Phatr_bicluster_0219 Residual: 0.22
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_0219 0.22 Phaeodactylum tricornutum
Displaying 1 - 18 of 18
PHATRDRAFT_10260 nadbeta subunit (PNTB superfamily)

PHATRDRAFT_10260 - nadbeta subunit (PNTB superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10260
PHATRDRAFT_10581 nadalpha subunit (pntA)

PHATRDRAFT_10581 - nadalpha subunit (pntA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10581
PHATRDRAFT_12416 hydroxylamine reductase (HCP_like superfamily)

PHATRDRAFT_12416 - hydroxylamine reductase (HCP_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12416
PHATRDRAFT_35217

PHATRDRAFT_35217 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35217
PHATRDRAFT_35400

PHATRDRAFT_35400 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35400
PHATRDRAFT_35909

PHATRDRAFT_35909 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35909
PHATRDRAFT_36928 cupin region (Cupin_2)

PHATRDRAFT_36928 - cupin region (Cupin_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36928
PHATRDRAFT_42502

PHATRDRAFT_42502 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42502
PHATRDRAFT_43261

PHATRDRAFT_43261 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43261
PHATRDRAFT_44259 smooth muscle myosin heavy chain

PHATRDRAFT_44259 - smooth muscle myosin heavy chain

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44259
PHATRDRAFT_45104

PHATRDRAFT_45104 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45104
PHATRDRAFT_45472 rhb1a (ring-h2 finger b1a) protein binding zinc ion binding

PHATRDRAFT_45472 - rhb1a (ring-h2 finger b1a) protein binding zinc ion binding

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45472
PHATRDRAFT_45603

PHATRDRAFT_45603 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45603
PHATRDRAFT_45672 general substrate transporter (2A0115)

PHATRDRAFT_45672 - general substrate transporter (2A0115)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45672
PHATRDRAFT_45826 mgc82090 protein (hscB)

PHATRDRAFT_45826 - mgc82090 protein (hscB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45826
PHATRDRAFT_46030

PHATRDRAFT_46030 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46030
PHATRDRAFT_46243 cell wall surface anchor family protein

PHATRDRAFT_46243 - cell wall surface anchor family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46243
PHATRDRAFT_51511 member ras oncogene family (Rab5_related)

PHATRDRAFT_51511 - member ras oncogene family (Rab5_related)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51511
GO ID Go Term p-value q-value Cluster
GO:0006118 electron transport 0.00808825 1 Phatr_bicluster_0219
GO:0015992 proton transport 0.0273521 1 Phatr_bicluster_0219
GO:0016567 protein ubiquitination 0.13382 1 Phatr_bicluster_0219
GO:0006457 protein folding 0.209255 1 Phatr_bicluster_0219
GO:0006810 transport 0.320848 1 Phatr_bicluster_0219
GO:0006508 proteolysis and peptidolysis 0.365994 1 Phatr_bicluster_0219
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