Phatr_bicluster_0069 Residual: 0.42
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_0069 0.42 Phaeodactylum tricornutum
Displaying 1 - 22 of 22
PHATRDRAFT_12969 haloacid dehalogenase-like hydrolase family protein (PLN02779)

PHATRDRAFT_12969 - haloacid dehalogenase-like hydrolase family protein (PLN02779)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12969
PHATRDRAFT_29014 dhx33 protein (HA2)

PHATRDRAFT_20335 - dhx33 protein (HA2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20335
PHATRDRAFT_32893 fructose-bisphosphate aldolase (FBP_aldolase_IIA)

PHATRDRAFT_29014 - fructose-bisphosphate aldolase (FBP_aldolase_IIA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29014
PHATRDRAFT_34751

PHATRDRAFT_32893 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32893
PHATRDRAFT_36309

PHATRDRAFT_34751 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34751
PHATRDRAFT_39477 heavy metal translocating p-type atpase

PHATRDRAFT_36309 - heavy metal translocating p-type atpase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36309
PHATRDRAFT_40644

PHATRDRAFT_39477 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39477
PHATRDRAFT_43365 (AlgLyase superfamily)

PHATRDRAFT_40644 - (AlgLyase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40644
PHATRDRAFT_43386

PHATRDRAFT_43365 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43365
PHATRDRAFT_44969 galactose-3-o-sulfotransferase 3

PHATRDRAFT_43386 - galactose-3-o-sulfotransferase 3

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43386
PHATRDRAFT_46399 abc1 familyprotein (AarF)

PHATRDRAFT_44969 - abc1 familyprotein (AarF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44969
PHATRDRAFT_46770 amineflavin-containing superfamily (Amino_oxidase)

PHATRDRAFT_46399 - amineflavin-containing superfamily (Amino_oxidase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46399
PHATRDRAFT_47408 y2104_arath uncharacterized methyltransferasechloroplast precursor (AdoMet_MTases)

PHATRDRAFT_46770 - y2104_arath uncharacterized methyltransferasechloroplast precursor (AdoMet_MTases)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46770
PHATRDRAFT_49103

PHATRDRAFT_47408 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47408
PHATRDRAFT_49701

PHATRDRAFT_49103 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49103
PHATRDRAFT_50055 (ANK)

PHATRDRAFT_49701 - (ANK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49701
PHATRDRAFT_50634 ankyrin repeat (ANK)

PHATRDRAFT_50055 - ankyrin repeat (ANK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50055
PHATRDRAFT_52539

PHATRDRAFT_50634 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50634
PHATRDRAFT_7208 succinate dehydrogenase (PLN00129)

PHATRDRAFT_52539 - succinate dehydrogenase (PLN00129)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52539
PHATRDRAFT_8171 cmp dcmpzinc-binding protein (nucleoside_deaminase)

PHATRDRAFT_7208 - cmp dcmpzinc-binding protein (nucleoside_deaminase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7208
PHATRDRAFT_8945 thioredoxin (TRX_family)

PHATRDRAFT_8171 - thioredoxin (TRX_family)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8171

PHATRDRAFT_8945 - aminotransferase class-iii (BioA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8945
GO ID Go Term p-value q-value Cluster
GO:0006096 glycolysis 0.0671528 1 Phatr_bicluster_0069
GO:0006118 electron transport 0.0711586 1 Phatr_bicluster_0069
GO:0008152 metabolism 0.109996 1 Phatr_bicluster_0069
GO:0006468 protein amino acid phosphorylation 0.2936 1 Phatr_bicluster_0069
GO:0006355 regulation of transcription, DNA-dependent 0.359328 1 Phatr_bicluster_0069
GO:0006508 proteolysis and peptidolysis 0.365994 1 Phatr_bicluster_0069
Log in to post comments