Phatr_bicluster_0205 Residual: 0.32
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_0205 0.32 Phaeodactylum tricornutum
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Displaying 1 - 31 of 31
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PHATRDRAFT_14391 abc transporter related (Uup)

PHATRDRAFT_14391 - abc transporter related (Uup)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14391
PHATRDRAFT_15482 membrane protein (Rhomboid)

PHATRDRAFT_15482 - membrane protein (Rhomboid)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15482
PHATRDRAFT_23833 prolyl-trna synthetase-like (YbaK_like)

PHATRDRAFT_23833 - prolyl-trna synthetase-like (YbaK_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23833
PHATRDRAFT_37441 arystal structure of xc6422 from xanthomonas campestris: a member of ab serine hydrolase without lid atresolution (Abhydrolase_5)

PHATRDRAFT_37441 - arystal structure of xc6422 from xanthomonas campestris: a member of ab serine hydrolase without lid atresolution (Abhydrolase_5)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37441
PHATRDRAFT_38535

PHATRDRAFT_38535 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38535
PHATRDRAFT_40690 peptidase m48 ste24p (HtpX)

PHATRDRAFT_40690 - peptidase m48 ste24p (HtpX)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40690
PHATRDRAFT_40919 lipolytic protein g-d-s-l family (SGNH_hydrolase superfamily)

PHATRDRAFT_40919 - lipolytic protein g-d-s-l family (SGNH_hydrolase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40919
PHATRDRAFT_43931 methyltransferase type 11 (SmtA)

PHATRDRAFT_43931 - methyltransferase type 11 (SmtA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43931
PHATRDRAFT_47467

PHATRDRAFT_47467 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47467
PHATRDRAFT_47469

PHATRDRAFT_47469 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47469
PHATRDRAFT_47594 leader peptidase i (sigpep_I_bact)

PHATRDRAFT_47594 - leader peptidase i (sigpep_I_bact)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47594
PHATRDRAFT_47863

PHATRDRAFT_47863 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47863
PHATRDRAFT_48178 (Ion_trans_2)

PHATRDRAFT_48178 - (Ion_trans_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48178
PHATRDRAFT_48184

PHATRDRAFT_48184 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48184
PHATRDRAFT_48230

PHATRDRAFT_48230 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48230
PHATRDRAFT_48343 (Nucleotid_trans superfamily)

PHATRDRAFT_48343 - (Nucleotid_trans superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48343
PHATRDRAFT_48386 solute carrier family 22 (organic cation transporter)member 18 (MFS_1)

PHATRDRAFT_48386 - solute carrier family 22 (organic cation transporter)member 18 (MFS_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48386
PHATRDRAFT_48473 jumonji domain containing 4

PHATRDRAFT_48473 - jumonji domain containing 4

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48473
PHATRDRAFT_48717 rhomboid family protein (Rhomboid superfamily)

PHATRDRAFT_48717 - rhomboid family protein (Rhomboid superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48717
PHATRDRAFT_48787

PHATRDRAFT_48787 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48787
PHATRDRAFT_48968

PHATRDRAFT_48968 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48968
PHATRDRAFT_49058 metal transport protein

PHATRDRAFT_49058 - metal transport protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49058
PHATRDRAFT_49124

PHATRDRAFT_49124 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49124
PHATRDRAFT_49379

PHATRDRAFT_49379 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49379
PHATRDRAFT_49443

PHATRDRAFT_49443 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49443
PHATRDRAFT_49568 (Aa_trans superfamily)

PHATRDRAFT_49568 - (Aa_trans superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49568
PHATRDRAFT_49955

PHATRDRAFT_49955 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49955
PHATRDRAFT_50416 (Nucleotid_trans superfamily)

PHATRDRAFT_50416 - (Nucleotid_trans superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50416
PHATRDRAFT_50614 serine threonine protein kinase and signal transduction histidine kinase (COG3899)

PHATRDRAFT_50614 - serine threonine protein kinase and signal transduction histidine kinase (COG3899)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50614
PHATRDRAFT_52208 alcohol dehydrogenasedomain protein (Zn_ADH5)

PHATRDRAFT_52208 - alcohol dehydrogenasedomain protein (Zn_ADH5)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52208
PHATRDRAFT_6789 peroxisomal coenzyme a diphosphatase nudt7 (nucleoside diphosphate-linked moiety x motif 7) (nudix motif 7) (CoAse)

PHATRDRAFT_6789 - peroxisomal coenzyme a diphosphatase nudt7 (nucleoside diphosphate-linked moiety x motif 7) (nudix motif 7) (CoAse)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6789
GO ID Go Term p-value q-value Cluster
GO:0006508 proteolysis and peptidolysis 0.010945 1 Phatr_bicluster_0205
GO:0006811 ion transport 0.0242101 1 Phatr_bicluster_0205
GO:0006813 potassium ion transport 0.0436294 1 Phatr_bicluster_0205
GO:0000160 two-component signal transduction system (phosphorelay) 0.056384 1 Phatr_bicluster_0205
GO:0006812 cation transport 0.058495 1 Phatr_bicluster_0205
GO:0006865 amino acid transport 0.0606018 1 Phatr_bicluster_0205
GO:0006355 regulation of transcription, DNA-dependent 0.394049 1 Phatr_bicluster_0205
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