Phatr_bicluster_0190 Residual: 0.25
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_0190 0.25 Phaeodactylum tricornutum
Displaying 1 - 32 of 32
PHATRDRAFT_10824 smt1_orysj cycloartenol-c-24-methyltransferase 1 (24-sterol c-methyltransferase 1) (sterol c-methyltransferase 1) (AdoMet_MTases)

PHATRDRAFT_10824 - smt1_orysj cycloartenol-c-24-methyltransferase 1 (24-sterol c-methyltransferase 1) (sterol c-methyltransferase 1) (AdoMet_MTases)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10824
PHATRDRAFT_12233 ubiquinol-cytochrome c reductase iron-sulfurmitochondrial precursor (Rieske_cytochrome_bc1)

PHATRDRAFT_12233 - ubiquinol-cytochrome c reductase iron-sulfurmitochondrial precursor (Rieske_cytochrome_bc1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12233
PHATRDRAFT_12620 n-ethylmaleimide-sensitive factor nsf sec18p (AAA)

PHATRDRAFT_12620 - n-ethylmaleimide-sensitive factor nsf sec18p (AAA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12620
PHATRDRAFT_12989 1 aminotransferase family protein (AAT_I superfamily)

PHATRDRAFT_12989 - 1 aminotransferase family protein (AAT_I superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12989
PHATRDRAFT_13034 sideroflexin 5 (Mtc superfamily)

PHATRDRAFT_13034 - sideroflexin 5 (Mtc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13034
PHATRDRAFT_13123 dehydrogenase kinase (BCDHK_Adom3)

PHATRDRAFT_13123 - dehydrogenase kinase (BCDHK_Adom3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13123
PHATRDRAFT_17967 homolog 1 (FtsJ)

PHATRDRAFT_17967 - homolog 1 (FtsJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17967
PHATRDRAFT_19699 1-aminocyclopropane-1-carboxylate synthase (AAT_like)

PHATRDRAFT_19699 - 1-aminocyclopropane-1-carboxylate synthase (AAT_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19699
PHATRDRAFT_21420 n-terminal acetyltransferase (NARP1)

PHATRDRAFT_21420 - n-terminal acetyltransferase (NARP1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21420
PHATRDRAFT_28833 zincste24 homolog (Peptidase_M48)

PHATRDRAFT_28833 - zincste24 homolog (Peptidase_M48)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28833
PHATRDRAFT_31713

PHATRDRAFT_31713 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31713
PHATRDRAFT_32976 cg13865-isoform a (COG0790)

PHATRDRAFT_32976 - cg13865-isoform a (COG0790)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32976
PHATRDRAFT_33675

PHATRDRAFT_33675 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33675
PHATRDRAFT_35154

PHATRDRAFT_35154 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35154
PHATRDRAFT_35336 (DUF2997)

PHATRDRAFT_35336 - (DUF2997)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35336
PHATRDRAFT_35647 heme oxygenase (HemeO superfamily)

PHATRDRAFT_35647 - heme oxygenase (HemeO superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35647
PHATRDRAFT_37124

PHATRDRAFT_37124 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37124
PHATRDRAFT_42650 (PHA03247)

PHATRDRAFT_42650 - (PHA03247)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42650
PHATRDRAFT_44748

PHATRDRAFT_44748 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44748
PHATRDRAFT_45207 fibronectin-binding protein (DUF814 superfamily)

PHATRDRAFT_45207 - fibronectin-binding protein (DUF814 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45207
PHATRDRAFT_4550 ac010924_18 ests gb

PHATRDRAFT_4550 - ac010924_18 ests gb

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_4550
PHATRDRAFT_45813 pap9_arath probable plastid-lipid-associated proteinchloroplast precursor (fibrillin-9) (PAP_fibrillin superfamily)

PHATRDRAFT_45813 - pap9_arath probable plastid-lipid-associated proteinchloroplast precursor (fibrillin-9) (PAP_fibrillin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45813
PHATRDRAFT_45899 homeodomain protein (Gst)

PHATRDRAFT_45899 - homeodomain protein (Gst)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45899
PHATRDRAFT_46174 (DUF1826 superfamily)

PHATRDRAFT_46174 - (DUF1826 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46174
PHATRDRAFT_48613 tpr repeat

PHATRDRAFT_48613 - tpr repeat

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48613
PHATRDRAFT_49056 threonine synthase (PRK09225)

PHATRDRAFT_49056 - threonine synthase (PRK09225)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49056
PHATRDRAFT_51757 sterol c-22 desaturase -like (p450 superfamily)

PHATRDRAFT_51757 - sterol c-22 desaturase -like (p450 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51757
PHATRDRAFT_5423 thiamin pyrophosphokinase 1 (PLN02714)

PHATRDRAFT_5423 - thiamin pyrophosphokinase 1 (PLN02714)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5423
PHATRDRAFT_5762 ac079935_17pyridoxamine 5-phosphate oxidase (PLN03050)

PHATRDRAFT_5762 - ac079935_17pyridoxamine 5-phosphate oxidase (PLN03050)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5762
PHATRDRAFT_7294 snat_bovin serotonin n-acetyltransferase (RimI)

PHATRDRAFT_7293 - snat_bovin serotonin n-acetyltransferase (RimI)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7293
PHATRDRAFT_9634 snat_bovin serotonin n-acetyltransferase (RimI)

PHATRDRAFT_7294 - snat_bovin serotonin n-acetyltransferase (RimI)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7294

PHATRDRAFT_9634 - abc1at (arabidopsis thaliana abc transporter 1) (AarF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9634
GO ID Go Term p-value q-value Cluster
GO:0009229 thiamin diphosphate biosynthesis 0.00321067 1 Phatr_bicluster_0190
GO:0006788 heme oxidation 0.00960348 1 Phatr_bicluster_0190
GO:0009088 threonine biosynthesis 0.00960348 1 Phatr_bicluster_0190
GO:0016310 phosphorylation 0.0440926 1 Phatr_bicluster_0190
GO:0006520 amino acid metabolism 0.0744808 1 Phatr_bicluster_0190
GO:0006812 cation transport 0.0834219 1 Phatr_bicluster_0190
GO:0009058 biosynthesis 0.135415 1 Phatr_bicluster_0190
GO:0006468 protein amino acid phosphorylation 0.431733 1 Phatr_bicluster_0190
GO:0006810 transport 0.466944 1 Phatr_bicluster_0190
GO:0006355 regulation of transcription, DNA-dependent 0.515177 1 Phatr_bicluster_0190
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