Phatr_bicluster_0185 Residual: 0.34
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_0185 0.34 Phaeodactylum tricornutum
Displaying 1 - 28 of 28
PHATRDRAFT_10799 malonyl-decarboxylase (MCD superfamily)

PHATRDRAFT_10799 - malonyl-decarboxylase (MCD superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10799
PHATRDRAFT_11183 transmembrane protein 34 (Solute_trans_a)

PHATRDRAFT_11183 - transmembrane protein 34 (Solute_trans_a)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11183
PHATRDRAFT_13418 ammonium transporter (Ammonium_transp superfamily)

PHATRDRAFT_13418 - ammonium transporter (Ammonium_transp superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13418
PHATRDRAFT_17199 solute carrier family 24 (sodium potassium calcium exchanger)member 2 (TIGR00367)

PHATRDRAFT_17199 - solute carrier family 24 (sodium potassium calcium exchanger)member 2 (TIGR00367)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17199
PHATRDRAFT_18180 light harvesting complex protein (Chloroa_b-bind)

PHATRDRAFT_18180 - light harvesting complex protein (Chloroa_b-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18180
PHATRDRAFT_34899

PHATRDRAFT_34899 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34899
PHATRDRAFT_34920 basic helix-loop-helixfamily protein (AAA_33)

PHATRDRAFT_34920 - basic helix-loop-helixfamily protein (AAA_33)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34920
PHATRDRAFT_36842 tubulin tyrosine ligase-likememberisoform cra_c (TTL superfamily)

PHATRDRAFT_34966 - tubulin tyrosine ligase-likememberisoform cra_c (TTL superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34966
PHATRDRAFT_37254 protein pns1 (Choline_transpo superfamily)

PHATRDRAFT_36842 - protein pns1 (Choline_transpo superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36842
PHATRDRAFT_42997 serine protease (Tryp_SPc)

PHATRDRAFT_37254 - serine protease (Tryp_SPc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37254
PHATRDRAFT_43686

PHATRDRAFT_42997 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42997
PHATRDRAFT_43699 (PTZ00445 superfamily)

PHATRDRAFT_43686 - (PTZ00445 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43686
PHATRDRAFT_44527

PHATRDRAFT_43699 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43699
PHATRDRAFT_44984 (Trypsin_2)

PHATRDRAFT_44527 - (Trypsin_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44527
PHATRDRAFT_45037 adenosylmethionine-8-amino-7-oxononanoate aminotransferase (AAT_I superfamily)

PHATRDRAFT_44984 - adenosylmethionine-8-amino-7-oxononanoate aminotransferase (AAT_I superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44984
PHATRDRAFT_45136

PHATRDRAFT_45037 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45037
PHATRDRAFT_45616

PHATRDRAFT_45136 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45136
PHATRDRAFT_46110

PHATRDRAFT_45616 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45616
PHATRDRAFT_46143 fuct c3 protein (Glyco_transf_10 superfamily)

PHATRDRAFT_46110 - fuct c3 protein (Glyco_transf_10 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46110
PHATRDRAFT_46370

PHATRDRAFT_46143 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46143
PHATRDRAFT_46378

PHATRDRAFT_46370 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46370
PHATRDRAFT_46500

PHATRDRAFT_46378 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46378
PHATRDRAFT_46540

PHATRDRAFT_46500 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46500
PHATRDRAFT_46952

PHATRDRAFT_46540 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46540
PHATRDRAFT_47898

PHATRDRAFT_46952 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46952
PHATRDRAFT_5651

PHATRDRAFT_47898 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47898

PHATRDRAFT_48704 - sarcosine-dimethylglycine methyltransferase (AdoMet_MTases)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48704

PHATRDRAFT_5651 - ywhae protein (14-3-3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5651
GO ID Go Term p-value q-value Cluster
GO:0006633 fatty acid biosynthesis 0.0127857 1 Phatr_bicluster_0185
GO:0009765 photosynthesis light harvesting 0.0379888 1 Phatr_bicluster_0185
GO:0006810 transport 0.175813 1 Phatr_bicluster_0185
GO:0006508 proteolysis and peptidolysis 0.203663 1 Phatr_bicluster_0185
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