Phatr_bicluster_0231 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_0231 0.29 Phaeodactylum tricornutum
Displaying 1 - 26 of 26
PHATRDRAFT_10073 kynurenine aminotransferase (PRK08912)

PHATRDRAFT_10073 - kynurenine aminotransferase (PRK08912)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10073
PHATRDRAFT_10718 alpha beta hydrolase fold-1 (Hydrolase_4 superfamily)

PHATRDRAFT_10718 - alpha beta hydrolase fold-1 (Hydrolase_4 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10718
PHATRDRAFT_12269 p-hydroxybenzoate polyprenyltransferase (PT_UbiA_COQ2)

PHATRDRAFT_12269 - p-hydroxybenzoate polyprenyltransferase (PT_UbiA_COQ2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12269
PHATRDRAFT_14339 n-terminal acetyltransferase complex ard1 subunit (RimI)

PHATRDRAFT_14339 - n-terminal acetyltransferase complex ard1 subunit (RimI)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14339
PHATRDRAFT_15683 oxidoreductase nad-binding domain-containing protein (FNR_like superfamily)

PHATRDRAFT_15683 - oxidoreductase nad-binding domain-containing protein (FNR_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15683
PHATRDRAFT_20460 o-acyltransferase (membrane bound) domain containing 2 (PLN02332)

PHATRDRAFT_20460 - o-acyltransferase (membrane bound) domain containing 2 (PLN02332)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20460
PHATRDRAFT_31968

PHATRDRAFT_31968 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31968
PHATRDRAFT_32681 peptide methionine sulfoxide reductase (PMSR superfamily)

PHATRDRAFT_32681 - peptide methionine sulfoxide reductase (PMSR superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32681
PHATRDRAFT_33845

PHATRDRAFT_33845 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33845
PHATRDRAFT_34924

PHATRDRAFT_34924 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34924
PHATRDRAFT_36970 protein kinase (Pkinase)

PHATRDRAFT_36322 - protein kinase (Pkinase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36322
PHATRDRAFT_43218 (PPR_2)

PHATRDRAFT_36970 - (PPR_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36970
PHATRDRAFT_43490

PHATRDRAFT_43218 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43218
PHATRDRAFT_43754 retinal pigment epithelial membrane (RPE65 superfamily)

PHATRDRAFT_43490 - retinal pigment epithelial membrane (RPE65 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43490
PHATRDRAFT_44279 major facilitator superfamily mfs_1 (MFS_1)

PHATRDRAFT_43754 - major facilitator superfamily mfs_1 (MFS_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43754
PHATRDRAFT_45258

PHATRDRAFT_44279 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44279
PHATRDRAFT_45400 cg9164-isoform a (Sulfotransfer_1 superfamily)

PHATRDRAFT_45258 - cg9164-isoform a (Sulfotransfer_1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45258
PHATRDRAFT_46233 auxin-regulated protein (Thioredoxin_like superfamily)

PHATRDRAFT_45400 - auxin-regulated protein (Thioredoxin_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45400
PHATRDRAFT_46236 map kinase kinase kinase (S_TKc)

PHATRDRAFT_46233 - map kinase kinase kinase (S_TKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46233
PHATRDRAFT_46282

PHATRDRAFT_46236 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46236
PHATRDRAFT_46796

PHATRDRAFT_46282 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46282
PHATRDRAFT_54049

PHATRDRAFT_46796 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46796
PHATRDRAFT_9246 cg9706-isoform a isoform 1 (Acatn superfamily)

PHATRDRAFT_54049 - cg9706-isoform a isoform 1 (Acatn superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54049
PHATRDRAFT_9855 hypothetical 317 kda protein-nucleoside-diphosphate sugar epimerase (NADB_Rossmann superfamily)

PHATRDRAFT_9246 - hypothetical 317 kda protein-nucleoside-diphosphate sugar epimerase (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9246

PHATRDRAFT_9490 - kelch motif family protein (BTB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9490

PHATRDRAFT_9855 - rna polymerase sigma-70 factor (Sig70-cyanoRpoD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9855
GO ID Go Term p-value q-value Cluster
GO:0009058 biosynthesis 0.00513633 1 Phatr_bicluster_0231
GO:0015904 tetracycline transport 0.00984608 1 Phatr_bicluster_0231
GO:0006352 transcription initiation 0.0292769 1 Phatr_bicluster_0231
GO:0006468 protein amino acid phosphorylation 0.0645174 1 Phatr_bicluster_0231
GO:0006464 protein modification 0.14529 1 Phatr_bicluster_0231
GO:0006355 regulation of transcription, DNA-dependent 0.426896 1 Phatr_bicluster_0231
GO:0006508 proteolysis and peptidolysis 0.434343 1 Phatr_bicluster_0231
GO:0006118 electron transport 0.441702 1 Phatr_bicluster_0231
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