Phatr_bicluster_0147 Residual: 0.26
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_0147 0.26 Phaeodactylum tricornutum
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Displaying 1 - 26 of 26
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PHATRDRAFT_10499 tousled-like kinase 2 (S_TKc)

PHATRDRAFT_10499 - tousled-like kinase 2 (S_TKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10499
PHATRDRAFT_13675 cyclin-dependent kinase 9 (cdc2-related kinase) (S_TKc)

PHATRDRAFT_13675 - cyclin-dependent kinase 9 (cdc2-related kinase) (S_TKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13675
PHATRDRAFT_18622 dna replication licensing factorexpressed (MCM)

PHATRDRAFT_18622 - dna replication licensing factorexpressed (MCM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18622
PHATRDRAFT_2087 bifunctional dihydrofolate reductase-thymidylate synthase 2 dhfr-ts (TS_Pyrimidine_HMase)

PHATRDRAFT_2087 - bifunctional dihydrofolate reductase-thymidylate synthase 2 dhfr-ts (TS_Pyrimidine_HMase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_2087
PHATRDRAFT_21882 vacuolar-atpase c subunit (V_ATP_synt_C)

PHATRDRAFT_21882 - vacuolar-atpase c subunit (V_ATP_synt_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21882
PHATRDRAFT_32940 replication protein32kda (RPA2_DBD_D)

PHATRDRAFT_32940 - replication protein32kda (RPA2_DBD_D)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32940
PHATRDRAFT_36733

PHATRDRAFT_36733 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36733
PHATRDRAFT_37740

PHATRDRAFT_37740 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37740
PHATRDRAFT_38545

PHATRDRAFT_38545 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38545
PHATRDRAFT_45071 gcn5-related n-acetyltransferase (RimL)

PHATRDRAFT_44829 - gcn5-related n-acetyltransferase (RimL)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44829
PHATRDRAFT_45193 dna repair protein rad8 (HELICc)

PHATRDRAFT_45071 - dna repair protein rad8 (HELICc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45071
PHATRDRAFT_45320

PHATRDRAFT_45193 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45193
PHATRDRAFT_45334

PHATRDRAFT_45320 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45320
PHATRDRAFT_47159

PHATRDRAFT_45334 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45334
PHATRDRAFT_47678

PHATRDRAFT_47159 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47159
PHATRDRAFT_48150 (DEXDc)

PHATRDRAFT_47619 - (DEXDc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47619
PHATRDRAFT_48837 (DUF563)

PHATRDRAFT_47678 - (DUF563)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47678
PHATRDRAFT_49526

PHATRDRAFT_48150 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48150
PHATRDRAFT_49527

PHATRDRAFT_48837 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48837
PHATRDRAFT_49771 (SANT)

PHATRDRAFT_49526 - (SANT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49526
PHATRDRAFT_50189

PHATRDRAFT_49527 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49527
PHATRDRAFT_51279 (PI-PLC-X)

PHATRDRAFT_49771 - (PI-PLC-X)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49771
PHATRDRAFT_52607 atp adp (TLC superfamily)

PHATRDRAFT_50189 - atp adp (TLC superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50189
PHATRDRAFT_55197 protein kinase domain containing protein (STKc_CDK_like)

PHATRDRAFT_51279 - protein kinase domain containing protein (STKc_CDK_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51279

PHATRDRAFT_52607 - chromosome associated protein (Smc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52607

PHATRDRAFT_55197 - oligosaccharyl transferase (PMT_2 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55197
GO ID Go Term p-value q-value Cluster
GO:0006231 dTMP biosynthesis 0.00591934 1 Phatr_bicluster_0147
GO:0050757 thymidylate synthase biosynthesis 0.00886694 1 Phatr_bicluster_0147
GO:0006468 protein amino acid phosphorylation 0.0124819 1 Phatr_bicluster_0147
GO:0006270 DNA replication initiation 0.0176618 1 Phatr_bicluster_0147
GO:0006629 lipid metabolism 0.0521304 1 Phatr_bicluster_0147
GO:0015986 ATP synthesis coupled proton transport 0.104445 1 Phatr_bicluster_0147
GO:0007242 intracellular signaling cascade 0.117765 1 Phatr_bicluster_0147
GO:0007165 signal transduction 0.130903 1 Phatr_bicluster_0147
GO:0006355 regulation of transcription, DNA-dependent 0.487367 1 Phatr_bicluster_0147
GO:0006508 proteolysis and peptidolysis 0.495352 1 Phatr_bicluster_0147
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