Phatr_bicluster_0131 Residual: 0.25
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_0131 0.25 Phaeodactylum tricornutum
Displaying 1 - 23 of 23
PHATRDRAFT_11286 nucleosome binding protein (HMGB-UBF_HMG-box)

PHATRDRAFT_11286 - nucleosome binding protein (HMGB-UBF_HMG-box)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11286
PHATRDRAFT_13402 rna recognition (RRM_SF superfamily)

PHATRDRAFT_13402 - rna recognition (RRM_SF superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13402
PHATRDRAFT_13833 cbs domain-containing protein octicosapeptide phox bemp1domain-containing protein (CBS_pair superfamily)

PHATRDRAFT_13833 - cbs domain-containing protein octicosapeptide phox bemp1domain-containing protein (CBS_pair superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13833
PHATRDRAFT_14626 mta sah nucleosidase (PLN02584)

PHATRDRAFT_14626 - mta sah nucleosidase (PLN02584)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14626
PHATRDRAFT_14827 rab gdp-dissociation inhibitor (MRS6 superfamily)

PHATRDRAFT_14827 - rab gdp-dissociation inhibitor (MRS6 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14827
PHATRDRAFT_17259 26s proteasome regulatory subunit s12 (mov34 protein) (PLN03246)

PHATRDRAFT_17259 - 26s proteasome regulatory subunit s12 (mov34 protein) (PLN03246)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17259
PHATRDRAFT_17728 helicase smarcad1 (HepA)

PHATRDRAFT_17728 - helicase smarcad1 (HepA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17728
PHATRDRAFT_18239 chromatin-specific transcription elongation factor fact 140 kda subunit (COG5406)

PHATRDRAFT_18239 - chromatin-specific transcription elongation factor fact 140 kda subunit (COG5406)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18239
PHATRDRAFT_26256 adenylosuccinate synthase (AdSS)

PHATRDRAFT_26256 - adenylosuccinate synthase (AdSS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_26256
PHATRDRAFT_26948 (Peptidases_S8_Tripeptidyl_Aminopeptidase_II)

PHATRDRAFT_26948 - (Peptidases_S8_Tripeptidyl_Aminopeptidase_II)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_26948
PHATRDRAFT_34124

PHATRDRAFT_34124 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34124
PHATRDRAFT_36913 n-acetyl-gamma-glutamyl-phosphate reductase (PRK11863)

PHATRDRAFT_36913 - n-acetyl-gamma-glutamyl-phosphate reductase (PRK11863)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36913
PHATRDRAFT_37111 cog3781: membrane protein (Bestrophin superfamily)

PHATRDRAFT_37111 - cog3781: membrane protein (Bestrophin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37111
PHATRDRAFT_41092

PHATRDRAFT_41092 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41092
PHATRDRAFT_42750 (Racemase_4)

PHATRDRAFT_42750 - (Racemase_4)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42750
PHATRDRAFT_42872 (DUF3419 superfamily)

PHATRDRAFT_42872 - (DUF3419 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42872
PHATRDRAFT_44554 high mobility group (HMGB-UBF_HMG-box)

PHATRDRAFT_44554 - high mobility group (HMGB-UBF_HMG-box)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44554
PHATRDRAFT_46906 nup35 protein (RRM_Nup53_like)

PHATRDRAFT_46906 - nup35 protein (RRM_Nup53_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46906
PHATRDRAFT_47818 start domain-containing protein (DUF1336 superfamily)

PHATRDRAFT_47818 - start domain-containing protein (DUF1336 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47818
PHATRDRAFT_49325 mgc108224 protein (Trans_IPPS_HT)

PHATRDRAFT_49325 - mgc108224 protein (Trans_IPPS_HT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49325
PHATRDRAFT_50120 dpy-30-like protein (Dpy-30 superfamily)

PHATRDRAFT_50120 - dpy-30-like protein (Dpy-30 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50120
PHATRDRAFT_53939 prosomal p27k protein (proteasome_alpha_type_6)

PHATRDRAFT_53939 - prosomal p27k protein (proteasome_alpha_type_6)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_53939
PHATRDRAFT_8518 isoform cra_a (LSm6)

PHATRDRAFT_8518 - isoform cra_a (LSm6)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8518
GO ID Go Term p-value q-value Cluster
GO:0006164 purine nucleotide biosynthesis 0.0108267 1 Phatr_bicluster_0131
GO:0006526 arginine biosynthesis 0.0188766 1 Phatr_bicluster_0131
GO:0008299 isoprenoid biosynthesis 0.0242101 1 Phatr_bicluster_0131
GO:0009116 nucleoside metabolism 0.0242101 1 Phatr_bicluster_0131
GO:0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system 0.026867 1 Phatr_bicluster_0131
GO:0043087 regulation of GTPase activity 0.0295173 1 Phatr_bicluster_0131
GO:0006397 mRNA processing 0.0608128 1 Phatr_bicluster_0131
GO:0015031 protein transport 0.0811638 1 Phatr_bicluster_0131
GO:0006355 regulation of transcription, DNA-dependent 0.116151 1 Phatr_bicluster_0131
GO:0006508 proteolysis and peptidolysis 0.465714 1 Phatr_bicluster_0131
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