Phatr_bicluster_0184 Residual: 0.27
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_0184 0.27 Phaeodactylum tricornutum
Displaying 1 - 22 of 22
PHATRDRAFT_13157 small gtp-binding protein domain containing protein (Ras_like_GTPase superfamily)

PHATRDRAFT_13157 - small gtp-binding protein domain containing protein (Ras_like_GTPase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13157
PHATRDRAFT_36077 tim-barrelyjbn family (DUS_like_FMN)

PHATRDRAFT_34229 - tim-barrelyjbn family (DUS_like_FMN)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34229
PHATRDRAFT_37223 (Ten1_2 superfamily)

PHATRDRAFT_36077 - (Ten1_2 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36077
PHATRDRAFT_38927 gcn5-related n-acetyltransferase

PHATRDRAFT_37223 - gcn5-related n-acetyltransferase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37223
PHATRDRAFT_39329 ribosomal protein l11 methyltransferase

PHATRDRAFT_38927 - ribosomal protein l11 methyltransferase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38927
PHATRDRAFT_39520 temporarily assigned gene name family member (tag-30) (BTB)

PHATRDRAFT_39329 - temporarily assigned gene name family member (tag-30) (BTB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39329
PHATRDRAFT_42424

PHATRDRAFT_39520 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39520
PHATRDRAFT_42818 xenotropic and polytropic murine leukemia virus receptor xpr1 (EXS superfamily)

PHATRDRAFT_42424 - xenotropic and polytropic murine leukemia virus receptor xpr1 (EXS superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42424
PHATRDRAFT_43143

PHATRDRAFT_42818 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42818
PHATRDRAFT_43435 thioredoxin-like proteinexpressed (PITH)

PHATRDRAFT_43143 - thioredoxin-like proteinexpressed (PITH)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43143
PHATRDRAFT_43454 cog0457: fog: tpr repeat (COG4976)

PHATRDRAFT_43435 - cog0457: fog: tpr repeat (COG4976)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43435
PHATRDRAFT_43515

PHATRDRAFT_43454 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43454
PHATRDRAFT_44453 solute carrier family 29 (nucleoside transporters)memberisoform cra_b (Nucleoside_tran superfamily)

PHATRDRAFT_43515 - solute carrier family 29 (nucleoside transporters)memberisoform cra_b (Nucleoside_tran superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43515
PHATRDRAFT_45790 myeloid lymphoid or mixed-lineage leukemia (zf-CXXC)

PHATRDRAFT_44453 - myeloid lymphoid or mixed-lineage leukemia (zf-CXXC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44453
PHATRDRAFT_46920 (acyl_WS_DGAT)

PHATRDRAFT_45790 - (acyl_WS_DGAT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45790
PHATRDRAFT_47092

PHATRDRAFT_46920 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46920
PHATRDRAFT_47117 p-atpase family transporter: cadmium zinc ion heavy metal translocating p-type atpase family-like protein

PHATRDRAFT_47092 - p-atpase family transporter: cadmium zinc ion heavy metal translocating p-type atpase family-like protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47092
PHATRDRAFT_47603 (Gly_transf_sug superfamily)

PHATRDRAFT_47117 - (Gly_transf_sug superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47117
PHATRDRAFT_48029

PHATRDRAFT_47603 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47603
PHATRDRAFT_48569 abortive infection protein (Abi)

PHATRDRAFT_48029 - abortive infection protein (Abi)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48029
PHATRDRAFT_54834 (CpeT superfamily)

PHATRDRAFT_48569 - (CpeT superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48569

PHATRDRAFT_54834 - malate l-lactate dehydrogenase (PLN00105)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54834
GO ID Go Term p-value q-value Cluster
GO:0007264 small GTPase mediated signal transduction 0.0205926 1 Phatr_bicluster_0184
GO:0015031 protein transport 0.030286 1 Phatr_bicluster_0184
GO:0006886 intracellular protein transport 0.0389484 1 Phatr_bicluster_0184
GO:0006355 regulation of transcription, DNA-dependent 0.199489 1 Phatr_bicluster_0184
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