Phatr_bicluster_0139 Residual: 0.32
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_0139 0.32 Phaeodactylum tricornutum
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Displaying 1 - 28 of 28
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PHATRDRAFT_11099 guanosine-3-bis3-pyrophosphohydrolase (ppgpp synthase) (SpoT)

PHATRDRAFT_11099 - guanosine-3-bis3-pyrophosphohydrolase (ppgpp synthase) (SpoT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11099
PHATRDRAFT_11337 nucleic acid binding nabp (Pumilio)

PHATRDRAFT_11337 - nucleic acid binding nabp (Pumilio)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11337
PHATRDRAFT_13582 erythrocyte membrane-associated antigen (AAA_12 superfamily)

PHATRDRAFT_13582 - erythrocyte membrane-associated antigen (AAA_12 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13582
PHATRDRAFT_20262 cdc2-like kinase (PKc_like superfamily)

PHATRDRAFT_20262 - cdc2-like kinase (PKc_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20262
PHATRDRAFT_26382 nad-dependent epimerase dehydratase (SDR_a5)

PHATRDRAFT_26382 - nad-dependent epimerase dehydratase (SDR_a5)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_26382
PHATRDRAFT_26742 b-glycoside hydrolase family 3 protein (PRK15098)

PHATRDRAFT_26742 - b-glycoside hydrolase family 3 protein (PRK15098)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_26742
PHATRDRAFT_27817 pmt3_schpo ubiquitin-like protein pmt3 smt3 precursor (UBQ superfamily)

PHATRDRAFT_27817 - pmt3_schpo ubiquitin-like protein pmt3 smt3 precursor (UBQ superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27817
PHATRDRAFT_33498 s-layer-like region

PHATRDRAFT_33498 - s-layer-like region

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33498
PHATRDRAFT_34373 molybdopterin synthase sulfurylase (ThiF_MoeB_HesA_family)

PHATRDRAFT_34373 - molybdopterin synthase sulfurylase (ThiF_MoeB_HesA_family)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34373
PHATRDRAFT_34489 alpha beta fold family protein (Abhydrolase_6)

PHATRDRAFT_34489 - alpha beta fold family protein (Abhydrolase_6)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34489
PHATRDRAFT_36848 hypothetical orf yor161cp (Choline_transpo superfamily)

PHATRDRAFT_36848 - hypothetical orf yor161cp (Choline_transpo superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36848
PHATRDRAFT_37237

PHATRDRAFT_37237 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37237
PHATRDRAFT_43180

PHATRDRAFT_43180 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43180
PHATRDRAFT_43184

PHATRDRAFT_43184 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43184
PHATRDRAFT_43395

PHATRDRAFT_43395 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43395
PHATRDRAFT_43483

PHATRDRAFT_43483 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43483
PHATRDRAFT_43687

PHATRDRAFT_43687 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43687
PHATRDRAFT_44767 (COG1112)

PHATRDRAFT_44767 - (COG1112)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44767
PHATRDRAFT_45341

PHATRDRAFT_45341 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45341
PHATRDRAFT_46493 choline dehydrogenase (BetA)

PHATRDRAFT_46493 - choline dehydrogenase (BetA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46493
PHATRDRAFT_46718

PHATRDRAFT_46718 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46718
PHATRDRAFT_46872 cold-active alkaline serine protease (Peptidases_S8_S53 superfamily)

PHATRDRAFT_46872 - cold-active alkaline serine protease (Peptidases_S8_S53 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46872
PHATRDRAFT_47109 2-oxoglutarate dehydrogenasedehydrogenaseand related enzyme (TPP_enzymes superfamily)

PHATRDRAFT_47109 - 2-oxoglutarate dehydrogenasedehydrogenaseand related enzyme (TPP_enzymes superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47109
PHATRDRAFT_47234

PHATRDRAFT_47234 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47234
PHATRDRAFT_50164

PHATRDRAFT_50164 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50164
PHATRDRAFT_54574

PHATRDRAFT_54574 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54574
PHATRDRAFT_55037 sensory transduction histidine kinase (HATPase_c)

PHATRDRAFT_55037 - sensory transduction histidine kinase (HATPase_c)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55037
PHATRDRAFT_7721 (PKc_like superfamily)

PHATRDRAFT_7721 - (PKc_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7721
GO ID Go Term p-value q-value Cluster
GO:0015969 guanosine tetraphosphate metabolism 0.00394818 1 Phatr_bicluster_0139
GO:0016071 mRNA metabolism 0.00788271 1 Phatr_bicluster_0139
GO:0006468 protein amino acid phosphorylation 0.0424353 1 Phatr_bicluster_0139
GO:0005975 carbohydrate metabolism 0.118 1 Phatr_bicluster_0139
GO:0006464 protein modification 0.118 1 Phatr_bicluster_0139
GO:0006508 proteolysis and peptidolysis 0.365994 1 Phatr_bicluster_0139
GO:0006118 electron transport 0.3726 1 Phatr_bicluster_0139
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