Phatr_bicluster_0015 Residual: 0.37
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_0015 0.37 Phaeodactylum tricornutum
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Displaying 1 - 49 of 49
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PHATRDRAFT_10640 chloroplast coproporphyrinogen iii oxidase (PLN02873)

PHATRDRAFT_10640 - chloroplast coproporphyrinogen iii oxidase (PLN02873)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10640
PHATRDRAFT_14857 2-c-methyl-d-erythritol 4-phosphate cytidyltransferase (Glyco_tranf_GTA_type superfamily)

PHATRDRAFT_14857 - 2-c-methyl-d-erythritol 4-phosphate cytidyltransferase (Glyco_tranf_GTA_type superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14857
PHATRDRAFT_14926 menaquinone biosynthesis

PHATRDRAFT_14926 - menaquinone biosynthesis

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14926
PHATRDRAFT_1494 hcf101 (high-chlorophyll-fluorescence 101) atp binding (MRP-like)

PHATRDRAFT_1494 - hcf101 (high-chlorophyll-fluorescence 101) atp binding (MRP-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_1494
PHATRDRAFT_15977 non-phototropic hypocotyl nph1 (PAS_9)

PHATRDRAFT_15977 - non-phototropic hypocotyl nph1 (PAS_9)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15977
PHATRDRAFT_16430 (PTZ00318)

PHATRDRAFT_16430 - (PTZ00318)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16430
PHATRDRAFT_21829 2-c-methyl-d-erythritol 4-phosphate cytidyltransferase (CDP-ME_synthetase)

PHATRDRAFT_21829 - 2-c-methyl-d-erythritol 4-phosphate cytidyltransferase (CDP-ME_synthetase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21829
PHATRDRAFT_21897 g-protein beta subunit 1 (WD40)

PHATRDRAFT_21897 - g-protein beta subunit 1 (WD40)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21897
PHATRDRAFT_33254 (DUF3110 superfamily)

PHATRDRAFT_33254 - (DUF3110 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33254
PHATRDRAFT_36312 dictyostelium discoideum (slime mold)r1062 protein (DUF221 superfamily)

PHATRDRAFT_36312 - dictyostelium discoideum (slime mold)r1062 protein (DUF221 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36312
PHATRDRAFT_36606 duf1325 family protein (DUF1325 superfamily)

PHATRDRAFT_36606 - duf1325 family protein (DUF1325 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36606
PHATRDRAFT_37956 (GAT_1 superfamily)

PHATRDRAFT_37956 - (GAT_1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37956
PHATRDRAFT_39681 l-3-hydroxyacyl-dehydrogenase subunit precursor (PLN02545)

PHATRDRAFT_39681 - l-3-hydroxyacyl-dehydrogenase subunit precursor (PLN02545)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39681
PHATRDRAFT_4283 at4g22260 t10i14_90 (Ferritin_like superfamily)

PHATRDRAFT_4283 - at4g22260 t10i14_90 (Ferritin_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_4283
PHATRDRAFT_43069

PHATRDRAFT_43069 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43069
PHATRDRAFT_43370

PHATRDRAFT_43370 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43370
PHATRDRAFT_43465 (SRPBCC superfamily)

PHATRDRAFT_43465 - (SRPBCC superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43465
PHATRDRAFT_43557 jumonji domain containing 4 (Cupin_8 superfamily)

PHATRDRAFT_43557 - jumonji domain containing 4 (Cupin_8 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43557
PHATRDRAFT_43934

PHATRDRAFT_43934 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43934
PHATRDRAFT_44122

PHATRDRAFT_44122 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44122
PHATRDRAFT_44174 (MPP_superfamily superfamily)

PHATRDRAFT_44174 - (MPP_superfamily superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44174
PHATRDRAFT_44266

PHATRDRAFT_44266 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44266
PHATRDRAFT_44429

PHATRDRAFT_44429 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44429
PHATRDRAFT_44593

PHATRDRAFT_44593 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44593
PHATRDRAFT_45070 diguanylate cyclase (GAF)

PHATRDRAFT_45070 - diguanylate cyclase (GAF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45070
PHATRDRAFT_45464 serine incorporatorisoform cra_a (Serinc superfamily)

PHATRDRAFT_45464 - serine incorporatorisoform cra_a (Serinc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45464
PHATRDRAFT_46819

PHATRDRAFT_46819 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46819
PHATRDRAFT_47347

PHATRDRAFT_47347 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47347
PHATRDRAFT_47802 folate biopterin (BT1)

PHATRDRAFT_47802 - folate biopterin (BT1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47802
PHATRDRAFT_47944 g-box binding factor 1

PHATRDRAFT_47944 - g-box binding factor 1

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47944
PHATRDRAFT_48064

PHATRDRAFT_48064 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48064
PHATRDRAFT_48229

PHATRDRAFT_48229 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48229
PHATRDRAFT_48552

PHATRDRAFT_48552 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48552
PHATRDRAFT_48876 (ABC_ATPase superfamily)

PHATRDRAFT_48876 - (ABC_ATPase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48876
PHATRDRAFT_48917

PHATRDRAFT_48917 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48917
PHATRDRAFT_4950 2og-fe oxygenase familyexpressed (P4Hc)

PHATRDRAFT_4950 - 2og-fe oxygenase familyexpressed (P4Hc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_4950
PHATRDRAFT_49617

PHATRDRAFT_49617 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49617
PHATRDRAFT_49728 ygrg_schpo uncharacterized membrane protein

PHATRDRAFT_49728 - ygrg_schpo uncharacterized membrane protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49728
PHATRDRAFT_49971 (DUF1275)

PHATRDRAFT_49971 - (DUF1275)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49971
PHATRDRAFT_50356 sulfolipid synthase (PLN02871)

PHATRDRAFT_50356 - sulfolipid synthase (PLN02871)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50356
PHATRDRAFT_50519 (DUF285)

PHATRDRAFT_50519 - (DUF285)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50519
PHATRDRAFT_50556

PHATRDRAFT_50556 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50556
PHATRDRAFT_50742 triose or hexose phosphate phosphate (PTZ00343)

PHATRDRAFT_50742 - triose or hexose phosphate phosphate (PTZ00343)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50742
PHATRDRAFT_52368 atpase class i type 8b member 4 (ATPase_P-type)

PHATRDRAFT_52368 - atpase class i type 8b member 4 (ATPase_P-type)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52368
PHATRDRAFT_52655 glutamate-trna ligase (PLN02627)

PHATRDRAFT_52655 - glutamate-trna ligase (PLN02627)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52655
PHATRDRAFT_54791 cytochrome c biogenesistransmembrane region (CcdA)

PHATRDRAFT_54791 - cytochrome c biogenesistransmembrane region (CcdA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54791
PHATRDRAFT_54872 (Peptidase_C14)

PHATRDRAFT_54872 - (Peptidase_C14)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54872
PHATRDRAFT_55070 heat shock factor (HSF_DNA-bind)

PHATRDRAFT_55070 - heat shock factor (HSF_DNA-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55070
PHATRDRAFT_5605 phosphoglycerate mutase (HP_PGM_like)

PHATRDRAFT_5605 - phosphoglycerate mutase (HP_PGM_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5605
GO ID Go Term p-value q-value Cluster
GO:0006631 fatty acid metabolism 0.0118109 1 Phatr_bicluster_0015
GO:0009058 biosynthesis 0.0131292 1 Phatr_bicluster_0015
GO:0046677 response to antibiotic 0.0157187 1 Phatr_bicluster_0015
GO:0008299 isoprenoid biosynthesis 0.0350414 1 Phatr_bicluster_0015
GO:0006779 porphyrin biosynthesis 0.0388631 1 Phatr_bicluster_0015
GO:0007186 G-protein coupled receptor protein signaling pathway 0.0502429 1 Phatr_bicluster_0015
GO:0006096 glycolysis 0.129916 1 Phatr_bicluster_0015
GO:0019538 protein metabolism 0.133385 1 Phatr_bicluster_0015
GO:0007165 signal transduction 0.170689 1 Phatr_bicluster_0015
GO:0006468 protein amino acid phosphorylation 0.50135 1 Phatr_bicluster_0015
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