Phatr_bicluster_0241 Residual: 0.23
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_0241 0.23 Phaeodactylum tricornutum
Displaying 1 - 24 of 24
PHATRDRAFT_12520 glucose transporter type 3 (Sugar_tr)

PHATRDRAFT_12520 - glucose transporter type 3 (Sugar_tr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12520
PHATRDRAFT_13549 pq-loop repeat family protein transmembrane family protein

PHATRDRAFT_13549 - pq-loop repeat family protein transmembrane family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13549
PHATRDRAFT_14636 light induced protein like (MPC superfamily)

PHATRDRAFT_14636 - light induced protein like (MPC superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14636
PHATRDRAFT_15423 dihydroorotate dehydrogenase (DHOD_2_like)

PHATRDRAFT_15423 - dihydroorotate dehydrogenase (DHOD_2_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15423
PHATRDRAFT_15844 cg17332-isoform a isoform 2 (V-ATPase_H_C superfamily)

PHATRDRAFT_15844 - cg17332-isoform a isoform 2 (V-ATPase_H_C superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15844
PHATRDRAFT_16960 mgc80429 protein (FKBP_C)

PHATRDRAFT_16960 - mgc80429 protein (FKBP_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16960
PHATRDRAFT_19949 mercuric reductase (PRK06370)

PHATRDRAFT_19949 - mercuric reductase (PRK06370)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19949
PHATRDRAFT_27719 at5g60160 f15l12_20 (M18_DAP)

PHATRDRAFT_27719 - at5g60160 f15l12_20 (M18_DAP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27719
PHATRDRAFT_37608

PHATRDRAFT_37608 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37608
PHATRDRAFT_42688 mitochondrial protein (PPR_2)

PHATRDRAFT_42688 - mitochondrial protein (PPR_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42688
PHATRDRAFT_42723 pyrimidine 5-nucleotidase (HAD_2)

PHATRDRAFT_42723 - pyrimidine 5-nucleotidase (HAD_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42723
PHATRDRAFT_42749 component of oligomeric golgi complex 5 isoform 3

PHATRDRAFT_42749 - component of oligomeric golgi complex 5 isoform 3

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42749
PHATRDRAFT_43076 hd phosphohydrolase family protein (HDc superfamily)

PHATRDRAFT_43076 - hd phosphohydrolase family protein (HDc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43076
PHATRDRAFT_43174 gdp-fucose transporter (VRG4)

PHATRDRAFT_43174 - gdp-fucose transporter (VRG4)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43174
PHATRDRAFT_44816 (DUF938 superfamily)

PHATRDRAFT_44816 - (DUF938 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44816
PHATRDRAFT_46099

PHATRDRAFT_46099 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46099
PHATRDRAFT_46361

PHATRDRAFT_46361 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46361
PHATRDRAFT_46780 metal cationzinc (zn2+)-iron (fe2+) permeasefamily (Zip)

PHATRDRAFT_46780 - metal cationzinc (zn2+)-iron (fe2+) permeasefamily (Zip)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46780
PHATRDRAFT_48515

PHATRDRAFT_48515 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48515
PHATRDRAFT_48865 alpha-l-fucosidase precursor (Alpha_L_fucos)

PHATRDRAFT_48865 - alpha-l-fucosidase precursor (Alpha_L_fucos)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48865
PHATRDRAFT_49185 transmembrane and coiled-coil domains (DUF106 superfamily)

PHATRDRAFT_49185 - transmembrane and coiled-coil domains (DUF106 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49185
PHATRDRAFT_49495

PHATRDRAFT_49495 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49495
PHATRDRAFT_51869 inositol 2-dehydrogenase (MviM)

PHATRDRAFT_51869 - inositol 2-dehydrogenase (MviM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51869
PHATRDRAFT_9267 fkbp2_yarli fk506-binding protein 2 precursor (peptidyl-prolyl cis-trans isomerase) (FKBP_C)

PHATRDRAFT_9267 - fkbp2_yarli fk506-binding protein 2 precursor (peptidyl-prolyl cis-trans isomerase) (FKBP_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9267
GO ID Go Term p-value q-value Cluster
GO:0006207 'de novo' pyrimidine base biosynthesis 0.00984608 1 Phatr_bicluster_0241
GO:0006457 protein folding 0.0320145 1 Phatr_bicluster_0241
GO:0030001 metal ion transport 0.0388631 1 Phatr_bicluster_0241
GO:0008643 carbohydrate transport 0.0388631 1 Phatr_bicluster_0241
GO:0005975 carbohydrate metabolism 0.14529 1 Phatr_bicluster_0241
GO:0006810 transport 0.38354 1 Phatr_bicluster_0241
GO:0006508 proteolysis and peptidolysis 0.434343 1 Phatr_bicluster_0241
GO:0006118 electron transport 0.441702 1 Phatr_bicluster_0241
GO:0008152 metabolism 0.529843 1 Phatr_bicluster_0241
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