Phatr_bicluster_0188 Residual: 0.15
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_0188 0.15 Phaeodactylum tricornutum
Displaying 1 - 20 of 20
PHATRDRAFT_12732 adenylate kinase cytosolic (adk)

PHATRDRAFT_12732 - adenylate kinase cytosolic (adk)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12732
PHATRDRAFT_13261 at4g39970 t5j17_140 (PLN02779)

PHATRDRAFT_13261 - at4g39970 t5j17_140 (PLN02779)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13261
PHATRDRAFT_18337 glutamine-dependent asparagine synthetase (PLN02549)

PHATRDRAFT_18337 - glutamine-dependent asparagine synthetase (PLN02549)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18337
PHATRDRAFT_21388 (COG1204)

PHATRDRAFT_21388 - (COG1204)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21388
PHATRDRAFT_26813 homoserine dehydrogenase (ThrA)

PHATRDRAFT_26813 - homoserine dehydrogenase (ThrA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_26813
PHATRDRAFT_32202 lysyl-trna synthetase (lysS)

PHATRDRAFT_32202 - lysyl-trna synthetase (lysS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32202
PHATRDRAFT_34093

PHATRDRAFT_34093 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34093
PHATRDRAFT_34747 n-anthranilate isomerase (PRAI)

PHATRDRAFT_34747 - n-anthranilate isomerase (PRAI)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34747
PHATRDRAFT_34933 peptidylprolyl isomeraselike (cyclophilin_ABH_like)

PHATRDRAFT_34933 - peptidylprolyl isomeraselike (cyclophilin_ABH_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34933
PHATRDRAFT_41721 cpn60 protein (groEL)

PHATRDRAFT_41721 - cpn60 protein (groEL)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41721
PHATRDRAFT_45306 (PLDc_SF superfamily)

PHATRDRAFT_45306 - (PLDc_SF superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45306
PHATRDRAFT_45434 at5g28840 f7p1_20 (PLN02695)

PHATRDRAFT_45434 - at5g28840 f7p1_20 (PLN02695)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45434
PHATRDRAFT_46281 cg9915-isoform b

PHATRDRAFT_46281 - cg9915-isoform b

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46281
PHATRDRAFT_46333 heat shock protein 70 (HSP70_NBD)

PHATRDRAFT_46333 - heat shock protein 70 (HSP70_NBD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46333
PHATRDRAFT_46394

PHATRDRAFT_46394 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46394
PHATRDRAFT_46438 cytochrome p450-like protein (p450 superfamily)

PHATRDRAFT_46438 - cytochrome p450-like protein (p450 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46438
PHATRDRAFT_46599 clathrin light chain (Clathrin_lg_ch superfamily)

PHATRDRAFT_46599 - clathrin light chain (Clathrin_lg_ch superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46599
PHATRDRAFT_49082

PHATRDRAFT_49082 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49082
PHATRDRAFT_49304

PHATRDRAFT_49304 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49304
PHATRDRAFT_54590 (Tic22 superfamily)

PHATRDRAFT_54590 - (Tic22 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54590
GO ID Go Term p-value q-value Cluster
GO:0006430 lysyl-tRNA aminoacylation 0.00641182 1 Phatr_bicluster_0188
GO:0006529 asparagine biosynthesis 0.0127857 1 Phatr_bicluster_0188
GO:0006422 aspartyl-tRNA aminoacylation 0.0191218 1 Phatr_bicluster_0188
GO:0006568 tryptophan metabolism 0.0191218 1 Phatr_bicluster_0188
GO:0009225 nucleotide-sugar metabolism 0.0222757 1 Phatr_bicluster_0188
GO:0008652 amino acid biosynthesis 0.0222757 1 Phatr_bicluster_0188
GO:0044267 cellular protein metabolism 0.0316815 1 Phatr_bicluster_0188
GO:0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolism 0.0347981 1 Phatr_bicluster_0188
GO:0006418 tRNA aminoacylation for protein translation 0.154889 1 Phatr_bicluster_0188
GO:0008152 metabolism 0.242573 1 Phatr_bicluster_0188
Log in to post comments