Phatr_bicluster_0145 Residual: 0.28
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_0145 0.28 Phaeodactylum tricornutum
Displaying 1 - 27 of 27
PHATRDRAFT_13553 duf580 domain protein (Choline_transpo superfamily)

PHATRDRAFT_13553 - duf580 domain protein (Choline_transpo superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13553
PHATRDRAFT_13617 serine threonine protein kinase (PKc_like superfamily)

PHATRDRAFT_13617 - serine threonine protein kinase (PKc_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13617
PHATRDRAFT_13975 y3911_agrt5 upf0317 protein atu3911 agr_l_1868 (PRK05463)

PHATRDRAFT_13975 - y3911_agrt5 upf0317 protein atu3911 agr_l_1868 (PRK05463)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13975
PHATRDRAFT_14646 beta-ig-h3 fasciclin (COG2335)

PHATRDRAFT_14646 - beta-ig-h3 fasciclin (COG2335)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14646
PHATRDRAFT_16222 probable cation-transporting atpase 13a3 (atpase family homolog up-regulated in senescence cells 1) (P-ATPase-V)

PHATRDRAFT_16222 - probable cation-transporting atpase 13a3 (atpase family homolog up-regulated in senescence cells 1) (P-ATPase-V)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16222
PHATRDRAFT_28374 iron-sulfur cluster scaffold homolog (IscU_like)

PHATRDRAFT_28374 - iron-sulfur cluster scaffold homolog (IscU_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28374
PHATRDRAFT_36063

PHATRDRAFT_36063 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36063
PHATRDRAFT_3676 outward rectifying potassium channel kco (Ion_trans_2)

PHATRDRAFT_3676 - outward rectifying potassium channel kco (Ion_trans_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3676
PHATRDRAFT_40753 d type cyclin

PHATRDRAFT_40753 - d type cyclin

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40753
PHATRDRAFT_42900

PHATRDRAFT_42900 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42900
PHATRDRAFT_43095 (NrfG)

PHATRDRAFT_43095 - (NrfG)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43095
PHATRDRAFT_43354 ankyrin repeat (ANK)

PHATRDRAFT_43354 - ankyrin repeat (ANK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43354
PHATRDRAFT_43469 mono- or diacylglycerol acyltransferase (LPLAT superfamily)

PHATRDRAFT_43469 - mono- or diacylglycerol acyltransferase (LPLAT superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43469
PHATRDRAFT_43879

PHATRDRAFT_43879 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43879
PHATRDRAFT_43885

PHATRDRAFT_43885 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43885
PHATRDRAFT_44600

PHATRDRAFT_44600 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44600
PHATRDRAFT_45155

PHATRDRAFT_45155 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45155
PHATRDRAFT_45403

PHATRDRAFT_45403 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45403
PHATRDRAFT_45782 ctl transporter (Choline_transpo)

PHATRDRAFT_45782 - ctl transporter (Choline_transpo)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45782
PHATRDRAFT_47520 (PqiA superfamily)

PHATRDRAFT_47520 - (PqiA superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47520
PHATRDRAFT_48084 vacuolar sorting receptor (PA superfamily)

PHATRDRAFT_48084 - vacuolar sorting receptor (PA superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48084
PHATRDRAFT_48950

PHATRDRAFT_48950 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48950
PHATRDRAFT_49164

PHATRDRAFT_49164 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49164
PHATRDRAFT_49834

PHATRDRAFT_49834 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49834
PHATRDRAFT_49880

PHATRDRAFT_49880 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49880
PHATRDRAFT_50027

PHATRDRAFT_50027 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50027
PHATRDRAFT_50642 (PqiA superfamily)

PHATRDRAFT_50642 - (PqiA superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50642
GO ID Go Term p-value q-value Cluster
GO:0006915 apoptosis 0.00665514 1 Phatr_bicluster_0145
GO:0007155 cell adhesion 0.0285555 1 Phatr_bicluster_0145
GO:0006813 potassium ion transport 0.0436294 1 Phatr_bicluster_0145
GO:0006812 cation transport 0.058495 1 Phatr_bicluster_0145
GO:0000074 regulation of cell cycle 0.0731548 1 Phatr_bicluster_0145
GO:0008152 metabolism 0.134877 1 Phatr_bicluster_0145
GO:0006468 protein amino acid phosphorylation 0.323667 1 Phatr_bicluster_0145
GO:0006508 proteolysis and peptidolysis 0.401138 1 Phatr_bicluster_0145
Log in to post comments