Phatr_bicluster_0052 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_0052 0.42 Phaeodactylum tricornutum
Displaying 1 - 31 of 31
PHATRDRAFT_10532 molybdenum cofactor biosynthesis protein c (MoaC superfamily)

PHATRDRAFT_10532 - molybdenum cofactor biosynthesis protein c (MoaC superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10532
PHATRDRAFT_15613 adf2_orysj actin-depolymerizing factor 2 (adf-2) (ADF_cofilin_like)

PHATRDRAFT_15613 - adf2_orysj actin-depolymerizing factor 2 (adf-2) (ADF_cofilin_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15613
PHATRDRAFT_16922 (Peptidase_M50B)

PHATRDRAFT_16922 - (Peptidase_M50B)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16922
PHATRDRAFT_18808 flagellar associated protein (DUF3228)

PHATRDRAFT_18808 - flagellar associated protein (DUF3228)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18808
PHATRDRAFT_23203 peptidyl-prolyl cis-transcyclophilin-type family protein (cyclophilin superfamily)

PHATRDRAFT_23203 - peptidyl-prolyl cis-transcyclophilin-type family protein (cyclophilin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23203
PHATRDRAFT_32120 mgc154358 protein (Mpv17_PMP22)

PHATRDRAFT_31437 - mgc154358 protein (Mpv17_PMP22)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31437
PHATRDRAFT_33876 sad1 and unc84 domain containing 1 (Sad1_UNC superfamily)

PHATRDRAFT_32120 - sad1 and unc84 domain containing 1 (Sad1_UNC superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32120
PHATRDRAFT_34302

PHATRDRAFT_33876 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33876
PHATRDRAFT_35262

PHATRDRAFT_34302 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34302
PHATRDRAFT_37885

PHATRDRAFT_35262 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35262
PHATRDRAFT_38445

PHATRDRAFT_37885 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37885
PHATRDRAFT_38787 zip family transporter: zinc ion (Zip superfamily)

PHATRDRAFT_38445 - zip family transporter: zinc ion (Zip superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38445
PHATRDRAFT_39325

PHATRDRAFT_38787 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38787
PHATRDRAFT_4003

PHATRDRAFT_39325 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39325
PHATRDRAFT_41192 calcium calmodulin-dependent protein kinase 1 (S_TKc)

PHATRDRAFT_4003 - calcium calmodulin-dependent protein kinase 1 (S_TKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_4003
PHATRDRAFT_42644

PHATRDRAFT_41192 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41192
PHATRDRAFT_42927

PHATRDRAFT_42644 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42644
PHATRDRAFT_43123 magnesium transporter (MgtE)

PHATRDRAFT_42927 - magnesium transporter (MgtE)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42927
PHATRDRAFT_43532

PHATRDRAFT_43123 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43123
PHATRDRAFT_45247 nica_arath nicastrin precursor (Zinc_peptidase_like superfamily)

PHATRDRAFT_43532 - nica_arath nicastrin precursor (Zinc_peptidase_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43532
PHATRDRAFT_45875 endonuclease exonuclease phosphatase familyexpressed (EEP superfamily)

PHATRDRAFT_45247 - endonuclease exonuclease phosphatase familyexpressed (EEP superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45247
PHATRDRAFT_45960

PHATRDRAFT_45875 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45875
PHATRDRAFT_47859 serine carboxypeptidase precursor (Peptidase_S10)

PHATRDRAFT_45960 - serine carboxypeptidase precursor (Peptidase_S10)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45960
PHATRDRAFT_48042 carbohydrate (n-acetylgalactosamine 4-0) sulfotransferase 8 (Sulfotransfer_2 superfamily)

PHATRDRAFT_47859 - carbohydrate (n-acetylgalactosamine 4-0) sulfotransferase 8 (Sulfotransfer_2 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47859
PHATRDRAFT_48173

PHATRDRAFT_48042 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48042
PHATRDRAFT_49224 rok family protein (COG2123)

PHATRDRAFT_48173 - rok family protein (COG2123)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48173
PHATRDRAFT_49547 (Ctr)

PHATRDRAFT_49224 - (Ctr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49224
PHATRDRAFT_50469

PHATRDRAFT_49547 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49547
PHATRDRAFT_52343

PHATRDRAFT_50469 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50469
PHATRDRAFT_5527 zinc transporter (Zip superfamily)

PHATRDRAFT_52343 - zinc transporter (Zip superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52343

PHATRDRAFT_5527 - enoyl-hydratase isomerase (crotonase-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5527
GO ID Go Term p-value q-value Cluster
GO:0006825 copper ion transport 0.00813004 1 Phatr_bicluster_0052
GO:0006777 Mo-molybdopterin cofactor biosynthesis 0.0162 1 Phatr_bicluster_0052
GO:0006820 anion transport 0.032161 1 Phatr_bicluster_0052
GO:0030001 metal ion transport 0.0426705 1 Phatr_bicluster_0052
GO:0006812 cation transport 0.0710389 1 Phatr_bicluster_0052
GO:0006508 proteolysis and peptidolysis 0.120633 1 Phatr_bicluster_0052
GO:0006396 RNA processing 0.142204 1 Phatr_bicluster_0052
GO:0006457 protein folding 0.275986 1 Phatr_bicluster_0052
GO:0006468 protein amino acid phosphorylation 0.380037 1 Phatr_bicluster_0052
GO:0008152 metabolism 0.564066 1 Phatr_bicluster_0052
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