Phatr_bicluster_0164 Residual: 0.35
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_0164 0.35 Phaeodactylum tricornutum
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Displaying 1 - 28 of 28
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PHATRDRAFT_20899 spx (syg1 pho81 xpr1) domain-containing

PHATRDRAFT_20899 - spx (syg1 pho81 xpr1) domain-containing

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20899
PHATRDRAFT_30092 ubiquitin-conjugating enzyme (UBCc)

PHATRDRAFT_30092 - ubiquitin-conjugating enzyme (UBCc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30092
PHATRDRAFT_30282 phosphoinositide-3-class 3 (PI3Kc_like superfamily)

PHATRDRAFT_30282 - phosphoinositide-3-class 3 (PI3Kc_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30282
PHATRDRAFT_32097 aaa family (AAA)

PHATRDRAFT_32097 - aaa family (AAA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32097
PHATRDRAFT_32815

PHATRDRAFT_32815 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32815
PHATRDRAFT_34003 embr-h2 protein jr700 (RING)

PHATRDRAFT_34003 - embr-h2 protein jr700 (RING)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34003
PHATRDRAFT_37889

PHATRDRAFT_37889 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37889
PHATRDRAFT_38828

PHATRDRAFT_38828 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38828
PHATRDRAFT_43235 (NADB_Rossmann superfamily)

PHATRDRAFT_43235 - (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43235
PHATRDRAFT_43815

PHATRDRAFT_43815 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43815
PHATRDRAFT_43857 (Fasciclin)

PHATRDRAFT_43857 - (Fasciclin)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43857
PHATRDRAFT_44694 m6 (immune inhibitor a) family (M6dom_TIGR03296)

PHATRDRAFT_44694 - m6 (immune inhibitor a) family (M6dom_TIGR03296)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44694
PHATRDRAFT_46222

PHATRDRAFT_46222 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46222
PHATRDRAFT_47472 (RNase_H_like superfamily)

PHATRDRAFT_47472 - (RNase_H_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47472
PHATRDRAFT_48252 refperecta protein (ZZ superfamily)

PHATRDRAFT_48252 - refperecta protein (ZZ superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48252
PHATRDRAFT_48415 novel protein (RabGAP-TBC superfamily)

PHATRDRAFT_48415 - novel protein (RabGAP-TBC superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48415
PHATRDRAFT_48684 (WD40 superfamily)

PHATRDRAFT_48684 - (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48684
PHATRDRAFT_48883 (UBCc)

PHATRDRAFT_48883 - (UBCc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48883
PHATRDRAFT_49003 cytochrome b5 (Cyt-b5)

PHATRDRAFT_49003 - cytochrome b5 (Cyt-b5)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49003
PHATRDRAFT_49525 myb-like dna-bindingshaqkyf class family protein (SANT)

PHATRDRAFT_49525 - myb-like dna-bindingshaqkyf class family protein (SANT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49525
PHATRDRAFT_49855

PHATRDRAFT_49855 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49855
PHATRDRAFT_49883 (Glyco_trans_1_2)

PHATRDRAFT_49883 - (Glyco_trans_1_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49883
PHATRDRAFT_49926 (Abi)

PHATRDRAFT_49926 - (Abi)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49926
PHATRDRAFT_49927

PHATRDRAFT_49927 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49927
PHATRDRAFT_50019 vacuolar transporter chaperone 4 (PolyPPase_VTC4_like)

PHATRDRAFT_50019 - vacuolar transporter chaperone 4 (PolyPPase_VTC4_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50019
PHATRDRAFT_50306

PHATRDRAFT_50306 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50306
PHATRDRAFT_50515

PHATRDRAFT_50515 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50515
PHATRDRAFT_8111 yippee-like proteinexpressed (Yippee-Mis18 superfamily)

PHATRDRAFT_8111 - yippee-like proteinexpressed (Yippee-Mis18 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8111
GO ID Go Term p-value q-value Cluster
GO:0006512 ubiquitin cycle 0.00231781 1 Phatr_bicluster_0164
GO:0006464 protein modification 0.00628141 1 Phatr_bicluster_0164
GO:0007155 cell adhesion 0.0254203 1 Phatr_bicluster_0164
GO:0016567 protein ubiquitination 0.13382 1 Phatr_bicluster_0164
GO:0006508 proteolysis and peptidolysis 0.365994 1 Phatr_bicluster_0164
GO:0008152 metabolism 0.453158 1 Phatr_bicluster_0164
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