Phatr_bicluster_0059 Residual: 0.40
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_0059 0.40 Phaeodactylum tricornutum
Displaying 1 - 39 of 39
PHATRDRAFT_14284 pyrophosphate--fructose-6-phosphate 1-phosphotransferase (PFK superfamily)

PHATRDRAFT_14284 - pyrophosphate--fructose-6-phosphate 1-phosphotransferase (PFK superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14284
PHATRDRAFT_14702 calcium calmodulin-dependent protein kinase ig (S_TKc)

PHATRDRAFT_14702 - calcium calmodulin-dependent protein kinase ig (S_TKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14702
PHATRDRAFT_15264 kinesin-like protein (Motor_domain superfamily)

PHATRDRAFT_15264 - kinesin-like protein (Motor_domain superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15264
PHATRDRAFT_19188 uroporphyrinogen decarboxylase (URO-D)

PHATRDRAFT_19188 - uroporphyrinogen decarboxylase (URO-D)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19188
PHATRDRAFT_23489 fkbp-type peptidyl-prolyl (FKBP_C)

PHATRDRAFT_23489 - fkbp-type peptidyl-prolyl (FKBP_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23489
PHATRDRAFT_2382 pt repeat family protein

PHATRDRAFT_2382 - pt repeat family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_2382
PHATRDRAFT_2444 kiaa0449 protein (Motor_domain superfamily)

PHATRDRAFT_2444 - kiaa0449 protein (Motor_domain superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_2444
PHATRDRAFT_24610 triose or hexose phosphate phosphate (tpt)

PHATRDRAFT_24610 - triose or hexose phosphate phosphate (tpt)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_24610
PHATRDRAFT_32487

PHATRDRAFT_32487 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32487
PHATRDRAFT_33147

PHATRDRAFT_33147 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33147
PHATRDRAFT_34245

PHATRDRAFT_34245 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34245
PHATRDRAFT_38086 flj00040 protein (ANK)

PHATRDRAFT_38086 - flj00040 protein (ANK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38086
PHATRDRAFT_38112 ctr2 family transporter: copper ion ctr-type copper transporter

PHATRDRAFT_38112 - ctr2 family transporter: copper ion ctr-type copper transporter

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38112
PHATRDRAFT_38917 dihydrofolate reductase (FSH1 superfamily)

PHATRDRAFT_38917 - dihydrofolate reductase (FSH1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38917
PHATRDRAFT_38966 serine protease a (Peptidases_S8_PCSK9_ProteinaseK_like)

PHATRDRAFT_38966 - serine protease a (Peptidases_S8_PCSK9_ProteinaseK_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38966
PHATRDRAFT_39307

PHATRDRAFT_39307 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39307
PHATRDRAFT_39311 sarcoma antigen ny-sar-41

PHATRDRAFT_39311 - sarcoma antigen ny-sar-41

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39311
PHATRDRAFT_39455 cog0432: uncharacterized conserved protein (UPF0047)

PHATRDRAFT_39455 - cog0432: uncharacterized conserved protein (UPF0047)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39455
PHATRDRAFT_39891

PHATRDRAFT_39891 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39891
PHATRDRAFT_40647 (CBM9_like_3)

PHATRDRAFT_40647 - (CBM9_like_3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40647
PHATRDRAFT_41555

PHATRDRAFT_41555 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41555
PHATRDRAFT_43335

PHATRDRAFT_43335 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43335
PHATRDRAFT_43804

PHATRDRAFT_43804 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43804
PHATRDRAFT_47563

PHATRDRAFT_47563 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47563
PHATRDRAFT_47738

PHATRDRAFT_47738 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47738
PHATRDRAFT_47779 bnr repeat domain protein

PHATRDRAFT_47779 - bnr repeat domain protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47779
PHATRDRAFT_47805 ctr2 family transporter: copper ion ctr-type copper transporter (Ctr)

PHATRDRAFT_47805 - ctr2 family transporter: copper ion ctr-type copper transporter (Ctr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47805
PHATRDRAFT_47872 epsilon frustilin

PHATRDRAFT_47872 - epsilon frustilin

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47872
PHATRDRAFT_48496 alkaline serine protease (Peptidases_S8_PCSK9_ProteinaseK_like)

PHATRDRAFT_48496 - alkaline serine protease (Peptidases_S8_PCSK9_ProteinaseK_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48496
PHATRDRAFT_48647 nucleoporin nsp1

PHATRDRAFT_48647 - nucleoporin nsp1

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48647
PHATRDRAFT_48834 lipopolysaccharide a protein (CAP10 superfamily)

PHATRDRAFT_48834 - lipopolysaccharide a protein (CAP10 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48834
PHATRDRAFT_49053 (Mt_ATP-synt_D superfamily)

PHATRDRAFT_49053 - (Mt_ATP-synt_D superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49053
PHATRDRAFT_49194

PHATRDRAFT_49194 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49194
PHATRDRAFT_49344

PHATRDRAFT_49344 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49344
PHATRDRAFT_49678 alkaline phosphatase (alkPPc superfamily)

PHATRDRAFT_49678 - alkaline phosphatase (alkPPc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49678
PHATRDRAFT_49716

PHATRDRAFT_49716 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49716
PHATRDRAFT_50171

PHATRDRAFT_50171 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50171
PHATRDRAFT_50210 aql1_theaqaqualysin-1 precursor (aqualysin i) (Peptidases_S8_PCSK9_ProteinaseK_like)

PHATRDRAFT_50210 - aql1_theaqaqualysin-1 precursor (aqualysin i) (Peptidases_S8_PCSK9_ProteinaseK_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50210
PHATRDRAFT_52709 cyclin dependent kinase c (PKc_like superfamily)

PHATRDRAFT_52709 - cyclin dependent kinase c (PKc_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52709
GO ID Go Term p-value q-value Cluster
GO:0007018 microtubule-based movement 0.0059714 1 Phatr_bicluster_0059
GO:0006508 proteolysis and peptidolysis 0.00979667 1 Phatr_bicluster_0059
GO:0006825 copper ion transport 0.0118109 1 Phatr_bicluster_0059
GO:0006779 porphyrin biosynthesis 0.0388631 1 Phatr_bicluster_0059
GO:0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system 0.0388631 1 Phatr_bicluster_0059
GO:0007186 G-protein coupled receptor protein signaling pathway 0.0502429 1 Phatr_bicluster_0059
GO:0006457 protein folding 0.0763282 1 Phatr_bicluster_0059
GO:0006096 glycolysis 0.129916 1 Phatr_bicluster_0059
GO:0006468 protein amino acid phosphorylation 0.50135 1 Phatr_bicluster_0059
GO:0006810 transport 0.539115 1 Phatr_bicluster_0059
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