Phatr_bicluster_0071 Residual: 0.39
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_0071 0.39 Phaeodactylum tricornutum
Displaying 1 - 22 of 22
PHATRDRAFT_12808 copper amine oxidase (Cu_amine_oxid)

PHATRDRAFT_12808 - copper amine oxidase (Cu_amine_oxid)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12808
PHATRDRAFT_14294 (PITH)

PHATRDRAFT_14294 - (PITH)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14294
PHATRDRAFT_25168 light harvesting protein (PLN00120)

PHATRDRAFT_25168 - light harvesting protein (PLN00120)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25168
PHATRDRAFT_27877 ammonium transporter (Ammonium_transp superfamily)

PHATRDRAFT_27877 - ammonium transporter (Ammonium_transp superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27877
PHATRDRAFT_28245 chloride channel 7 (Voltage_gated_ClC superfamily)

PHATRDRAFT_28245 - chloride channel 7 (Voltage_gated_ClC superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28245
PHATRDRAFT_35050 (Tmemb_14)

PHATRDRAFT_35050 - (Tmemb_14)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35050
PHATRDRAFT_35903

PHATRDRAFT_35903 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35903
PHATRDRAFT_36006 type i secretion target repeat

PHATRDRAFT_36006 - type i secretion target repeat

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36006
PHATRDRAFT_39534 conserved hypothetical membrane protein (Bestrophin superfamily)

PHATRDRAFT_39534 - conserved hypothetical membrane protein (Bestrophin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39534
PHATRDRAFT_40280 carbohydrate-binding protein

PHATRDRAFT_40280 - carbohydrate-binding protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40280
PHATRDRAFT_42902 (COG0523)

PHATRDRAFT_42902 - (COG0523)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42902
PHATRDRAFT_43479 (PDZ_signaling)

PHATRDRAFT_43479 - (PDZ_signaling)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43479
PHATRDRAFT_43708 mgc82689 protein (SET)

PHATRDRAFT_43708 - mgc82689 protein (SET)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43708
PHATRDRAFT_43723 novel protein (TPD)

PHATRDRAFT_43723 - novel protein (TPD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43723
PHATRDRAFT_44286

PHATRDRAFT_44286 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44286
PHATRDRAFT_44673 (DUF4336 superfamily)

PHATRDRAFT_44673 - (DUF4336 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44673
PHATRDRAFT_47436 5-nucleotidase 2-cyclic phosphodiesterase and related esterase (MPP_superfamily superfamily)

PHATRDRAFT_47436 - 5-nucleotidase 2-cyclic phosphodiesterase and related esterase (MPP_superfamily superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47436
PHATRDRAFT_47543

PHATRDRAFT_47543 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47543
PHATRDRAFT_47562

PHATRDRAFT_47562 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47562
PHATRDRAFT_49244 cax family of cationmembrane protein (PLN03151)

PHATRDRAFT_49244 - cax family of cationmembrane protein (PLN03151)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49244
PHATRDRAFT_5419 (HpcH_HpaI superfamily)

PHATRDRAFT_5419 - (HpcH_HpaI superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5419
PHATRDRAFT_9280 calcineurin-like phosphoesterase family protein (MPP_superfamily superfamily)

PHATRDRAFT_9280 - calcineurin-like phosphoesterase family protein (MPP_superfamily superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9280
GO ID Go Term p-value q-value Cluster
GO:0001682 tRNA 5'-leader removal 0.00123487 1 Phatr_bicluster_0071
GO:0006821 chloride transport 0.00861852 1 Phatr_bicluster_0071
GO:0009765 photosynthesis light harvesting 0.0472641 1 Phatr_bicluster_0071
GO:0005975 carbohydrate metabolism 0.0754495 1 Phatr_bicluster_0071
GO:0006810 transport 0.21473 1 Phatr_bicluster_0071
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