Phatr_bicluster_0177 Residual: 0.30
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_0177 0.30 Phaeodactylum tricornutum
Displaying 1 - 23 of 23
PHATRDRAFT_14401 isocitrate lyase (ICL_PEPM)

PHATRDRAFT_14401 - isocitrate lyase (ICL_PEPM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14401
PHATRDRAFT_17860 electron transfer flavoprotein beta-subunit (ETF_beta)

PHATRDRAFT_17860 - electron transfer flavoprotein beta-subunit (ETF_beta)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17860
PHATRDRAFT_25932 acyl-coenzyme ac-2 to c-3 short chain (SCAD_SBCAD)

PHATRDRAFT_25932 - acyl-coenzyme ac-2 to c-3 short chain (SCAD_SBCAD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25932
PHATRDRAFT_29666 (DUF389)

PHATRDRAFT_29666 - (DUF389)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29666
PHATRDRAFT_31650 (Xan_ur_permease)

PHATRDRAFT_31650 - (Xan_ur_permease)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31650
PHATRDRAFT_33773 protein familywith a coiled coil-4 domain (Methyltransf_22)

PHATRDRAFT_33773 - protein familywith a coiled coil-4 domain (Methyltransf_22)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33773
PHATRDRAFT_33814

PHATRDRAFT_33814 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33814
PHATRDRAFT_35240

PHATRDRAFT_35067 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35067
PHATRDRAFT_35691 hydroxyacyl-coenzyme a dehydrogenase 3-ketoacyl-coenzyme a thiolase enoyl-coenzyme a hydratase (trifunctional protein)alpha subunit (fadJ)

PHATRDRAFT_35240 - hydroxyacyl-coenzyme a dehydrogenase 3-ketoacyl-coenzyme a thiolase enoyl-coenzyme a hydratase (trifunctional protein)alpha subunit (fadJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35240
PHATRDRAFT_36106 thiamine-phosphate pyrophosphorylase (TMP_TenI)

PHATRDRAFT_35691 - thiamine-phosphate pyrophosphorylase (TMP_TenI)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35691
PHATRDRAFT_43269 (Alginate_lyase)

PHATRDRAFT_36106 - (Alginate_lyase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36106
PHATRDRAFT_43371

PHATRDRAFT_43269 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43269
PHATRDRAFT_44742

PHATRDRAFT_43371 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43371
PHATRDRAFT_45323

PHATRDRAFT_44742 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44742
PHATRDRAFT_45547 (FHA)

PHATRDRAFT_45323 - (FHA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45323
PHATRDRAFT_45676 dumpy cg33196-pb

PHATRDRAFT_45547 - dumpy cg33196-pb

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45547
PHATRDRAFT_45877 (COG0398)

PHATRDRAFT_45676 - (COG0398)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45676
PHATRDRAFT_46323

PHATRDRAFT_45877 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45877
PHATRDRAFT_46622 mucin-associated surface protein

PHATRDRAFT_46323 - mucin-associated surface protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46323
PHATRDRAFT_47168

PHATRDRAFT_46622 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46622
PHATRDRAFT_48819

PHATRDRAFT_47168 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47168
PHATRDRAFT_49232 phosphoglucosamine mutase family protein (PLN02371)

PHATRDRAFT_48819 - phosphoglucosamine mutase family protein (PLN02371)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48819

PHATRDRAFT_49232 - atbrca1 (breast cancer susceptibility1) ubiquitin-protein ligase (RING)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49232
GO ID Go Term p-value q-value Cluster
GO:0006097 glyoxylate cycle 0.00246975 1 Phatr_bicluster_0177
GO:0009228 thiamin biosynthesis 0.00739277 1 Phatr_bicluster_0177
GO:0006631 fatty acid metabolism 0.00739277 1 Phatr_bicluster_0177
GO:0006118 electron transport 0.106225 1 Phatr_bicluster_0177
GO:0005975 carbohydrate metabolism 0.14529 1 Phatr_bicluster_0177
GO:0008152 metabolism 0.160846 1 Phatr_bicluster_0177
GO:0016567 protein ubiquitination 0.164415 1 Phatr_bicluster_0177
GO:0006810 transport 0.38354 1 Phatr_bicluster_0177
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