Phatr_bicluster_0127 Residual: 0.23
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_0127 0.23 Phaeodactylum tricornutum
Displaying 1 - 25 of 25
PHATRDRAFT_10251 (HELICc)

PHATRDRAFT_10251 - (HELICc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10251
PHATRDRAFT_1241 dna topoisomerase i (TOP1Ac)

PHATRDRAFT_1241 - dna topoisomerase i (TOP1Ac)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_1241
PHATRDRAFT_14149 rrp8_schpo ribosomal rna-processing protein 8 (AdoMet_MTases superfamily)

PHATRDRAFT_14149 - rrp8_schpo ribosomal rna-processing protein 8 (AdoMet_MTases superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14149
PHATRDRAFT_15233 5-3 exoribonuclease 2 (XRN_N superfamily)

PHATRDRAFT_15233 - 5-3 exoribonuclease 2 (XRN_N superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15233
PHATRDRAFT_18524 threonyl-trna synthetase (PLN02908)

PHATRDRAFT_18524 - threonyl-trna synthetase (PLN02908)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18524
PHATRDRAFT_23838 (COG0714)

PHATRDRAFT_23838 - (COG0714)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23838
PHATRDRAFT_24195 (CPSaseII_lrg)

PHATRDRAFT_24195 - (CPSaseII_lrg)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_24195
PHATRDRAFT_33217 riken cdna 2410002o22isoform cra_a (DUF974 superfamily)

PHATRDRAFT_33217 - riken cdna 2410002o22isoform cra_a (DUF974 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33217
PHATRDRAFT_3351 dimethyladenosine transferase

PHATRDRAFT_3351 - dimethyladenosine transferase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3351
PHATRDRAFT_3425 trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (tRNA_Me_trans)

PHATRDRAFT_3425 - trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (tRNA_Me_trans)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3425
PHATRDRAFT_38891 histidinol-phosphate aminotransferase (PLN03026)

PHATRDRAFT_38891 - histidinol-phosphate aminotransferase (PLN03026)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38891
PHATRDRAFT_39883

PHATRDRAFT_39883 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39883
PHATRDRAFT_4048 cg3645-isoform a (DUS_like_FMN)

PHATRDRAFT_4048 - cg3645-isoform a (DUS_like_FMN)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_4048
PHATRDRAFT_4049 cg3645-isoform a (DUS_like_FMN)

PHATRDRAFT_4049 - cg3645-isoform a (DUS_like_FMN)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_4049
PHATRDRAFT_40902

PHATRDRAFT_40902 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40902
PHATRDRAFT_41071 methyltransferase type 12 (AdoMet_MTases)

PHATRDRAFT_41071 - methyltransferase type 12 (AdoMet_MTases)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41071
PHATRDRAFT_44042 exonuclease family protein (DnaQ_like_exo superfamily)

PHATRDRAFT_44042 - exonuclease family protein (DnaQ_like_exo superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44042
PHATRDRAFT_48038

PHATRDRAFT_48038 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48038
PHATRDRAFT_49808

PHATRDRAFT_49808 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49808
PHATRDRAFT_50465 (Smc)

PHATRDRAFT_50465 - (Smc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50465
PHATRDRAFT_50527 nucleolar gtpase atpase p130 (SRP40_C superfamily)

PHATRDRAFT_50527 - nucleolar gtpase atpase p130 (SRP40_C superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50527
PHATRDRAFT_5175 solute carrier family 25 (mitochondrial carrier ornithine transporter) member 15 (Mito_carr)

PHATRDRAFT_5175 - solute carrier family 25 (mitochondrial carrier ornithine transporter) member 15 (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5175
PHATRDRAFT_7810 dead deah box helicase domain protein (SrmB)

PHATRDRAFT_7810 - dead deah box helicase domain protein (SrmB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7810
PHATRDRAFT_8000 rnafamily protein (SpoU_methylase superfamily)

PHATRDRAFT_8000 - rnafamily protein (SpoU_methylase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8000
PHATRDRAFT_8457 (RRM_SF superfamily)

PHATRDRAFT_8457 - (RRM_SF superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8457
GO ID Go Term p-value q-value Cluster
GO:0008033 tRNA processing 0.000171452 0.393825 Phatr_bicluster_0127
GO:0051341 regulation of oxidoreductase activity 0.00352946 1 Phatr_bicluster_0127
GO:0006435 threonyl-tRNA aminoacylation 0.01133 1 Phatr_bicluster_0127
GO:0000154 rRNA modification 0.01133 1 Phatr_bicluster_0127
GO:0019856 pyrimidine base biosynthesis 0.0169488 1 Phatr_bicluster_0127
GO:0006304 DNA modification 0.028095 1 Phatr_bicluster_0127
GO:0006268 DNA unwinding 0.028095 1 Phatr_bicluster_0127
GO:0006526 arginine biosynthesis 0.0391202 1 Phatr_bicluster_0127
GO:0006364 rRNA processing 0.0445878 1 Phatr_bicluster_0127
GO:0000105 histidine biosynthesis 0.0500257 1 Phatr_bicluster_0127
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