Phatr_bicluster_0199 Residual: 0.23
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_0199 0.23 Phaeodactylum tricornutum
Displaying 1 - 22 of 22
PHATRDRAFT_17238 anthranilate synthase (PRK13566)

PHATRDRAFT_17238 - anthranilate synthase (PRK13566)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17238
PHATRDRAFT_20934 3-isopropylmalate dehydrogenase (PRK00772)

PHATRDRAFT_20934 - 3-isopropylmalate dehydrogenase (PRK00772)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20934
PHATRDRAFT_24838 topoisomerase spo11 (PRK04342)

PHATRDRAFT_24838 - topoisomerase spo11 (PRK04342)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_24838
PHATRDRAFT_33853

PHATRDRAFT_31963 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31963
PHATRDRAFT_35973 methyltransferase like 2

PHATRDRAFT_33853 - methyltransferase like 2

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33853
PHATRDRAFT_36142 phenazine biosynthesis proteinfamily (COG0384)

PHATRDRAFT_35973 - phenazine biosynthesis proteinfamily (COG0384)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35973
PHATRDRAFT_37201 protein required for amino acid permease transport from the golgi to the cell surface (WD40)

PHATRDRAFT_36142 - protein required for amino acid permease transport from the golgi to the cell surface (WD40)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36142
PHATRDRAFT_42990 phosphoglycerate mutase family member 5 (HP_PGM_like)

PHATRDRAFT_37201 - phosphoglycerate mutase family member 5 (HP_PGM_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37201
PHATRDRAFT_43071 microneme proteinpartial

PHATRDRAFT_42990 - microneme proteinpartial

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42990
PHATRDRAFT_43516 rna (guanine-7-) methyltransferase (AdoMet_MTases superfamily)

PHATRDRAFT_43071 - rna (guanine-7-) methyltransferase (AdoMet_MTases superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43071
PHATRDRAFT_44910

PHATRDRAFT_43516 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43516
PHATRDRAFT_45904 dna polymerase eta (PolY superfamily)

PHATRDRAFT_44910 - dna polymerase eta (PolY superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44910
PHATRDRAFT_46242 pepsinogen a (pepsin_like)

PHATRDRAFT_45904 - pepsinogen a (pepsin_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45904
PHATRDRAFT_46417 protein lysyl hydroxylase fusion

PHATRDRAFT_46242 - protein lysyl hydroxylase fusion

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46242
PHATRDRAFT_46675 interferon-related developmental regulator family protein ifrd protein family (IFRD superfamily)

PHATRDRAFT_46417 - interferon-related developmental regulator family protein ifrd protein family (IFRD superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46417
PHATRDRAFT_46891 tetratricopeptide repeat protein (TPR)

PHATRDRAFT_46675 - tetratricopeptide repeat protein (TPR)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46675
PHATRDRAFT_47370 wd repeat domain 24 isoform 2 (WD40 superfamily)

PHATRDRAFT_46891 - wd repeat domain 24 isoform 2 (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46891
PHATRDRAFT_48497

PHATRDRAFT_47370 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47370
PHATRDRAFT_51819

PHATRDRAFT_48497 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48497
PHATRDRAFT_54110 adp-ribosylation factor-like 2 (Arl2)

PHATRDRAFT_51819 - adp-ribosylation factor-like 2 (Arl2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51819
PHATRDRAFT_5720 (TLC superfamily)

PHATRDRAFT_54110 - (TLC superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54110

PHATRDRAFT_5720 - septum formation protein maf-like protein (Maf_Ham1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5720
GO ID Go Term p-value q-value Cluster
GO:0006355 regulation of transcription, DNA-dependent 0.541484 1 Phatr_bicluster_0199
GO:0006508 proteolysis and peptidolysis 0.549807 1 Phatr_bicluster_0199
GO:0007131 meiotic recombination 0.00345764 1 Phatr_bicluster_0199
GO:0006370 mRNA capping 0.00345764 1 Phatr_bicluster_0199
GO:0009098 leucine biosynthesis 0.0103397 1 Phatr_bicluster_0199
GO:0000162 tryptophan biosynthesis 0.0103397 1 Phatr_bicluster_0199
GO:0006265 DNA topological change 0.0307218 1 Phatr_bicluster_0199
GO:0006259 DNA metabolism 0.0407661 1 Phatr_bicluster_0199
GO:0008152 metabolism 0.0758904 1 Phatr_bicluster_0199
GO:0000160 two-component signal transduction system (phosphorelay) 0.0863742 1 Phatr_bicluster_0199
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