Phatr_bicluster_0138 Residual: 0.26
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_0138 0.26 Phaeodactylum tricornutum
Displaying 1 - 21 of 21
PHATRDRAFT_13538 solute carrier familymember 36 (Mito_carr)

PHATRDRAFT_13538 - solute carrier familymember 36 (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13538
PHATRDRAFT_16537 chaperonin cpn10 (cpn10)

PHATRDRAFT_16537 - chaperonin cpn10 (cpn10)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16537
PHATRDRAFT_18551 serine carboxypeptidase ii (Peptidase_S10)

PHATRDRAFT_18551 - serine carboxypeptidase ii (Peptidase_S10)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18551
PHATRDRAFT_21922 gtp-binding protein era (era)

PHATRDRAFT_21922 - gtp-binding protein era (era)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21922
PHATRDRAFT_2271 gtp-binding protein (PRK00093)

PHATRDRAFT_2271 - gtp-binding protein (PRK00093)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_2271
PHATRDRAFT_23472 loc539613 protein

PHATRDRAFT_23472 - loc539613 protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23472
PHATRDRAFT_24792 queuine trna-ribosyltransferase (TGT superfamily)

PHATRDRAFT_24792 - queuine trna-ribosyltransferase (TGT superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_24792
PHATRDRAFT_30514 ornithine transcarbamylase (PLN02342)

PHATRDRAFT_30514 - ornithine transcarbamylase (PLN02342)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30514
PHATRDRAFT_3140 histidinol dehydrogenase (NTP-PPase_His4)

PHATRDRAFT_3140 - histidinol dehydrogenase (NTP-PPase_His4)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3140
PHATRDRAFT_31605 dnaj heat shock n-terminal domain-containing protein (DnaJ)

PHATRDRAFT_31605 - dnaj heat shock n-terminal domain-containing protein (DnaJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31605
PHATRDRAFT_43285 peptide chain release factor 1 (prfA)

PHATRDRAFT_36081 - peptide chain release factor 1 (prfA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36081
PHATRDRAFT_45212 (DUF3727 superfamily)

PHATRDRAFT_43285 - (DUF3727 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43285
PHATRDRAFT_47610 dna helicase (DEXDc)

PHATRDRAFT_43406 - dna helicase (DEXDc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43406
PHATRDRAFT_48756

PHATRDRAFT_43683 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43683
PHATRDRAFT_49134

PHATRDRAFT_45212 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45212
PHATRDRAFT_49783

PHATRDRAFT_47610 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47610
PHATRDRAFT_52173 pseudouridine synthase rlu family protein (PseudoU_synth_RluCD_like)

PHATRDRAFT_48756 - pseudouridine synthase rlu family protein (PseudoU_synth_RluCD_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48756
PHATRDRAFT_54289 (DUF2428 superfamily)

PHATRDRAFT_49134 - (DUF2428 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49134

PHATRDRAFT_49783 - sam-dependent methyltransferase-like protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49783

PHATRDRAFT_52173 - dna mismatch repair protein (MutS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52173

PHATRDRAFT_54289 - (PRK08565)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54289
GO ID Go Term p-value q-value Cluster
GO:0008616 queuosine biosynthesis 0.00960348 1 Phatr_bicluster_0138
GO:0006207 'de novo' pyrimidine base biosynthesis 0.0127857 1 Phatr_bicluster_0138
GO:0006400 tRNA modification 0.0127857 1 Phatr_bicluster_0138
GO:0006415 translational termination 0.0222757 1 Phatr_bicluster_0138
GO:0000105 histidine biosynthesis 0.0285555 1 Phatr_bicluster_0138
GO:0006457 protein folding 0.0524596 1 Phatr_bicluster_0138
GO:0008033 tRNA processing 0.0624342 1 Phatr_bicluster_0138
GO:0007264 small GTPase mediated signal transduction 0.0654593 1 Phatr_bicluster_0138
GO:0006520 amino acid metabolism 0.0744808 1 Phatr_bicluster_0138
GO:0006396 RNA processing 0.165834 1 Phatr_bicluster_0138
Log in to post comments