Phatr_bicluster_0211 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_0211 0.25 Phaeodactylum tricornutum
Displaying 1 - 27 of 27
PHATRDRAFT_11390 digalactosyldiacylglycerol synthaseexpressed (Glycos_transf_1 superfamily)

PHATRDRAFT_11390 - digalactosyldiacylglycerol synthaseexpressed (Glycos_transf_1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11390
PHATRDRAFT_12265 uncharacterized protein family upf0016 containingexpressed (COG2119)

PHATRDRAFT_12265 - uncharacterized protein family upf0016 containingexpressed (COG2119)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12265
PHATRDRAFT_17335 aldo keto reductase (Aldo_ket_red)

PHATRDRAFT_17335 - aldo keto reductase (Aldo_ket_red)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17335
PHATRDRAFT_33839

PHATRDRAFT_31984 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31984
PHATRDRAFT_33977 phosphoglycerate mutase 1 (HP_PGM_like)

PHATRDRAFT_33839 - phosphoglycerate mutase 1 (HP_PGM_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33839
PHATRDRAFT_34647

PHATRDRAFT_33977 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33977
PHATRDRAFT_34656

PHATRDRAFT_34647 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34647
PHATRDRAFT_34964

PHATRDRAFT_34656 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34656
PHATRDRAFT_35318 kynurenine 3- (UbiH)

PHATRDRAFT_34964 - kynurenine 3- (UbiH)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34964
PHATRDRAFT_35638 rhomboid family protein (Rhomboid superfamily)

PHATRDRAFT_35318 - rhomboid family protein (Rhomboid superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35318
PHATRDRAFT_43150 oxidoreductase domain protein (MviM)

PHATRDRAFT_35638 - oxidoreductase domain protein (MviM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35638
PHATRDRAFT_43583 (RING)

PHATRDRAFT_43150 - (RING)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43150
PHATRDRAFT_43715 rna methylase

PHATRDRAFT_43583 - rna methylase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43583
PHATRDRAFT_43770

PHATRDRAFT_43715 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43715
PHATRDRAFT_44702 (Amidohydro_2)

PHATRDRAFT_43770 - (Amidohydro_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43770
PHATRDRAFT_45250 (DUF3321 superfamily)

PHATRDRAFT_44702 - (DUF3321 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44702
PHATRDRAFT_45657 (Sad1_UNC superfamily)

PHATRDRAFT_45250 - (Sad1_UNC superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45250
PHATRDRAFT_45726 myo-inositol oxygenase (DUF706 superfamily)

PHATRDRAFT_45657 - myo-inositol oxygenase (DUF706 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45657
PHATRDRAFT_45795

PHATRDRAFT_45726 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45726
PHATRDRAFT_46142 cysteine endopeptidase (Peptidase_C1A)

PHATRDRAFT_45795 - cysteine endopeptidase (Peptidase_C1A)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45795
PHATRDRAFT_46336 binding protein 1 (BRCT)

PHATRDRAFT_46142 - binding protein 1 (BRCT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46142
PHATRDRAFT_46455 at3g61320 t20k12_220 (Bestrophin superfamily)

PHATRDRAFT_46336 - at3g61320 t20k12_220 (Bestrophin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46336
PHATRDRAFT_46850 crumbs homolog 1isoform cra_b

PHATRDRAFT_46455 - crumbs homolog 1isoform cra_b

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46455
PHATRDRAFT_49214 unusual protein kinase (AarF)

PHATRDRAFT_46850 - unusual protein kinase (AarF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46850
PHATRDRAFT_7072 isoform cra_b

PHATRDRAFT_49214 - isoform cra_b

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49214
PHATRDRAFT_9617 tata box binding protein-associated factor (COG1936)

PHATRDRAFT_7072 - tata box binding protein-associated factor (COG1936)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7072

PHATRDRAFT_9617 - af304372_1beta--glucan synthase (Glucan_synthase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9617
GO ID Go Term p-value q-value Cluster
GO:0006075 beta-1,3 glucan biosynthesis 0.00321067 1 Phatr_bicluster_0211
GO:0008152 metabolism 0.0115207 1 Phatr_bicluster_0211
GO:0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolism 0.0347981 1 Phatr_bicluster_0211
GO:0006725 aromatic compound metabolism 0.0624342 1 Phatr_bicluster_0211
GO:0006096 glycolysis 0.106876 1 Phatr_bicluster_0211
GO:0006508 proteolysis and peptidolysis 0.159337 1 Phatr_bicluster_0211
GO:0006118 electron transport 0.165064 1 Phatr_bicluster_0211
GO:0016567 protein ubiquitination 0.20832 1 Phatr_bicluster_0211
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