Phatr_bicluster_0212 Residual: 0.29
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_0212 0.29 Phaeodactylum tricornutum
Displaying 1 - 22 of 22
PHATRDRAFT_20588 ribonuclease iii (RIBOc superfamily)

PHATRDRAFT_13944 - ribonuclease iii (RIBOc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13944
PHATRDRAFT_21135 s-adenosyl-methyltransferase (AdoMet_MTases superfamily)

PHATRDRAFT_15884 - s-adenosyl-methyltransferase (AdoMet_MTases superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15884
PHATRDRAFT_31704 (Sm_like superfamily)

PHATRDRAFT_20588 - (Sm_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20588
PHATRDRAFT_31898 heat shock protein (PRK05456)

PHATRDRAFT_21135 - heat shock protein (PRK05456)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21135
PHATRDRAFT_36988

PHATRDRAFT_31704 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31704
PHATRDRAFT_39717 heat shock 105kda 110kda proteinisoform cra_a

PHATRDRAFT_31898 - heat shock 105kda 110kda proteinisoform cra_a

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31898
PHATRDRAFT_44712 heat shock protein hsp70 family protein

PHATRDRAFT_34252 - heat shock protein hsp70 family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34252
PHATRDRAFT_45409

PHATRDRAFT_36988 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36988
PHATRDRAFT_45546

PHATRDRAFT_39717 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39717
PHATRDRAFT_47373

PHATRDRAFT_44712 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44712
PHATRDRAFT_47820 sr protein related family member (rsr-1) (BRLZ)

PHATRDRAFT_45409 - sr protein related family member (rsr-1) (BRLZ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45409
PHATRDRAFT_48404 leucine rich repeat familyexpressed

PHATRDRAFT_45546 - leucine rich repeat familyexpressed

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45546
PHATRDRAFT_48573

PHATRDRAFT_47373 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47373
PHATRDRAFT_49351

PHATRDRAFT_47820 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47820
PHATRDRAFT_49647

PHATRDRAFT_48404 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48404
PHATRDRAFT_49827 telomeric repeat binding factorisoform cra_a (SANT_TRF)

PHATRDRAFT_48573 - telomeric repeat binding factorisoform cra_a (SANT_TRF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48573
PHATRDRAFT_50007

PHATRDRAFT_48857 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48857
PHATRDRAFT_50604

PHATRDRAFT_49351 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49351

PHATRDRAFT_49647 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49647

PHATRDRAFT_49827 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49827

PHATRDRAFT_50007 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50007

PHATRDRAFT_50604 - cell surface flocculin

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50604
GO ID Go Term p-value q-value Cluster
GO:0006397 mRNA processing 0.0169488 1 Phatr_bicluster_0212
GO:0006511 ubiquitin-dependent protein catabolism 0.0329804 1 Phatr_bicluster_0212
GO:0006355 regulation of transcription, DNA-dependent 0.15368 1 Phatr_bicluster_0212
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