Phatr_bicluster_0106 Residual: 0.31
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_0106 0.31 Phaeodactylum tricornutum
Displaying 1 - 16 of 16
PHATRDRAFT_12436 adenylate kinase (ADK)

PHATRDRAFT_12436 - adenylate kinase (ADK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12436
PHATRDRAFT_16711 prolylcarboxypeptidase (angiotensinase c) (Peptidase_S28 superfamily)

PHATRDRAFT_16711 - prolylcarboxypeptidase (angiotensinase c) (Peptidase_S28 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16711
PHATRDRAFT_17914 mc family transporter: folate (Mito_carr)

PHATRDRAFT_17914 - mc family transporter: folate (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17914
PHATRDRAFT_19604 dna mismatch repair protein (MutS_V)

PHATRDRAFT_19604 - dna mismatch repair protein (MutS_V)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19604
PHATRDRAFT_34636

PHATRDRAFT_34636 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34636
PHATRDRAFT_37371

PHATRDRAFT_37176 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37176
PHATRDRAFT_42546 c-5 sterol (ERG3)

PHATRDRAFT_37371 - c-5 sterol (ERG3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37371
PHATRDRAFT_42874

PHATRDRAFT_42546 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42546
PHATRDRAFT_43240

PHATRDRAFT_42874 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42874
PHATRDRAFT_43529 violaxanthin de-epoxidase-related-like

PHATRDRAFT_43240 - violaxanthin de-epoxidase-related-like

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43240
PHATRDRAFT_44510 histone stem-loop binding protein (SLBP_RNA_bind superfamily)

PHATRDRAFT_43529 - histone stem-loop binding protein (SLBP_RNA_bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43529
PHATRDRAFT_45814

PHATRDRAFT_44510 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44510
PHATRDRAFT_50507

PHATRDRAFT_45814 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45814
PHATRDRAFT_52260 ch032_bovinuncharacterized protein c8orf32 homolog (Nt_Gln_amidase superfamily)

PHATRDRAFT_50507 - ch032_bovinuncharacterized protein c8orf32 homolog (Nt_Gln_amidase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50507
PHATRDRAFT_768 argonaute-like protein (Piwi-like superfamily)

PHATRDRAFT_52260 - argonaute-like protein (Piwi-like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52260

PHATRDRAFT_768 - ac018727_22urea active transport protein (SLC5sbd_DUR3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_768
GO ID Go Term p-value q-value Cluster
GO:0006839 mitochondrial transport 0.00172882 1 Phatr_bicluster_0106
GO:0006298 mismatch repair 0.0103346 1 Phatr_bicluster_0106
GO:0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolism 0.0188766 1 Phatr_bicluster_0106
GO:0006810 transport 0.0397443 1 Phatr_bicluster_0106
GO:0006508 proteolysis and peptidolysis 0.328797 1 Phatr_bicluster_0106
GO:0008152 metabolism 0.410263 1 Phatr_bicluster_0106
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