Phatr_bicluster_0146 Residual: 0.20
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_0146 0.20 Phaeodactylum tricornutum
Displaying 1 - 20 of 20
PHATRDRAFT_12107 dihydropterin pyrophosphokinase dihydropteroate synthase (DHPS)

PHATRDRAFT_12107 - dihydropterin pyrophosphokinase dihydropteroate synthase (DHPS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12107
PHATRDRAFT_13476 serine acetyltransferase (cysE)

PHATRDRAFT_13476 - serine acetyltransferase (cysE)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13476
PHATRDRAFT_18197 atp-bindingsub-family c (cftr mrp)member 1 (ABCC_MRP_domain2)

PHATRDRAFT_18197 - atp-bindingsub-family c (cftr mrp)member 1 (ABCC_MRP_domain2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18197
PHATRDRAFT_18458 at5g58710 mzn1_160 (cyclophilin_ABH_like)

PHATRDRAFT_18458 - at5g58710 mzn1_160 (cyclophilin_ABH_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18458
PHATRDRAFT_33921 (DUF4281)

PHATRDRAFT_33921 - (DUF4281)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33921
PHATRDRAFT_35383

PHATRDRAFT_35383 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35383
PHATRDRAFT_35643 ornithine cyclodeaminase (PRK06199 superfamily)

PHATRDRAFT_35643 - ornithine cyclodeaminase (PRK06199 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35643
PHATRDRAFT_36143

PHATRDRAFT_36143 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36143
PHATRDRAFT_36641 dehydroascorbate reductase (GST_C_family superfamily)

PHATRDRAFT_36641 - dehydroascorbate reductase (GST_C_family superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36641
PHATRDRAFT_37266 cog0802: atpase or kinase (UPF0079 superfamily)

PHATRDRAFT_37266 - cog0802: atpase or kinase (UPF0079 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37266
PHATRDRAFT_42440 rrna methylase (rRNA_methylase superfamily)

PHATRDRAFT_42440 - rrna methylase (rRNA_methylase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42440
PHATRDRAFT_45350 (SbcC)

PHATRDRAFT_45350 - (SbcC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45350
PHATRDRAFT_45582

PHATRDRAFT_45582 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45582
PHATRDRAFT_45717 uncharacterized conserved protein (DUF1415 superfamily)

PHATRDRAFT_45717 - uncharacterized conserved protein (DUF1415 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45717
PHATRDRAFT_46365 at3g61320 t20k12_220 (Bestrophin superfamily)

PHATRDRAFT_46365 - at3g61320 t20k12_220 (Bestrophin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46365
PHATRDRAFT_46729 elg protein isoform 4 (DUF2414 superfamily)

PHATRDRAFT_46729 - elg protein isoform 4 (DUF2414 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46729
PHATRDRAFT_48620 muty homolog (MutY)

PHATRDRAFT_48620 - muty homolog (MutY)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48620
PHATRDRAFT_4896 gtp-binding protein (COG0218)

PHATRDRAFT_4896 - gtp-binding protein (COG0218)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_4896
PHATRDRAFT_50770 glycerol kinase (PLN02295)

PHATRDRAFT_50770 - glycerol kinase (PLN02295)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50770
PHATRDRAFT_8810 topoisomeraseiii beta (TopA)

PHATRDRAFT_8810 - topoisomeraseiii beta (TopA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8810
GO ID Go Term p-value q-value Cluster
GO:0006535 cysteine biosynthesis from serine 0.00739277 1 Phatr_bicluster_0146
GO:0006284 base-excision repair 0.00739277 1 Phatr_bicluster_0146
GO:0006072 glycerol-3-phosphate metabolism 0.00984608 1 Phatr_bicluster_0146
GO:0006304 DNA modification 0.0122939 1 Phatr_bicluster_0146
GO:0006268 DNA unwinding 0.0122939 1 Phatr_bicluster_0146
GO:0009396 folic acid and derivative biosynthesis 0.0196048 1 Phatr_bicluster_0146
GO:0006265 DNA topological change 0.0220309 1 Phatr_bicluster_0146
GO:0005975 carbohydrate metabolism 0.14529 1 Phatr_bicluster_0146
GO:0006457 protein folding 0.254387 1 Phatr_bicluster_0146
GO:0006810 transport 0.38354 1 Phatr_bicluster_0146
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