Phatr_bicluster_0249 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_0249 0.32 Phaeodactylum tricornutum
Displaying 1 - 30 of 30
PHATRDRAFT_10284 ribosomal large subunit pseudouridine synthase a (RluA)

PHATRDRAFT_10284 - ribosomal large subunit pseudouridine synthase a (RluA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10284
PHATRDRAFT_11674 multidrug resistance protein (ATM1)

PHATRDRAFT_11674 - multidrug resistance protein (ATM1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11674
PHATRDRAFT_13445 trna-binding protein (tRNA_bindingDomain superfamily)

PHATRDRAFT_13445 - trna-binding protein (tRNA_bindingDomain superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13445
PHATRDRAFT_19835 (dna directed) polypeptide h (RPB7)

PHATRDRAFT_19835 - (dna directed) polypeptide h (RPB7)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19835
PHATRDRAFT_22919 nduv2_caeel probable nadh dehydrogenaseflavoproteinmitochondrial precursor (2Fe-2S_thioredx)

PHATRDRAFT_22919 - nduv2_caeel probable nadh dehydrogenaseflavoproteinmitochondrial precursor (2Fe-2S_thioredx)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22919
PHATRDRAFT_24474 20s proteasome subunit pac1 (Ntn_hydrolase superfamily)

PHATRDRAFT_24474 - 20s proteasome subunit pac1 (Ntn_hydrolase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_24474
PHATRDRAFT_25331 transcription factor protein (HMGB-UBF_HMG-box)

PHATRDRAFT_24886 - transcription factor protein (HMGB-UBF_HMG-box)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_24886
PHATRDRAFT_28620 at4g39280 t22f8_180 (PLN02853)

PHATRDRAFT_25331 - at4g39280 t22f8_180 (PLN02853)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25331
PHATRDRAFT_33639 nadh dehydrogenase1 alpha13 (GRIM-19 superfamily)

PHATRDRAFT_28620 - nadh dehydrogenase1 alpha13 (GRIM-19 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28620
PHATRDRAFT_34775

PHATRDRAFT_33639 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33639
PHATRDRAFT_35061 ornithine cyclodeaminase (PRK08618)

PHATRDRAFT_34775 - ornithine cyclodeaminase (PRK08618)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34775
PHATRDRAFT_39868

PHATRDRAFT_35061 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35061
PHATRDRAFT_42832 y601_synpx upf0090 protein synw0601 (Sm_like superfamily)

PHATRDRAFT_39868 - y601_synpx upf0090 protein synw0601 (Sm_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39868
PHATRDRAFT_42910 manganese superoxide dismutase (SodA)

PHATRDRAFT_42832 - manganese superoxide dismutase (SodA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42832
PHATRDRAFT_43097 (RF-1)

PHATRDRAFT_42910 - (RF-1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42910
PHATRDRAFT_43179 prolyl-trna synthetase (PRK08661)

PHATRDRAFT_43097 - prolyl-trna synthetase (PRK08661)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43097
PHATRDRAFT_43373 microrchidia 4 (zf-CW)

PHATRDRAFT_43179 - microrchidia 4 (zf-CW)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43179
PHATRDRAFT_43451

PHATRDRAFT_43373 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43373
PHATRDRAFT_43537

PHATRDRAFT_43451 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43451
PHATRDRAFT_44930

PHATRDRAFT_43537 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43537
PHATRDRAFT_45777 cog0439: biotin carboxylase (ATP-grasp_4)

PHATRDRAFT_44930 - cog0439: biotin carboxylase (ATP-grasp_4)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44930
PHATRDRAFT_45987

PHATRDRAFT_45777 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45777
PHATRDRAFT_46133 (Bromodomain)

PHATRDRAFT_45987 - (Bromodomain)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45987
PHATRDRAFT_46146 ubiquinol-cytochrome c reductase complex 14 kda (UCR_14kD superfamily)

PHATRDRAFT_46133 - ubiquinol-cytochrome c reductase complex 14 kda (UCR_14kD superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46133
PHATRDRAFT_46460 acyl-activating enzyme 14 (AFD_class_I superfamily)

PHATRDRAFT_46146 - acyl-activating enzyme 14 (AFD_class_I superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46146
PHATRDRAFT_48464 (DnaQ_like_exo superfamily)

PHATRDRAFT_46460 - (DnaQ_like_exo superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46460
PHATRDRAFT_49038

PHATRDRAFT_48464 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48464
PHATRDRAFT_54323 (TauE)

PHATRDRAFT_49038 - (TauE)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49038
PHATRDRAFT_54642 polyubiquitin homolog (UBQ superfamily)

PHATRDRAFT_54323 - polyubiquitin homolog (UBQ superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54323

PHATRDRAFT_54642 - cell division cycle proteinexpressed (CDC48)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54642
GO ID Go Term p-value q-value Cluster
GO:0006306 DNA methylation 0.0808874 1 Phatr_bicluster_0249
GO:0006118 electron transport 0.629073 1 Phatr_bicluster_0249
GO:0007242 intracellular signaling cascade 0.162734 1 Phatr_bicluster_0249
GO:0008152 metabolism 0.723107 1 Phatr_bicluster_0249
GO:0006120 mitochondrial electron transport, NADH to ubiquinone 0.012546 1 Phatr_bicluster_0249
GO:0006122 mitochondrial electron transport, ubiquinol to cytochrome c 0.00419857 1 Phatr_bicluster_0249
GO:0006432 phenylalanyl-tRNA aminoacylation 0.012546 1 Phatr_bicluster_0249
GO:0006412 protein biosynthesis 0.499011 1 Phatr_bicluster_0249
GO:0006355 regulation of transcription, DNA-dependent 0.61218 1 Phatr_bicluster_0249
GO:0006396 RNA processing 0.211193 1 Phatr_bicluster_0249
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