Phatr_bicluster_0208 Residual: 0.30
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_0208 0.30 Phaeodactylum tricornutum
Displaying 1 - 22 of 22
PHATRDRAFT_11236 dna repair protein (PRK11823)

PHATRDRAFT_11236 - dna repair protein (PRK11823)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11236
PHATRDRAFT_15042 topoisomerase 6 subunit b (top6b)

PHATRDRAFT_15042 - topoisomerase 6 subunit b (top6b)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15042
PHATRDRAFT_3171 mitochondrial translocase complex component (NIF)

PHATRDRAFT_3171 - mitochondrial translocase complex component (NIF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3171
PHATRDRAFT_35516

PHATRDRAFT_35516 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35516
PHATRDRAFT_36197 soul3-like protein

PHATRDRAFT_36197 - soul3-like protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36197
PHATRDRAFT_36252

PHATRDRAFT_36252 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36252
PHATRDRAFT_37127 membrane bound o-acyl transferasefamily protein wax synthase-related (MBOAT_2)

PHATRDRAFT_37127 - membrane bound o-acyl transferasefamily protein wax synthase-related (MBOAT_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37127
PHATRDRAFT_37133

PHATRDRAFT_37133 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37133
PHATRDRAFT_42744 (FSH1 superfamily)

PHATRDRAFT_42744 - (FSH1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42744
PHATRDRAFT_42752

PHATRDRAFT_42752 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42752
PHATRDRAFT_42864 httm domain protein (HTTM superfamily)

PHATRDRAFT_42864 - httm domain protein (HTTM superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42864
PHATRDRAFT_43425 salicylate hydroxylase (UbiH)

PHATRDRAFT_43425 - salicylate hydroxylase (UbiH)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43425
PHATRDRAFT_43598 kelch motif family protein

PHATRDRAFT_43598 - kelch motif family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43598
PHATRDRAFT_44801 possible acetyltransferasefamily protein

PHATRDRAFT_44801 - possible acetyltransferasefamily protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44801
PHATRDRAFT_45766 (DUF3054)

PHATRDRAFT_45766 - (DUF3054)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45766
PHATRDRAFT_46451

PHATRDRAFT_46451 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46451
PHATRDRAFT_46706 biotin lipoate protein ligase-like protein (PTZ00276)

PHATRDRAFT_46706 - biotin lipoate protein ligase-like protein (PTZ00276)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46706
PHATRDRAFT_46878

PHATRDRAFT_46878 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46878
PHATRDRAFT_47254

PHATRDRAFT_47254 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47254
PHATRDRAFT_48762 oxidoreductase family protein (MviM)

PHATRDRAFT_48762 - oxidoreductase family protein (MviM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48762
PHATRDRAFT_49372 tha1 (threonine aldolase 1) aldehyde-lyase (PLN02721)

PHATRDRAFT_49372 - tha1 (threonine aldolase 1) aldehyde-lyase (PLN02721)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49372
PHATRDRAFT_8940 fkbp-type peptidyl-prolyl cis-trans isomerase (FKBP_C)

PHATRDRAFT_8940 - fkbp-type peptidyl-prolyl cis-trans isomerase (FKBP_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8940
GO ID Go Term p-value q-value Cluster
GO:0006813 potassium ion transport 0.0388725 1 Phatr_bicluster_0208
GO:0006725 aromatic compound metabolism 0.0388725 1 Phatr_bicluster_0208
GO:0006464 protein modification 0.118 1 Phatr_bicluster_0208
GO:0006457 protein folding 0.209255 1 Phatr_bicluster_0208
GO:0006810 transport 0.320848 1 Phatr_bicluster_0208
GO:0006508 proteolysis and peptidolysis 0.365994 1 Phatr_bicluster_0208
GO:0006118 electron transport 0.3726 1 Phatr_bicluster_0208
GO:0008152 metabolism 0.453158 1 Phatr_bicluster_0208
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