Phatr_bicluster_0038 Residual: 0.40
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_0038 0.40 Phaeodactylum tricornutum
Displaying 1 - 28 of 28
PHATRDRAFT_14688 abc1 family protein (AarF)

PHATRDRAFT_14688 - abc1 family protein (AarF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14688
PHATRDRAFT_33664

PHATRDRAFT_33664 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33664
PHATRDRAFT_33726 dmt family transporter: drug metabolite (RhaT)

PHATRDRAFT_33726 - dmt family transporter: drug metabolite (RhaT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33726
PHATRDRAFT_3639 p7 protein (SBF superfamily)

PHATRDRAFT_36253 - p7 protein (SBF superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36253
PHATRDRAFT_37171 inositol 2-dehydrogenase (MviM)

PHATRDRAFT_3639 - inositol 2-dehydrogenase (MviM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3639
PHATRDRAFT_37916 (Chalcone superfamily)

PHATRDRAFT_37171 - (Chalcone superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37171
PHATRDRAFT_38665

PHATRDRAFT_37916 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37916
PHATRDRAFT_38744

PHATRDRAFT_38665 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38665
PHATRDRAFT_39282

PHATRDRAFT_38744 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38744
PHATRDRAFT_43099 fuco_mousetissue alpha-l-fucosidase precursor (alpha-l-fucosidase i) (alpha-l-fucoside fucohydrolase) (Alpha_L_fucos)

PHATRDRAFT_39282 - fuco_mousetissue alpha-l-fucosidase precursor (alpha-l-fucosidase i) (alpha-l-fucoside fucohydrolase) (Alpha_L_fucos)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39282
PHATRDRAFT_43556 probable 1-acyl-sn-glycerol-3-phosphate acyltransferase (LPLAT_AGPAT-like)

PHATRDRAFT_43099 - probable 1-acyl-sn-glycerol-3-phosphate acyltransferase (LPLAT_AGPAT-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43099
PHATRDRAFT_43695 thylakoid lumenkda protein (TPM)

PHATRDRAFT_43556 - thylakoid lumenkda protein (TPM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43556
PHATRDRAFT_44610 pentatricopeptiderepeat-containing protein (PPR_2)

PHATRDRAFT_43695 - pentatricopeptiderepeat-containing protein (PPR_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43695
PHATRDRAFT_45438 uroporphyrinogen iii synthase (HemD)

PHATRDRAFT_44610 - uroporphyrinogen iii synthase (HemD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44610
PHATRDRAFT_45902

PHATRDRAFT_45438 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45438
PHATRDRAFT_47570 protein with 8 transmembrane domains (TRAM_LAG1_CLN8)

PHATRDRAFT_45902 - protein with 8 transmembrane domains (TRAM_LAG1_CLN8)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45902
PHATRDRAFT_47828

PHATRDRAFT_47570 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47570
PHATRDRAFT_48533

PHATRDRAFT_47828 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47828
PHATRDRAFT_48985

PHATRDRAFT_48533 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48533
PHATRDRAFT_49508 (SQS_PSY)

PHATRDRAFT_48985 - (SQS_PSY)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48985
PHATRDRAFT_49590 cbix protein (CbiX_SirB_N)

PHATRDRAFT_49508 - cbix protein (CbiX_SirB_N)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49508
PHATRDRAFT_50567

PHATRDRAFT_49590 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49590
PHATRDRAFT_54017 (LON)

PHATRDRAFT_50567 - (LON)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50567
PHATRDRAFT_55102 phosphate phosphoenolpyruvate translocator precursor (tpt)

PHATRDRAFT_54017 - phosphate phosphoenolpyruvate translocator precursor (tpt)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54017
PHATRDRAFT_5668 phytoene desaturase (phytoene_desat)

PHATRDRAFT_55102 - phytoene desaturase (phytoene_desat)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55102
PHATRDRAFT_5851 immunophilin fkbp-type peptidyl-prolyl cis-trans isomerase-like protein (FKBP_C)

PHATRDRAFT_5668 - immunophilin fkbp-type peptidyl-prolyl cis-trans isomerase-like protein (FKBP_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5668
PHATRDRAFT_7774 heme oxygenase (HemeO)

PHATRDRAFT_5851 - heme oxygenase (HemeO)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5851

PHATRDRAFT_7774 - tkl family protein kinase (PKc_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7774
GO ID Go Term p-value q-value Cluster
GO:0006510 ATP-dependent proteolysis 0.00960348 1 Phatr_bicluster_0038
GO:0006783 heme biosynthesis 0.0127857 1 Phatr_bicluster_0038
GO:0005975 carbohydrate metabolism 0.016644 1 Phatr_bicluster_0038
GO:0006779 porphyrin biosynthesis 0.0316815 1 Phatr_bicluster_0038
GO:0007264 small GTPase mediated signal transduction 0.0654593 1 Phatr_bicluster_0038
GO:0009058 biosynthesis 0.135415 1 Phatr_bicluster_0038
GO:0008152 metabolism 0.242573 1 Phatr_bicluster_0038
GO:0006457 protein folding 0.317339 1 Phatr_bicluster_0038
GO:0006468 protein amino acid phosphorylation 0.431733 1 Phatr_bicluster_0038
GO:0006810 transport 0.466944 1 Phatr_bicluster_0038
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