Phatr_bicluster_0068 Residual: 0.33
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_0068 0.33 Phaeodactylum tricornutum
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Displaying 1 - 23 of 23
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PHATRDRAFT_15627 ubiquitin-protein ligase (HECTc)

PHATRDRAFT_15627 - ubiquitin-protein ligase (HECTc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15627
PHATRDRAFT_16586 cytochrome p450 (p450 superfamily)

PHATRDRAFT_16586 - cytochrome p450 (p450 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16586
PHATRDRAFT_35118 aspartate-beta-hydroxylaseisoform cra_a (Asp_Arg_Hydrox superfamily)

PHATRDRAFT_35118 - aspartate-beta-hydroxylaseisoform cra_a (Asp_Arg_Hydrox superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35118
PHATRDRAFT_36744

PHATRDRAFT_36744 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36744
PHATRDRAFT_37042

PHATRDRAFT_37042 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37042
PHATRDRAFT_38559 translation-associated gtpase (PRK09601)

PHATRDRAFT_38559 - translation-associated gtpase (PRK09601)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38559
PHATRDRAFT_43791 (NADB_Rossmann superfamily)

PHATRDRAFT_43791 - (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43791
PHATRDRAFT_47868

PHATRDRAFT_47868 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47868
PHATRDRAFT_48100 aldo-keto reductase (Aldo_ket_red)

PHATRDRAFT_48100 - aldo-keto reductase (Aldo_ket_red)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48100
PHATRDRAFT_48133 probable proline iminopeptidase pip (prolyl aminopeptidase) (pro_imino_pep_2)

PHATRDRAFT_48133 - probable proline iminopeptidase pip (prolyl aminopeptidase) (pro_imino_pep_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48133
PHATRDRAFT_48162

PHATRDRAFT_48162 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48162
PHATRDRAFT_48468 pheromone shutdown protein (TraB superfamily)

PHATRDRAFT_48468 - pheromone shutdown protein (TraB superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48468
PHATRDRAFT_48655 viral a-type inclusion

PHATRDRAFT_48655 - viral a-type inclusion

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48655
PHATRDRAFT_48689

PHATRDRAFT_48689 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48689
PHATRDRAFT_48772

PHATRDRAFT_48772 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48772
PHATRDRAFT_48785

PHATRDRAFT_48785 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48785
PHATRDRAFT_48902

PHATRDRAFT_48902 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48902
PHATRDRAFT_49252 sjchgc02338 protein (Mmp37 superfamily)

PHATRDRAFT_49252 - sjchgc02338 protein (Mmp37 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49252
PHATRDRAFT_49498 (FPL superfamily)

PHATRDRAFT_49498 - (FPL superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49498
PHATRDRAFT_49710

PHATRDRAFT_49710 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49710
PHATRDRAFT_50072 amino acid transporter (Aa_trans superfamily)

PHATRDRAFT_50072 - amino acid transporter (Aa_trans superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50072
PHATRDRAFT_50578 (Peptidase_C97)

PHATRDRAFT_50578 - (Peptidase_C97)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50578
PHATRDRAFT_54969 aliphatic amidase (aliphatic_amidase)

PHATRDRAFT_54969 - aliphatic amidase (aliphatic_amidase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54969
GO ID Go Term p-value q-value Cluster
GO:0006865 amino acid transport 0.0474487 1 Phatr_bicluster_0068
GO:0006118 electron transport 0.33492 1 Phatr_bicluster_0068
GO:0008152 metabolism 0.410263 1 Phatr_bicluster_0068
GO:0018193 peptidyl-amino acid modification 0.00861852 1 Phatr_bicluster_0068
GO:0006464 protein modification 0.104035 1 Phatr_bicluster_0068
GO:0006508 proteolysis and peptidolysis 0.328797 1 Phatr_bicluster_0068
GO:0006512 ubiquitin cycle 0.0639203 1 Phatr_bicluster_0068
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