Phatr_bicluster_0232 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_0232 0.25 Phaeodactylum tricornutum
Displaying 1 - 26 of 26
PHATRDRAFT_11003 pyruvate formate lyase activating enzyme 2 fe-s cluster domain (Radical_SAM)

PHATRDRAFT_11003 - pyruvate formate lyase activating enzyme 2 fe-s cluster domain (Radical_SAM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11003
PHATRDRAFT_11615 probable adp atp translocase (TLC superfamily)

PHATRDRAFT_11615 - probable adp atp translocase (TLC superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11615
PHATRDRAFT_18945 at4g27720 t29a15_210 (MFS_1)

PHATRDRAFT_18945 - at4g27720 t29a15_210 (MFS_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18945
PHATRDRAFT_19831 riken cdna 0710008k08isoform cra_a (YXKO-related)

PHATRDRAFT_19831 - riken cdna 0710008k08isoform cra_a (YXKO-related)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19831
PHATRDRAFT_21183 h+-ppase family transporter: proton (hppA)

PHATRDRAFT_21183 - h+-ppase family transporter: proton (hppA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21183
PHATRDRAFT_25127 nucleoside diphosphate kinase b (NDPk_I)

PHATRDRAFT_25127 - nucleoside diphosphate kinase b (NDPk_I)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25127
PHATRDRAFT_26422 cytochrome p450 (p450 superfamily)

PHATRDRAFT_26422 - cytochrome p450 (p450 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_26422
PHATRDRAFT_32316

PHATRDRAFT_32316 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32316
PHATRDRAFT_33844 (PsbP superfamily)

PHATRDRAFT_33844 - (PsbP superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33844
PHATRDRAFT_33864 cdp-ethanolamine:dag ethanolamine phosphotransferase (CDP-OH_P_transf superfamily)

PHATRDRAFT_33864 - cdp-ethanolamine:dag ethanolamine phosphotransferase (CDP-OH_P_transf superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33864
PHATRDRAFT_34521 (ADPRase_NUDT5)

PHATRDRAFT_34521 - (ADPRase_NUDT5)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34521
PHATRDRAFT_34522 (Nudix_Hydrolase superfamily)

PHATRDRAFT_34522 - (Nudix_Hydrolase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34522
PHATRDRAFT_39045 (HMGB-UBF_HMG-box)

PHATRDRAFT_39045 - (HMGB-UBF_HMG-box)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39045
PHATRDRAFT_43057

PHATRDRAFT_43057 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43057
PHATRDRAFT_43307

PHATRDRAFT_43307 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43307
PHATRDRAFT_43427 (PH)

PHATRDRAFT_43427 - (PH)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43427
PHATRDRAFT_43471 fertility restorer homologue c

PHATRDRAFT_43471 - fertility restorer homologue c

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43471
PHATRDRAFT_44302

PHATRDRAFT_44302 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44302
PHATRDRAFT_44757 (DOT1 superfamily)

PHATRDRAFT_44757 - (DOT1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44757
PHATRDRAFT_44989 (Hydrolase_4 superfamily)

PHATRDRAFT_44989 - (Hydrolase_4 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44989
PHATRDRAFT_45252 thioredoxin family protein (TRX_family)

PHATRDRAFT_45252 - thioredoxin family protein (TRX_family)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45252
PHATRDRAFT_45836

PHATRDRAFT_45836 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45836
PHATRDRAFT_45961 (Tryp_SPc)

PHATRDRAFT_45961 - (Tryp_SPc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45961
PHATRDRAFT_46491 phosphoglycerate mutase family

PHATRDRAFT_46491 - phosphoglycerate mutase family

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46491
PHATRDRAFT_51422 1-aminocyclopropane-1-carboxylate synthase (PLN02450)

PHATRDRAFT_51422 - 1-aminocyclopropane-1-carboxylate synthase (PLN02450)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51422
PHATRDRAFT_51700 ripening-associated protein (PRK02534)

PHATRDRAFT_51700 - ripening-associated protein (PRK02534)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51700
GO ID Go Term p-value q-value Cluster
GO:0006241 CTP biosynthesis 0.00886694 1 Phatr_bicluster_0232
GO:0006183 GTP biosynthesis 0.00886694 1 Phatr_bicluster_0232
GO:0006228 UTP biosynthesis 0.00886694 1 Phatr_bicluster_0232
GO:0008654 phospholipid biosynthesis 0.026385 1 Phatr_bicluster_0232
GO:0015992 proton transport 0.0407661 1 Phatr_bicluster_0232
GO:0006810 transport 0.107111 1 Phatr_bicluster_0232
GO:0006508 proteolysis and peptidolysis 0.13969 1 Phatr_bicluster_0232
GO:0006118 electron transport 0.144823 1 Phatr_bicluster_0232
GO:0006355 regulation of transcription, DNA-dependent 0.487367 1 Phatr_bicluster_0232
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