Phatr_bicluster_0149 Residual: 0.22
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_0149 0.22 Phaeodactylum tricornutum
Displaying 1 - 23 of 23
PHATRDRAFT_2171 nitrate transporter (2A0108)

PHATRDRAFT_2171 - nitrate transporter (2A0108)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_2171
PHATRDRAFT_24019 transcriptional co-repressor sin3a isoform 6 (Sin3_corepress)

PHATRDRAFT_24019 - transcriptional co-repressor sin3a isoform 6 (Sin3_corepress)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_24019
PHATRDRAFT_34216 phosducin family protein (Thioredoxin_like superfamily)

PHATRDRAFT_34216 - phosducin family protein (Thioredoxin_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34216
PHATRDRAFT_34384

PHATRDRAFT_34384 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34384
PHATRDRAFT_34385 peptidylprolyl isomerase fk506-binding protein (FKBP_C)

PHATRDRAFT_34385 - peptidylprolyl isomerase fk506-binding protein (FKBP_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34385
PHATRDRAFT_36589

PHATRDRAFT_36589 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36589
PHATRDRAFT_43115 ring-15 protein (RING)

PHATRDRAFT_43115 - ring-15 protein (RING)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43115
PHATRDRAFT_43121

PHATRDRAFT_43121 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43121
PHATRDRAFT_43375 (zf-C3HC superfamily)

PHATRDRAFT_43375 - (zf-C3HC superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43375
PHATRDRAFT_43396

PHATRDRAFT_43396 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43396
PHATRDRAFT_43880 (LRR_RI superfamily)

PHATRDRAFT_43880 - (LRR_RI superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43880
PHATRDRAFT_44536 proteophosphoglycan 5

PHATRDRAFT_44536 - proteophosphoglycan 5

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44536
PHATRDRAFT_45483

PHATRDRAFT_45483 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45483
PHATRDRAFT_45955 phospholipase carboxylesterase familyexpressed (COG1054)

PHATRDRAFT_45955 - phospholipase carboxylesterase familyexpressed (COG1054)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45955
PHATRDRAFT_46214 dienelactone hydrolase (COG0412)

PHATRDRAFT_46214 - dienelactone hydrolase (COG0412)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46214
PHATRDRAFT_46360 uncharacterised protein family containingexpressed (Bestrophin superfamily)

PHATRDRAFT_46360 - uncharacterised protein family containingexpressed (Bestrophin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46360
PHATRDRAFT_46578 tocopherol cyclase

PHATRDRAFT_46578 - tocopherol cyclase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46578
PHATRDRAFT_47127 atp-dependent dna helicase (KU superfamily)

PHATRDRAFT_47127 - atp-dependent dna helicase (KU superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47127
PHATRDRAFT_47879 (SH2_2)

PHATRDRAFT_47879 - (SH2_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47879
PHATRDRAFT_48345 phosphodiesterasecalmodulin-dependentisoform cra_a

PHATRDRAFT_48345 - phosphodiesterasecalmodulin-dependentisoform cra_a

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48345
PHATRDRAFT_49982

PHATRDRAFT_49982 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49982
PHATRDRAFT_9278 histone deacetylase superfamily (HDAC_classIV)

PHATRDRAFT_9278 - histone deacetylase superfamily (HDAC_classIV)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9278
PHATRDRAFT_9612 ribose phosphate pyrophosphokinase (PLN02297)

PHATRDRAFT_9612 - ribose phosphate pyrophosphokinase (PLN02297)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9612
GO ID Go Term p-value q-value Cluster
GO:0006303 double-strand break repair via nonhomologous end-joining 0.00394818 1 Phatr_bicluster_0149
GO:0009165 nucleotide biosynthesis 0.00788271 1 Phatr_bicluster_0149
GO:0009116 nucleoside metabolism 0.0176596 1 Phatr_bicluster_0149
GO:0006520 amino acid metabolism 0.0464863 1 Phatr_bicluster_0149
GO:0016567 protein ubiquitination 0.13382 1 Phatr_bicluster_0149
GO:0006457 protein folding 0.209255 1 Phatr_bicluster_0149
GO:0006355 regulation of transcription, DNA-dependent 0.359328 1 Phatr_bicluster_0149
GO:0006508 proteolysis and peptidolysis 0.365994 1 Phatr_bicluster_0149
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