporter (Uup)

PHATRDRAFT_41351 - atp-binding component of abc transporter (Uup)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41351
PHATRDRAFT_42123 ubiquitin protein ligase (HECTc)

PHATRDRAFT_42123 - ubiquitin protein ligase (HECTc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42123
PHATRDRAFT_43807 (DUF819 superfamily)

PHATRDRAFT_43807 - (DUF819 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43807
PHATRDRAFT_44362 leucine-rich repeat containing protein (COG4886)

PHATRDRAFT_44362 - leucine-rich repeat containing protein (COG4886)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44362
PHATRDRAFT_47389 loc100036841 protein (PIP5K)

PHATRDRAFT_47389 - loc100036841 protein (PIP5K)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47389
PHATRDRAFT_47746 (Tub_2 superfamily)

PHATRDRAFT_47746 - (Tub_2 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47746
PHATRDRAFT_47795 l-sorbosone dehydrogenase

PHATRDRAFT_47795 - l-sorbosone dehydrogenase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47795
PHATRDRAFT_47841 (START_2)

PHATRDRAFT_47841 - (START_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47841
PHATRDRAFT_48638 flap endonuclease 1 (PIN_FEN1)

PHATRDRAFT_48638 - flap endonuclease 1 (PIN_FEN1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48638
PHATRDRAFT_48646 subunit of escrt-iii complex (Snf7 superfamily)

PHATRDRAFT_48646 - subunit of escrt-iii complex (Snf7 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48646
PHATRDRAFT_49091 peptidasecarboxypeptidase a (Peptidase_M14_like superfamily)

PHATRDRAFT_49091 - peptidasecarboxypeptidase a (Peptidase_M14_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49091
PHATRDRAFT_49175

PHATRDRAFT_49175 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49175
PHATRDRAFT_49575 dehydrogenase reductase (sdr family) member 7 (NADB_Rossmann superfamily)

PHATRDRAFT_49575 - dehydrogenase reductase (sdr family) member 7 (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49575
PHATRDRAFT_50054

PHATRDRAFT_50054 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50054
PHATRDRAFT_50138 (Nipped-B_C)

PHATRDRAFT_50138 - (Nipped-B_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50138
PHATRDRAFT_50201 (DUF1275)

PHATRDRAFT_50201 - (DUF1275)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50201
PHATRDRAFT_50474

PHATRDRAFT_50474 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50474
GO ID Go Term p-value q-value Cluster
GO:0051336 regulation of hydrolase activity 0.0132709 1 Phatr_bicluster_0050
GO:0006564 L-serine biosynthesis 0.0176596 1 Phatr_bicluster_0050
GO:0006281 DNA repair 0.0731548 1 Phatr_bicluster_0050
GO:0006512 ubiquitin cycle 0.0814404 1 Phatr_bicluster_0050
GO:0006464 protein modification 0.13175 1 Phatr_bicluster_0050
GO:0008152 metabolism 0.134877 1 Phatr_bicluster_0050
GO:0006355 regulation of transcription, DNA-dependent 0.394049 1 Phatr_bicluster_0050
GO:0006508 proteolysis and peptidolysis 0.401138 1 Phatr_bicluster_0050
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