Phatr_bicluster_0224 Residual: 0.21
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_0224 0.21 Phaeodactylum tricornutum
Displaying 1 - 18 of 18
PHATRDRAFT_10800 (DUF819 superfamily)

PHATRDRAFT_10800 - (DUF819 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10800
PHATRDRAFT_11387 ca2+ h+ antiporter (cax)

PHATRDRAFT_11387 - ca2+ h+ antiporter (cax)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11387
PHATRDRAFT_15125 gdp-4-keto-6-deoxy-d-mannose epimerase-reductase (PLN02725)

PHATRDRAFT_15125 - gdp-4-keto-6-deoxy-d-mannose epimerase-reductase (PLN02725)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15125
PHATRDRAFT_18323 inositol-phosphate phosphatase (IMPase)

PHATRDRAFT_18323 - inositol-phosphate phosphatase (IMPase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18323
PHATRDRAFT_21006 protein kinase domain containing protein (Pkinase)

PHATRDRAFT_21006 - protein kinase domain containing protein (Pkinase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21006
PHATRDRAFT_32849 branched-chain amino acid aminotransferase (BCAT_beta_family)

PHATRDRAFT_32849 - branched-chain amino acid aminotransferase (BCAT_beta_family)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32849
PHATRDRAFT_33037 (Methyltransf_28)

PHATRDRAFT_33037 - (Methyltransf_28)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33037
PHATRDRAFT_38394 3-ketoacyl-(acyl-carrier-protein) reductase (SDR_c)

PHATRDRAFT_38394 - 3-ketoacyl-(acyl-carrier-protein) reductase (SDR_c)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38394
PHATRDRAFT_39827

PHATRDRAFT_39827 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39827
PHATRDRAFT_44054

PHATRDRAFT_44054 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44054
PHATRDRAFT_44902 aspartate--ammonia ligase (PRK05425)

PHATRDRAFT_44902 - aspartate--ammonia ligase (PRK05425)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44902
PHATRDRAFT_45495 two-component response regulator (PAS_9)

PHATRDRAFT_45495 - two-component response regulator (PAS_9)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45495
PHATRDRAFT_45572 ero1-like beta (ERO1 superfamily)

PHATRDRAFT_45572 - ero1-like beta (ERO1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45572
PHATRDRAFT_45803

PHATRDRAFT_45803 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45803
PHATRDRAFT_48342

PHATRDRAFT_48342 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48342
PHATRDRAFT_50964 o-acetylhomoserine o-acetylserine sulfhydrylase (CGS_like)

PHATRDRAFT_50964 - o-acetylhomoserine o-acetylserine sulfhydrylase (CGS_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50964
PHATRDRAFT_5780 3-ketoacyl-(acyl-carrier-protein) reductase (SDR_c)

PHATRDRAFT_5780 - 3-ketoacyl-(acyl-carrier-protein) reductase (SDR_c)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5780
PHATRDRAFT_8301 (DUF3593 superfamily)

PHATRDRAFT_8301 - (DUF3593 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8301
GO ID Go Term p-value q-value Cluster
GO:0009081 branched chain family amino acid metabolism 0.00591714 1 Phatr_bicluster_0224
GO:0006529 asparagine biosynthesis 0.00788271 1 Phatr_bicluster_0224
GO:0008152 metabolism 0.0161272 1 Phatr_bicluster_0224
GO:0006520 amino acid metabolism 0.0464863 1 Phatr_bicluster_0224
GO:0006418 tRNA aminoacylation for protein translation 0.0983212 1 Phatr_bicluster_0224
GO:0006468 protein amino acid phosphorylation 0.2936 1 Phatr_bicluster_0224
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