Phatr_bicluster_0153 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_0153 0.26 Phaeodactylum tricornutum
Displaying 1 - 19 of 19
PHATRDRAFT_23399 (metH)

PHATRDRAFT_23399 - (metH)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23399
PHATRDRAFT_28841 hypothetical maltose o-acetyltransferase (LbH_MAT_GAT)

PHATRDRAFT_28841 - hypothetical maltose o-acetyltransferase (LbH_MAT_GAT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28841
PHATRDRAFT_29812 actin a (ACTIN)

PHATRDRAFT_29812 - actin a (ACTIN)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29812
PHATRDRAFT_31068 atp binding (ATP_bind_1)

PHATRDRAFT_31068 - atp binding (ATP_bind_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31068
PHATRDRAFT_37927

PHATRDRAFT_37927 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37927
PHATRDRAFT_43152 peptidyl-prolyl cis-transcyclophilin-type (cyclophilin_ABH_like)

PHATRDRAFT_43152 - peptidyl-prolyl cis-transcyclophilin-type (cyclophilin_ABH_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43152
PHATRDRAFT_44488

PHATRDRAFT_44488 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44488
PHATRDRAFT_47498

PHATRDRAFT_47378 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47378
PHATRDRAFT_47702

PHATRDRAFT_47498 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47498
PHATRDRAFT_48279 pentatricopeptide repeat protein

PHATRDRAFT_47702 - pentatricopeptide repeat protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47702
PHATRDRAFT_48744 glycosylfamily 2 (Glyco_tranf_GTA_type superfamily)

PHATRDRAFT_48279 - glycosylfamily 2 (Glyco_tranf_GTA_type superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48279
PHATRDRAFT_49339

PHATRDRAFT_48744 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48744
PHATRDRAFT_51136 (PRK12999)

PHATRDRAFT_49339 - (PRK12999)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49339
PHATRDRAFT_51157 phosphoenolpyruvate carboxylase (PEPcase)

PHATRDRAFT_51136 - phosphoenolpyruvate carboxylase (PEPcase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51136
PHATRDRAFT_54935 actin a (ACTIN)

PHATRDRAFT_51157 - actin a (ACTIN)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51157
PHATRDRAFT_55192 clathrin coat assembly (APS2)

PHATRDRAFT_54935 - clathrin coat assembly (APS2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54935
PHATRDRAFT_55198 enoyl-hydratase isomerase (PRK05862)

PHATRDRAFT_55192 - enoyl-hydratase isomerase (PRK05862)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55192
PHATRDRAFT_9904 oligosaccharyl transferase subunit (PMT_2 superfamily)

PHATRDRAFT_55198 - oligosaccharyl transferase subunit (PMT_2 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55198

PHATRDRAFT_9904 - haloacid dehalogenase-like hydrolase-like (Hydrolase_3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9904
GO ID Go Term p-value q-value Cluster
GO:0009086 methionine biosynthesis 0.00689992 1 Phatr_bicluster_0153
GO:0006094 gluconeogenesis 0.00861852 1 Phatr_bicluster_0153
GO:0006099 tricarboxylic acid cycle 0.013759 1 Phatr_bicluster_0153
GO:0009396 folic acid and derivative biosynthesis 0.013759 1 Phatr_bicluster_0153
GO:0006520 amino acid metabolism 0.0407909 1 Phatr_bicluster_0153
GO:0006457 protein folding 0.185684 1 Phatr_bicluster_0153
GO:0008152 metabolism 0.410263 1 Phatr_bicluster_0153
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