Phatr_bicluster_0210 Residual: 0.20
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_0210 0.20 Phaeodactylum tricornutum
Displaying 1 - 20 of 20
PHATRDRAFT_10757 aspartate-semialdehyde dehydrogenase (PLN02383)

PHATRDRAFT_10757 - aspartate-semialdehyde dehydrogenase (PLN02383)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10757
PHATRDRAFT_12254 fkbp-type peptidyl-prolyl cis-trans isomerase (FkpA)

PHATRDRAFT_12254 - fkbp-type peptidyl-prolyl cis-trans isomerase (FkpA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12254
PHATRDRAFT_12963 (ATP_bind_1)

PHATRDRAFT_12963 - (ATP_bind_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12963
PHATRDRAFT_13119 atp-binding family protein (ATP_bind_1)

PHATRDRAFT_13119 - atp-binding family protein (ATP_bind_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13119
PHATRDRAFT_13174 ascorbate peroxidase (ascorbate_peroxidase)

PHATRDRAFT_13174 - ascorbate peroxidase (ascorbate_peroxidase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13174
PHATRDRAFT_19413 drosophila melanogaster cg18001 (Ribosomal_L38e)

PHATRDRAFT_19413 - drosophila melanogaster cg18001 (Ribosomal_L38e)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19413
PHATRDRAFT_21929 (Coatomer_WDAD)

PHATRDRAFT_21929 - (Coatomer_WDAD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21929
PHATRDRAFT_27851 40s ribosomal protein s10 (S10_plectin)

PHATRDRAFT_27851 - 40s ribosomal protein s10 (S10_plectin)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27851
PHATRDRAFT_28147 40s ribosomal protein s29-a (Ribosomal_S14 superfamily)

PHATRDRAFT_28147 - 40s ribosomal protein s29-a (Ribosomal_S14 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28147
PHATRDRAFT_32272

PHATRDRAFT_32272 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32272
PHATRDRAFT_33660 40s ribosomal protein (PTZ00084)

PHATRDRAFT_33660 - 40s ribosomal protein (PTZ00084)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33660
PHATRDRAFT_34526 argininosuccinate lyase (PLN02646)

PHATRDRAFT_34526 - argininosuccinate lyase (PLN02646)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34526
PHATRDRAFT_36226 ribosomal protein l18a (RPL20A)

PHATRDRAFT_36226 - ribosomal protein l18a (RPL20A)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36226
PHATRDRAFT_36420 lsu ribosomal protein l9p (Ribosomal_L9_N)

PHATRDRAFT_36420 - lsu ribosomal protein l9p (Ribosomal_L9_N)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36420
PHATRDRAFT_41252 (OTU)

PHATRDRAFT_41252 - (OTU)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41252
PHATRDRAFT_42104 nucleoside diphosphate kinase (NDPk_I)

PHATRDRAFT_42104 - nucleoside diphosphate kinase (NDPk_I)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42104
PHATRDRAFT_44291 ribosomal protein (Ribosomal_L34e superfamily)

PHATRDRAFT_44291 - ribosomal protein (Ribosomal_L34e superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44291
PHATRDRAFT_44971

PHATRDRAFT_44971 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44971
PHATRDRAFT_50701 yeast ribosomal protein s28 homologue (Ribosomal_S23)

PHATRDRAFT_50701 - yeast ribosomal protein s28 homologue (Ribosomal_S23)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50701
PHATRDRAFT_8058 ankyrin repeat protein mbp3_16 (ANK)

PHATRDRAFT_8058 - ankyrin repeat protein mbp3_16 (ANK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8058
GO ID Go Term p-value q-value Cluster
GO:0006412 protein biosynthesis 0.0000207 0.0479151 Phatr_bicluster_0210
GO:0006241 CTP biosynthesis 0.0118109 1 Phatr_bicluster_0210
GO:0006183 GTP biosynthesis 0.0118109 1 Phatr_bicluster_0210
GO:0006228 UTP biosynthesis 0.0118109 1 Phatr_bicluster_0210
GO:0009088 threonine biosynthesis 0.0118109 1 Phatr_bicluster_0210
GO:0009086 methionine biosynthesis 0.0157187 1 Phatr_bicluster_0210
GO:0006414 translational elongation 0.0540081 1 Phatr_bicluster_0210
GO:0006979 response to oxidative stress 0.0908976 1 Phatr_bicluster_0210
GO:0006520 amino acid metabolism 0.0908976 1 Phatr_bicluster_0210
GO:0006886 intracellular protein transport 0.147128 1 Phatr_bicluster_0210
Log in to post comments