Phatr_bicluster_0207 Residual: 0.26
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_0207 0.26 Phaeodactylum tricornutum
Displaying 1 - 22 of 22
PHATRDRAFT_28056 5-methyltetrahydropteroyltriglutamate--homocysteine s-methyltransferase (PLN02475)

PHATRDRAFT_28056 - 5-methyltetrahydropteroyltriglutamate--homocysteine s-methyltransferase (PLN02475)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28056
PHATRDRAFT_32292 saccharopine dehydrogenase (NADB_Rossmann superfamily)

PHATRDRAFT_32292 - saccharopine dehydrogenase (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32292
PHATRDRAFT_34794 duf962 domain protein (DUF962 superfamily)

PHATRDRAFT_34794 - duf962 domain protein (DUF962 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34794
PHATRDRAFT_41374

PHATRDRAFT_36133 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36133
PHATRDRAFT_42895 nod3 protein (LRR_RI superfamily)

PHATRDRAFT_41374 - nod3 protein (LRR_RI superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41374
PHATRDRAFT_43101

PHATRDRAFT_42895 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42895
PHATRDRAFT_43191 phosphatidylinositoln-acetylglucosaminyltransfe ra sesubunit (GPI2 superfamily)

PHATRDRAFT_43101 - phosphatidylinositoln-acetylglucosaminyltransfe ra sesubunit (GPI2 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43101
PHATRDRAFT_44192

PHATRDRAFT_43191 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43191
PHATRDRAFT_44613

PHATRDRAFT_44192 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44192
PHATRDRAFT_44987

PHATRDRAFT_44613 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44613
PHATRDRAFT_45018

PHATRDRAFT_44987 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44987
PHATRDRAFT_45046

PHATRDRAFT_45018 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45018
PHATRDRAFT_45440 signal-transduction protein with cbs domains (CBS_pair)

PHATRDRAFT_45046 - signal-transduction protein with cbs domains (CBS_pair)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45046
PHATRDRAFT_45639

PHATRDRAFT_45440 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45440
PHATRDRAFT_45716 kiaa0859 isoform 1

PHATRDRAFT_45639 - kiaa0859 isoform 1

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45639
PHATRDRAFT_46329

PHATRDRAFT_45716 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45716
PHATRDRAFT_46492

PHATRDRAFT_46329 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46329
PHATRDRAFT_46698 glycoside hydrolase family 28 protein polygalacturonasefamily protein (Pectate_lyase_3 superfamily)

PHATRDRAFT_46492 - glycoside hydrolase family 28 protein polygalacturonasefamily protein (Pectate_lyase_3 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46492
PHATRDRAFT_48976 poly polymerase and dna-ligase zn-finger region family protein (zf-PARP)

PHATRDRAFT_46698 - poly polymerase and dna-ligase zn-finger region family protein (zf-PARP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46698
PHATRDRAFT_50414

PHATRDRAFT_48976 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48976
PHATRDRAFT_8876 nod3 protein (LRR_RI superfamily)

PHATRDRAFT_50414 - nod3 protein (LRR_RI superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50414

PHATRDRAFT_8876 - dephospho-kinase (DPCK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8876
GO ID Go Term p-value q-value Cluster
GO:0009086 methionine biosynthesis 0.00197506 1 Phatr_bicluster_0207
GO:0005975 carbohydrate metabolism 0.0308805 1 Phatr_bicluster_0207
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