Phatr_bicluster_0049 Residual: 0.33
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_0049 0.33 Phaeodactylum tricornutum
Displaying 1 - 30 of 30
PHATRDRAFT_10724 ubiquitin-conjugating enzyme (UBCc)

PHATRDRAFT_10724 - ubiquitin-conjugating enzyme (UBCc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10724
PHATRDRAFT_11462 ac068562_11est gb

PHATRDRAFT_11462 - ac068562_11est gb

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11462
PHATRDRAFT_12346 at1g32080 f3c3_12 (LrgB superfamily)

PHATRDRAFT_12346 - at1g32080 f3c3_12 (LrgB superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12346
PHATRDRAFT_18769 catalytic coenzyme binding (NADB_Rossmann superfamily)

PHATRDRAFT_18769 - catalytic coenzyme binding (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18769
PHATRDRAFT_18877 trna-ia37 modification enzyme (PRK14333)

PHATRDRAFT_18877 - trna-ia37 modification enzyme (PRK14333)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18877
PHATRDRAFT_18927 congested-like trachea cg3057-isoform a (Mito_carr)

PHATRDRAFT_18927 - congested-like trachea cg3057-isoform a (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18927
PHATRDRAFT_21868 gtp cyclohydrolase i (GTP_cyclohydro1)

PHATRDRAFT_21868 - gtp cyclohydrolase i (GTP_cyclohydro1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21868
PHATRDRAFT_22993 plastid c1 class ii fructose bisphosphate aldolase (FBP_aldolase_IIA)

PHATRDRAFT_22993 - plastid c1 class ii fructose bisphosphate aldolase (FBP_aldolase_IIA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22993
PHATRDRAFT_32822

PHATRDRAFT_32822 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32822
PHATRDRAFT_33356 gene product (TRX_family)

PHATRDRAFT_33356 - gene product (TRX_family)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33356
PHATRDRAFT_35509 amine oxidase (phytoene_desat)

PHATRDRAFT_35509 - amine oxidase (phytoene_desat)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35509
PHATRDRAFT_36165 8-amino-7-oxononanoate synthase (BioF)

PHATRDRAFT_36165 - 8-amino-7-oxononanoate synthase (BioF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36165
PHATRDRAFT_39133 glutaredoxin 3 (Thioredoxin_like superfamily)

PHATRDRAFT_39133 - glutaredoxin 3 (Thioredoxin_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39133
PHATRDRAFT_41150 (AdoMet_MTases)

PHATRDRAFT_41150 - (AdoMet_MTases)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41150
PHATRDRAFT_42116 na+ h+ antiporter precursor (PLN00137)

PHATRDRAFT_42116 - na+ h+ antiporter precursor (PLN00137)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42116
PHATRDRAFT_42619 gtp cyclohydrolase ii (PRK07198)

PHATRDRAFT_42619 - gtp cyclohydrolase ii (PRK07198)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42619
PHATRDRAFT_42982 fg-gap repeat family protein

PHATRDRAFT_42982 - fg-gap repeat family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42982
PHATRDRAFT_43950 (Trigger_N superfamily)

PHATRDRAFT_43950 - (Trigger_N superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43950
PHATRDRAFT_44393

PHATRDRAFT_44393 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44393
PHATRDRAFT_44529 (DUF1995 superfamily)

PHATRDRAFT_44529 - (DUF1995 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44529
PHATRDRAFT_46454

PHATRDRAFT_46454 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46454
PHATRDRAFT_46468

PHATRDRAFT_46468 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46468
PHATRDRAFT_47157 (DUF1499 superfamily)

PHATRDRAFT_47157 - (DUF1499 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47157
PHATRDRAFT_47708

PHATRDRAFT_47708 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47708
PHATRDRAFT_49437 nad dependent epimerase dehydratase familyexpressed (NADB_Rossmann superfamily)

PHATRDRAFT_49437 - nad dependent epimerase dehydratase familyexpressed (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49437
PHATRDRAFT_52200 twin-arginine translocation e family subunit (MttA_Hcf106 superfamily)

PHATRDRAFT_52200 - twin-arginine translocation e family subunit (MttA_Hcf106 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52200
PHATRDRAFT_54365

PHATRDRAFT_54365 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54365
PHATRDRAFT_9241 glutaredoxin-related protein (GRX_PICOT_like)

PHATRDRAFT_9035 - glutaredoxin-related protein (GRX_PICOT_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9035
PHATRDRAFT_9462 signal peptidase i family protein (sigpep_I_bact)

PHATRDRAFT_9241 - signal peptidase i family protein (sigpep_I_bact)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9241

PHATRDRAFT_9462 - hsc70-interacting protein (TPR)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9462
GO ID Go Term p-value q-value Cluster
GO:0045454 cell redox homeostasis 0.0176618 1 Phatr_bicluster_0049
GO:0006118 electron transport 0.0268615 1 Phatr_bicluster_0049
GO:0006096 glycolysis 0.0990654 1 Phatr_bicluster_0049
GO:0006512 ubiquitin cycle 0.107123 1 Phatr_bicluster_0049
GO:0009058 biosynthesis 0.125669 1 Phatr_bicluster_0049
GO:0006418 tRNA aminoacylation for protein translation 0.143861 1 Phatr_bicluster_0049
GO:0006464 protein modification 0.171749 1 Phatr_bicluster_0049
GO:0006810 transport 0.440472 1 Phatr_bicluster_0049
GO:0006355 regulation of transcription, DNA-dependent 0.487367 1 Phatr_bicluster_0049
GO:0006508 proteolysis and peptidolysis 0.495352 1 Phatr_bicluster_0049
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