Phatr_bicluster_0063 Residual: 0.36
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_0063 0.36 Phaeodactylum tricornutum
Displaying 1 - 25 of 25
PHATRDRAFT_12990 dead-box protein abstrakt (PRK10590)

PHATRDRAFT_12990 - dead-box protein abstrakt (PRK10590)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12990
PHATRDRAFT_16120 cytoplasmic protein of eukaryotic origin-like (DUF2419 superfamily)

PHATRDRAFT_16120 - cytoplasmic protein of eukaryotic origin-like (DUF2419 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16120
PHATRDRAFT_23306 vacuolar protein sorting 13b (VacB)

PHATRDRAFT_23306 - vacuolar protein sorting 13b (VacB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23306
PHATRDRAFT_25 (COG1204)

PHATRDRAFT_25 - (COG1204)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25
PHATRDRAFT_267 insulin degrading enzyme (Ptr)

PHATRDRAFT_267 - insulin degrading enzyme (Ptr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_267
PHATRDRAFT_33266 solute carrier family 34 (sodium phosphate)member 1 (2a58)

PHATRDRAFT_33266 - solute carrier family 34 (sodium phosphate)member 1 (2a58)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33266
PHATRDRAFT_33499

PHATRDRAFT_33499 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33499
PHATRDRAFT_36016 homology subfamily a member 5 (DnaJ)

PHATRDRAFT_36016 - homology subfamily a member 5 (DnaJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36016
PHATRDRAFT_37734 (Nop25 superfamily)

PHATRDRAFT_37734 - (Nop25 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37734
PHATRDRAFT_42441

PHATRDRAFT_42441 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42441
PHATRDRAFT_42676

PHATRDRAFT_42676 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42676
PHATRDRAFT_44423

PHATRDRAFT_44423 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44423
PHATRDRAFT_44564 (DUF4246)

PHATRDRAFT_44564 - (DUF4246)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44564
PHATRDRAFT_44627 gtp-binding protein (Obg)

PHATRDRAFT_44627 - gtp-binding protein (Obg)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44627
PHATRDRAFT_47281 pentatricopeptiderepeat-containing protein

PHATRDRAFT_47281 - pentatricopeptiderepeat-containing protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47281
PHATRDRAFT_47705 ribosome receptor

PHATRDRAFT_47705 - ribosome receptor

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47705
PHATRDRAFT_49439 cbf1 interacting corepressor cir (Cir_N)

PHATRDRAFT_49439 - cbf1 interacting corepressor cir (Cir_N)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49439
PHATRDRAFT_49534 biopterin transport-related protein bt1 (BT1)

PHATRDRAFT_49534 - biopterin transport-related protein bt1 (BT1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49534
PHATRDRAFT_49540 (MFS)

PHATRDRAFT_49540 - (MFS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49540
PHATRDRAFT_49642 pentatrichopeptide repeatprotein (PPR_2)

PHATRDRAFT_49642 - pentatrichopeptide repeatprotein (PPR_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49642
PHATRDRAFT_49765 (Peptidase_C48 superfamily)

PHATRDRAFT_49765 - (Peptidase_C48 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49765
PHATRDRAFT_49919 splicing endonuclease positive effector sen1 (AAA_12 superfamily)

PHATRDRAFT_49919 - splicing endonuclease positive effector sen1 (AAA_12 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49919
PHATRDRAFT_52346 mgc88910 protein (Glyco_hydro_47)

PHATRDRAFT_52346 - mgc88910 protein (Glyco_hydro_47)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52346
PHATRDRAFT_8821 atp-bindingsub-family b (mdr tap)member 10 (ABC_ATPase superfamily)

PHATRDRAFT_8821 - atp-bindingsub-family b (mdr tap)member 10 (ABC_ATPase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8821
PHATRDRAFT_9078 photosystem ii 11 kd protein (PSII_Pbs27)

PHATRDRAFT_9078 - photosystem ii 11 kd protein (PSII_Pbs27)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9078
GO ID Go Term p-value q-value Cluster
GO:0006817 phosphate transport 0.0120481 1 Phatr_bicluster_0063
GO:0006508 proteolysis and peptidolysis 0.053216 1 Phatr_bicluster_0063
GO:0006418 tRNA aminoacylation for protein translation 0.08657 1 Phatr_bicluster_0063
GO:0006457 protein folding 0.185684 1 Phatr_bicluster_0063
GO:0006412 protein biosynthesis 0.247414 1 Phatr_bicluster_0063
GO:0006118 electron transport 0.33492 1 Phatr_bicluster_0063
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