Phatr_bicluster_0220 Residual: 0.29
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_0220 0.29 Phaeodactylum tricornutum
Displaying 1 - 29 of 29
PHATRDRAFT_10068 enoyl-acyl carrier reductase (PLN02730)

PHATRDRAFT_10068 - enoyl-acyl carrier reductase (PLN02730)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10068
PHATRDRAFT_10896 solute carrier protein (Mito_carr)

PHATRDRAFT_10896 - solute carrier protein (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10896
PHATRDRAFT_13895 photosystem ii stability assembly factor hcf136 (PLN00033)

PHATRDRAFT_13895 - photosystem ii stability assembly factor hcf136 (PLN00033)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13895
PHATRDRAFT_14529 inorganic pyrophosphatase-like protein (pyrophosphatase)

PHATRDRAFT_14529 - inorganic pyrophosphatase-like protein (pyrophosphatase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14529
PHATRDRAFT_20657 chloroplast atpase gamma subunit precursor (F1-ATPase_gamma)

PHATRDRAFT_20657 - chloroplast atpase gamma subunit precursor (F1-ATPase_gamma)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20657
PHATRDRAFT_22122 glyceraldehyde-3-phosphate dehydrogenase precursor (GapA)

PHATRDRAFT_22122 - glyceraldehyde-3-phosphate dehydrogenase precursor (GapA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22122
PHATRDRAFT_32708 (PLN02307)

PHATRDRAFT_32708 - (PLN02307)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32708
PHATRDRAFT_34270

PHATRDRAFT_34270 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34270
PHATRDRAFT_35386 methyltransferase type 11 (Methyltransf_12)

PHATRDRAFT_35386 - methyltransferase type 11 (Methyltransf_12)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35386
PHATRDRAFT_35587 mopfamily transporter: multidrug efflux (MATE_like superfamily)

PHATRDRAFT_35587 - mopfamily transporter: multidrug efflux (MATE_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35587
PHATRDRAFT_36724

PHATRDRAFT_36724 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36724
PHATRDRAFT_41038 glutaredoxin 2 (PRK10387)

PHATRDRAFT_38124 - glutaredoxin 2 (PRK10387)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38124
PHATRDRAFT_42282

PHATRDRAFT_41038 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41038
PHATRDRAFT_43233 atp sulfurylase (sulfate adenylyltransferase) (sopT)

PHATRDRAFT_42282 - atp sulfurylase (sulfate adenylyltransferase) (sopT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42282
PHATRDRAFT_44603 low-co2 inducible protein

PHATRDRAFT_43233 - low-co2 inducible protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43233
PHATRDRAFT_44999 atp synthase h+-transporting mitochondrial f1 complex o subunit (OSCP)

PHATRDRAFT_44603 - atp synthase h+-transporting mitochondrial f1 complex o subunit (OSCP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44603
PHATRDRAFT_45190 (alpha-crystallin-Hsps_p23-like superfamily)

PHATRDRAFT_44999 - (alpha-crystallin-Hsps_p23-like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44999
PHATRDRAFT_45465 gnat family (RimI)

PHATRDRAFT_45190 - gnat family (RimI)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45190
PHATRDRAFT_46376

PHATRDRAFT_45465 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45465
PHATRDRAFT_46608

PHATRDRAFT_46376 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46376
PHATRDRAFT_46930 deoxyxylulose-5-phosphate synthase (TIP120 superfamily)

PHATRDRAFT_46608 - deoxyxylulose-5-phosphate synthase (TIP120 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46608
PHATRDRAFT_47103 (Methyltransf_16 superfamily)

PHATRDRAFT_46930 - (Methyltransf_16 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46930
PHATRDRAFT_49229

PHATRDRAFT_47103 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47103
PHATRDRAFT_49779 10-formyltetrahydrofolate synthetase (FTHFS)

PHATRDRAFT_49229 - 10-formyltetrahydrofolate synthetase (FTHFS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49229
PHATRDRAFT_50215

PHATRDRAFT_49779 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49779
PHATRDRAFT_51837

PHATRDRAFT_50215 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50215
PHATRDRAFT_8747 glutaredoxin type i (Thioredoxin_like superfamily)

PHATRDRAFT_51837 - glutaredoxin type i (Thioredoxin_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51837
PHATRDRAFT_9709 (COG1739)

PHATRDRAFT_8747 - (COG1739)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8747

PHATRDRAFT_9709 - acyl carrier protein (acpP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9709
GO ID Go Term p-value q-value Cluster
GO:0015986 ATP synthesis coupled proton transport 0.00690102 1 Phatr_bicluster_0220
GO:0000103 sulfate assimilation 0.00690418 1 Phatr_bicluster_0220
GO:0006855 multidrug transport 0.0137641 1 Phatr_bicluster_0220
GO:0045454 cell redox homeostasis 0.02058 1 Phatr_bicluster_0220
GO:0006006 glucose metabolism 0.0239715 1 Phatr_bicluster_0220
GO:0009396 folic acid and derivative biosynthesis 0.0273521 1 Phatr_bicluster_0220
GO:0006633 fatty acid biosynthesis 0.0440926 1 Phatr_bicluster_0220
GO:0006096 glycolysis 0.114621 1 Phatr_bicluster_0220
GO:0005975 carbohydrate metabolism 0.197401 1 Phatr_bicluster_0220
GO:0008152 metabolism 0.270353 1 Phatr_bicluster_0220
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