Phatr_bicluster_0113 Residual: 0.23
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_0113 0.23 Phaeodactylum tricornutum
Displaying 1 - 24 of 24
PHATRDRAFT_12188 emb1241 (embryo defective 1241) adenyl-nucleotide exchange factor chaperone binding protein binding protein homodimerization (GrpE)

PHATRDRAFT_12188 - emb1241 (embryo defective 1241) adenyl-nucleotide exchange factor chaperone binding protein binding protein homodimerization (GrpE)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12188
PHATRDRAFT_12572 der1-like domainmember 3 (DER1 superfamily)

PHATRDRAFT_12572 - der1-like domainmember 3 (DER1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12572
PHATRDRAFT_3061 c-terminal processing peptidase (Peptidase_S41_CPP)

PHATRDRAFT_3061 - c-terminal processing peptidase (Peptidase_S41_CPP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3061
PHATRDRAFT_32554 magnesium-dependent phosphatase 1 (Acid_PPase)

PHATRDRAFT_32554 - magnesium-dependent phosphatase 1 (Acid_PPase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32554
PHATRDRAFT_36597 transitional endoplasmic reticulum atpase ter94 (CDC48)

PHATRDRAFT_36597 - transitional endoplasmic reticulum atpase ter94 (CDC48)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36597
PHATRDRAFT_41850 cell division cycle proteinexpressed (SpoVK)

PHATRDRAFT_41850 - cell division cycle proteinexpressed (SpoVK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41850
PHATRDRAFT_42426 prolyl 4-hydroxylase alpha subunit (2OG-FeII_Oxy_3 superfamily)

PHATRDRAFT_42426 - prolyl 4-hydroxylase alpha subunit (2OG-FeII_Oxy_3 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42426
PHATRDRAFT_42903 thioredoxin

PHATRDRAFT_42903 - thioredoxin

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42903
PHATRDRAFT_42980 phytoene dehydrogenase and related protein (COG1233)

PHATRDRAFT_42980 - phytoene dehydrogenase and related protein (COG1233)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42980
PHATRDRAFT_43060

PHATRDRAFT_43060 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43060
PHATRDRAFT_43309

PHATRDRAFT_43309 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43309
PHATRDRAFT_44315 protein kinasereceptor type precursor

PHATRDRAFT_44315 - protein kinasereceptor type precursor

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44315
PHATRDRAFT_44344 inositol polyphosphate-5-phosphatase inp51p (EEP superfamily)

PHATRDRAFT_44344 - inositol polyphosphate-5-phosphatase inp51p (EEP superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44344
PHATRDRAFT_44790 phosphatidylinositol glycan anchorclass b (Glyco_transf_22 superfamily)

PHATRDRAFT_44790 - phosphatidylinositol glycan anchorclass b (Glyco_transf_22 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44790
PHATRDRAFT_45935

PHATRDRAFT_45935 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45935
PHATRDRAFT_46792

PHATRDRAFT_46792 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46792
PHATRDRAFT_49120

PHATRDRAFT_49120 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49120
PHATRDRAFT_49377

PHATRDRAFT_49377 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49377
PHATRDRAFT_49509

PHATRDRAFT_49509 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49509
PHATRDRAFT_54068 glycosylgroup 1 family protein (GT1_PIG-A_like)

PHATRDRAFT_54068 - glycosylgroup 1 family protein (GT1_PIG-A_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54068
PHATRDRAFT_54197 chloroplast envelope protein translocase (cept or tic-toc) family protein (Tic22 superfamily)

PHATRDRAFT_54197 - chloroplast envelope protein translocase (cept or tic-toc) family protein (Tic22 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54197
PHATRDRAFT_6554 (FMN_red superfamily)

PHATRDRAFT_6554 - (FMN_red superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6554
PHATRDRAFT_7525 atp-dependent clp protease adaptor proteincontaining protein (ClpS)

PHATRDRAFT_7525 - atp-dependent clp protease adaptor proteincontaining protein (ClpS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7525
PHATRDRAFT_9956 ac008051_10identical to gene zw10 from arabidopsis thaliana gb (His_Phos_1)

PHATRDRAFT_9956 - ac008051_10identical to gene zw10 from arabidopsis thaliana gb (His_Phos_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9956
GO ID Go Term p-value q-value Cluster
GO:0019538 protein metabolism 0.0264433 1 Phatr_bicluster_0113
GO:0006457 protein folding 0.0842275 1 Phatr_bicluster_0113
GO:0006508 proteolysis and peptidolysis 0.156991 1 Phatr_bicluster_0113
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