Phatr_bicluster_0238 Residual: 0.34
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_0238 0.34 Phaeodactylum tricornutum
Displaying 1 - 28 of 28
PHATRDRAFT_12878 methylmalonic aciduria type a (Fer4_NifH superfamily)

PHATRDRAFT_12878 - methylmalonic aciduria type a (Fer4_NifH superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12878
PHATRDRAFT_13710 (Acetyltransf_6 superfamily)

PHATRDRAFT_13710 - (Acetyltransf_6 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13710
PHATRDRAFT_14380 peptidase s8 andsedolisin (Peptidases_S8_PCSK9_ProteinaseK_like)

PHATRDRAFT_14380 - peptidase s8 andsedolisin (Peptidases_S8_PCSK9_ProteinaseK_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14380
PHATRDRAFT_14802 cg6000-isoform a (RHOD superfamily)

PHATRDRAFT_14802 - cg6000-isoform a (RHOD superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14802
PHATRDRAFT_16844 pyrophosphate-dependent phosphofructo-1-kinase-like protein (PFK superfamily)

PHATRDRAFT_16844 - pyrophosphate-dependent phosphofructo-1-kinase-like protein (PFK superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16844
PHATRDRAFT_28874 atelc elc ubiquitin binding (UEV superfamily)

PHATRDRAFT_28874 - atelc elc ubiquitin binding (UEV superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28874
PHATRDRAFT_34685 abc transporter family protein (3a01204)

PHATRDRAFT_34685 - abc transporter family protein (3a01204)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34685
PHATRDRAFT_38509 (Arginase)

PHATRDRAFT_38509 - (Arginase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38509
PHATRDRAFT_39095 kelch domain containing 1

PHATRDRAFT_39095 - kelch domain containing 1

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39095
PHATRDRAFT_42887

PHATRDRAFT_42887 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42887
PHATRDRAFT_43310

PHATRDRAFT_43310 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43310
PHATRDRAFT_43424

PHATRDRAFT_43424 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43424
PHATRDRAFT_44092

PHATRDRAFT_44092 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44092
PHATRDRAFT_44234

PHATRDRAFT_44234 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44234
PHATRDRAFT_44260 probable hydrolase (Abhydrolase_6)

PHATRDRAFT_44260 - probable hydrolase (Abhydrolase_6)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44260
PHATRDRAFT_44413

PHATRDRAFT_44413 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44413
PHATRDRAFT_44558

PHATRDRAFT_44558 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44558
PHATRDRAFT_45394

PHATRDRAFT_45394 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45394
PHATRDRAFT_46965 novel 2og-feoxygenase superfamily protein (2OG-FeII_Oxy_3 superfamily)

PHATRDRAFT_46965 - novel 2og-feoxygenase superfamily protein (2OG-FeII_Oxy_3 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46965
PHATRDRAFT_47758 (Arrestin_C)

PHATRDRAFT_47758 - (Arrestin_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47758
PHATRDRAFT_47797 (Abi)

PHATRDRAFT_47797 - (Abi)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47797
PHATRDRAFT_48226 enzyme with alpha beta-hydrolase domain (COG0429)

PHATRDRAFT_48226 - enzyme with alpha beta-hydrolase domain (COG0429)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48226
PHATRDRAFT_48484 alkaline serine protease (Peptidases_S8_PCSK9_ProteinaseK_like)

PHATRDRAFT_48484 - alkaline serine protease (Peptidases_S8_PCSK9_ProteinaseK_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48484
PHATRDRAFT_48802 rhodanese domain protein (RHOD)

PHATRDRAFT_48802 - rhodanese domain protein (RHOD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48802
PHATRDRAFT_50499

PHATRDRAFT_50499 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50499
PHATRDRAFT_51134 aaa atpase domain-containing protein (chaperone_ClpB)

PHATRDRAFT_51134 - aaa atpase domain-containing protein (chaperone_ClpB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51134
PHATRDRAFT_54765 (pepsin_retropepsin_like superfamily)

PHATRDRAFT_54765 - (pepsin_retropepsin_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54765
PHATRDRAFT_54800 all-trans--dihydroretinol saturase (COG1233)

PHATRDRAFT_54800 - all-trans--dihydroretinol saturase (COG1233)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54800
GO ID Go Term p-value q-value Cluster
GO:0019538 protein metabolism 0.00402011 1 Phatr_bicluster_0238
GO:0006527 arginine catabolism 0.00542673 1 Phatr_bicluster_0238
GO:0043086 negative regulation of enzyme activity 0.0135166 1 Phatr_bicluster_0238
GO:0006865 amino acid transport 0.0735796 1 Phatr_bicluster_0238
GO:0015031 protein transport 0.0811638 1 Phatr_bicluster_0238
GO:0006096 glycolysis 0.0911882 1 Phatr_bicluster_0238
GO:0006512 ubiquitin cycle 0.0986411 1 Phatr_bicluster_0238
GO:0006508 proteolysis and peptidolysis 0.120633 1 Phatr_bicluster_0238
GO:0006464 protein modification 0.158622 1 Phatr_bicluster_0238
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