Phatr_bicluster_0156 Residual: 0.31
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_0156 0.31 Phaeodactylum tricornutum
Displaying 1 - 26 of 26
PHATRDRAFT_10089 hal3a protein (Flavoprotein superfamily)

PHATRDRAFT_10089 - hal3a protein (Flavoprotein superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10089
PHATRDRAFT_10102 (RRM_CNOT4)

PHATRDRAFT_10102 - (RRM_CNOT4)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10102
PHATRDRAFT_11352 membrance occupation and recognition nexus protein 1 (MORN superfamily)

PHATRDRAFT_11352 - membrance occupation and recognition nexus protein 1 (MORN superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11352
PHATRDRAFT_12595 methionyl aminopeptidase 1 (PLN03158)

PHATRDRAFT_12595 - methionyl aminopeptidase 1 (PLN03158)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12595
PHATRDRAFT_12868 eukaryotic translation initiation factor 1b (eIF1_SUI1)

PHATRDRAFT_12868 - eukaryotic translation initiation factor 1b (eIF1_SUI1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12868
PHATRDRAFT_15371 uncharacterized membrane protein (bPH_2)

PHATRDRAFT_15371 - uncharacterized membrane protein (bPH_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15371
PHATRDRAFT_16807 zgc:162229 protein (Nudix_Hydrolase superfamily)

PHATRDRAFT_16807 - zgc:162229 protein (Nudix_Hydrolase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16807
PHATRDRAFT_21441 mfs family transporter: sugar (MFS)

PHATRDRAFT_21441 - mfs family transporter: sugar (MFS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21441
PHATRDRAFT_29423 conserved hypotheical protein (UPF0061 superfamily)

PHATRDRAFT_29423 - conserved hypotheical protein (UPF0061 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29423
PHATRDRAFT_32094

PHATRDRAFT_32094 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32094
PHATRDRAFT_32507

PHATRDRAFT_32507 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32507
PHATRDRAFT_34422 family dioxygenase (TauD)

PHATRDRAFT_34422 - family dioxygenase (TauD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34422
PHATRDRAFT_36969 cg9240-pa isoform 3 (S26_SPase_I)

PHATRDRAFT_36969 - cg9240-pa isoform 3 (S26_SPase_I)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36969
PHATRDRAFT_42432

PHATRDRAFT_42432 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42432
PHATRDRAFT_44014 at1g22850 f29g20_19 (COG0398)

PHATRDRAFT_44014 - at1g22850 f29g20_19 (COG0398)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44014
PHATRDRAFT_44076 ankyrin repeat

PHATRDRAFT_44076 - ankyrin repeat

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44076
PHATRDRAFT_44224 (TRAM_LAG1_CLN8)

PHATRDRAFT_44224 - (TRAM_LAG1_CLN8)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44224
PHATRDRAFT_44303 2-oxoglutarate and iron-dependent oxygenase domain containing 2 (2OG-FeII_Oxy_3 superfamily)

PHATRDRAFT_44303 - 2-oxoglutarate and iron-dependent oxygenase domain containing 2 (2OG-FeII_Oxy_3 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44303
PHATRDRAFT_44519

PHATRDRAFT_44519 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44519
PHATRDRAFT_45931 homo sapienskiaa0041 protein

PHATRDRAFT_45931 - homo sapienskiaa0041 protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45931
PHATRDRAFT_46090 gcn5-related n-acetyltransferase (NAT_SF)

PHATRDRAFT_46090 - gcn5-related n-acetyltransferase (NAT_SF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46090
PHATRDRAFT_46195

PHATRDRAFT_46195 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46195
PHATRDRAFT_46273 (ubiquitin)

PHATRDRAFT_46273 - (ubiquitin)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46273
PHATRDRAFT_50545 (DUF2854 superfamily)

PHATRDRAFT_48524 - (DUF2854 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48524
PHATRDRAFT_5132

PHATRDRAFT_50545 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50545

PHATRDRAFT_5132 - (AIM24)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5132
GO ID Go Term p-value q-value Cluster
GO:0006413 translational initiation 0.0407909 1 Phatr_bicluster_0156
GO:0006508 proteolysis and peptidolysis 0.053216 1 Phatr_bicluster_0156
GO:0019538 protein metabolism 0.0606456 1 Phatr_bicluster_0156
GO:0006464 protein modification 0.104035 1 Phatr_bicluster_0156
GO:0016567 protein ubiquitination 0.118111 1 Phatr_bicluster_0156
GO:0006810 transport 0.287164 1 Phatr_bicluster_0156
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