Phatr_bicluster_0135 Residual: 0.29
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_0135 0.29 Phaeodactylum tricornutum
Displaying 1 - 36 of 36
PHATRDRAFT_14143 transcription factor cmyb isoform 1 (SANT)

PHATRDRAFT_14143 - transcription factor cmyb isoform 1 (SANT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14143
PHATRDRAFT_16408 lysosomal trafficking regulator lyst and related beach and wd40 repeat proteins (Beach)

PHATRDRAFT_16408 - lysosomal trafficking regulator lyst and related beach and wd40 repeat proteins (Beach)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16408
PHATRDRAFT_16608 rufy1 isoform 4 (FYVE)

PHATRDRAFT_16608 - rufy1 isoform 4 (FYVE)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16608
PHATRDRAFT_16649 hydroxymethylglutaryl coenzyme a synthase (PLN02577)

PHATRDRAFT_16649 - hydroxymethylglutaryl coenzyme a synthase (PLN02577)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16649
PHATRDRAFT_16891 adapter-related protein complex 4 epsilon 1 (Adaptin_N)

PHATRDRAFT_16891 - adapter-related protein complex 4 epsilon 1 (Adaptin_N)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16891
PHATRDRAFT_29736 urate oxidase (TFold superfamily)

PHATRDRAFT_29736 - urate oxidase (TFold superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29736
PHATRDRAFT_32513

PHATRDRAFT_32513 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32513
PHATRDRAFT_33571 heat shock protein 83-1

PHATRDRAFT_33571 - heat shock protein 83-1

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33571
PHATRDRAFT_37058

PHATRDRAFT_37058 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37058
PHATRDRAFT_37460 cyclin serine peptidase familypeptidase (GAT_1 superfamily)

PHATRDRAFT_37460 - cyclin serine peptidase familypeptidase (GAT_1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37460
PHATRDRAFT_40317

PHATRDRAFT_40317 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40317
PHATRDRAFT_40578 ubiquitin-protein ligase e3-alpha-like protein (zf-UBR)

PHATRDRAFT_40578 - ubiquitin-protein ligase e3-alpha-like protein (zf-UBR)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40578
PHATRDRAFT_40677 (PH_BEACH)

PHATRDRAFT_40677 - (PH_BEACH)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40677
PHATRDRAFT_41011 hect e3 ubiquitin ligase (RCC1)

PHATRDRAFT_41011 - hect e3 ubiquitin ligase (RCC1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41011
PHATRDRAFT_41214 (Apc1 superfamily)

PHATRDRAFT_41214 - (Apc1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41214
PHATRDRAFT_43825

PHATRDRAFT_43825 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43825
PHATRDRAFT_43898 (Sgf11)

PHATRDRAFT_43898 - (Sgf11)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43898
PHATRDRAFT_43966

PHATRDRAFT_43966 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43966
PHATRDRAFT_44803 conserved protein (fungal and protazoan) (DUF2009 superfamily)

PHATRDRAFT_44803 - conserved protein (fungal and protazoan) (DUF2009 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44803
PHATRDRAFT_45008 camk family protein kinase (PKc_like superfamily)

PHATRDRAFT_45008 - camk family protein kinase (PKc_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45008
PHATRDRAFT_47166

PHATRDRAFT_47166 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47166
PHATRDRAFT_47516 c3hc4 zinc-binding integral peroxisomal membrane protein (RING)

PHATRDRAFT_47516 - c3hc4 zinc-binding integral peroxisomal membrane protein (RING)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47516
PHATRDRAFT_48346

PHATRDRAFT_48346 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48346
PHATRDRAFT_49474

PHATRDRAFT_49474 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49474
PHATRDRAFT_49706 (E_set_GO_C)

PHATRDRAFT_49706 - (E_set_GO_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49706
PHATRDRAFT_49775

PHATRDRAFT_49775 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49775
PHATRDRAFT_49835

PHATRDRAFT_49835 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49835
PHATRDRAFT_49954 core 1 udp-galactose:n-acetylgalactosamine-alpha-r beta- galactosy

PHATRDRAFT_49954 - core 1 udp-galactose:n-acetylgalactosamine-alpha-r beta- galactosy

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49954
PHATRDRAFT_50139

PHATRDRAFT_50139 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50139
PHATRDRAFT_50388

PHATRDRAFT_50388 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50388
PHATRDRAFT_50612

PHATRDRAFT_50612 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50612
PHATRDRAFT_54772 cop9 complex homolog subunit 1 b cg3889-pa (RPN7 superfamily)

PHATRDRAFT_54772 - cop9 complex homolog subunit 1 b cg3889-pa (RPN7 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54772
PHATRDRAFT_55114 gap related family member (rbg-3) (TBC)

PHATRDRAFT_55114 - gap related family member (rbg-3) (TBC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55114
PHATRDRAFT_7866 dna mismatch repair protein muts (ABC_ATPase superfamily)

PHATRDRAFT_7866 - dna mismatch repair protein muts (ABC_ATPase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7866
PHATRDRAFT_7867 s-adenosylmethionine decarboxylase related (AdoMet_dc)

PHATRDRAFT_7867 - s-adenosylmethionine decarboxylase related (AdoMet_dc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7867
PHATRDRAFT_8141 dna damage response protein

PHATRDRAFT_8141 - dna damage response protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8141
GO ID Go Term p-value q-value Cluster
GO:0006084 acetyl-CoA metabolism 0.00271672 1 Phatr_bicluster_0135
GO:0006144 purine base metabolism 0.00271672 1 Phatr_bicluster_0135
GO:0006298 mismatch repair 0.0162 1 Phatr_bicluster_0135
GO:0006512 ubiquitin cycle 0.0986411 1 Phatr_bicluster_0135
GO:0006508 proteolysis and peptidolysis 0.120633 1 Phatr_bicluster_0135
GO:0016567 protein ubiquitination 0.17931 1 Phatr_bicluster_0135
GO:0008152 metabolism 0.187614 1 Phatr_bicluster_0135
GO:0006457 protein folding 0.275986 1 Phatr_bicluster_0135
GO:0006468 protein amino acid phosphorylation 0.380037 1 Phatr_bicluster_0135
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