Phatr_bicluster_0055 Residual: 0.36
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_0055 0.36 Phaeodactylum tricornutum
Displaying 1 - 34 of 34
PHATRDRAFT_12655 protein kinase a regulatory subunit (CAP_ED)

PHATRDRAFT_12655 - protein kinase a regulatory subunit (CAP_ED)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12655
PHATRDRAFT_13633 chromosome 1 open reading frame 91 (UPF0546 superfamily)

PHATRDRAFT_13633 - chromosome 1 open reading frame 91 (UPF0546 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13633
PHATRDRAFT_16168 aspartic protease (pepsin_retropepsin_like superfamily)

PHATRDRAFT_16168 - aspartic protease (pepsin_retropepsin_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16168
PHATRDRAFT_19089 gelsolin (gelsolin_S1_like)

PHATRDRAFT_19089 - gelsolin (gelsolin_S1_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19089
PHATRDRAFT_25840 nadp transhydrogenase (pntA)

PHATRDRAFT_25840 - nadp transhydrogenase (pntA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25840
PHATRDRAFT_28191 succinic semialdehyde dehydrogenase (ALDH_F5_SSADH_GabD)

PHATRDRAFT_28191 - succinic semialdehyde dehydrogenase (ALDH_F5_SSADH_GabD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28191
PHATRDRAFT_33088

PHATRDRAFT_33088 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33088
PHATRDRAFT_34403 dual specificity protein phosphatase (DSPc superfamily)

PHATRDRAFT_34403 - dual specificity protein phosphatase (DSPc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34403
PHATRDRAFT_36828 mitochondrial carrier protein (Mito_carr)

PHATRDRAFT_36828 - mitochondrial carrier protein (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36828
PHATRDRAFT_39093 classes i and ii superfamily (AAT_like)

PHATRDRAFT_39093 - classes i and ii superfamily (AAT_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39093
PHATRDRAFT_42481 hypothetical hydrolase acyltransferase (MhpC)

PHATRDRAFT_42481 - hypothetical hydrolase acyltransferase (MhpC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42481
PHATRDRAFT_44012 ser thr protein phosphatase family (MPP_YHR202W_N)

PHATRDRAFT_44012 - ser thr protein phosphatase family (MPP_YHR202W_N)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44012
PHATRDRAFT_44109 mgc108373 protein (Annexin)

PHATRDRAFT_44109 - mgc108373 protein (Annexin)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44109
PHATRDRAFT_44203 (Peptidase_M11 superfamily)

PHATRDRAFT_44203 - (Peptidase_M11 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44203
PHATRDRAFT_45802 (HECTc superfamily)

PHATRDRAFT_45802 - (HECTc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45802
PHATRDRAFT_45870

PHATRDRAFT_45870 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45870
PHATRDRAFT_45981

PHATRDRAFT_45981 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45981
PHATRDRAFT_46555 viral a-type inclusion

PHATRDRAFT_46555 - viral a-type inclusion

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46555
PHATRDRAFT_47097 (CIA30 superfamily)

PHATRDRAFT_47097 - (CIA30 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47097
PHATRDRAFT_47387

PHATRDRAFT_47387 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47387
PHATRDRAFT_47663 alpha beta hydrolase fold (MhpC)

PHATRDRAFT_47663 - alpha beta hydrolase fold (MhpC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47663
PHATRDRAFT_47839 (G8)

PHATRDRAFT_47839 - (G8)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47839
PHATRDRAFT_47952 hsf-type dna-binding domain containing protein (HSF_DNA-bind superfamily)

PHATRDRAFT_47952 - hsf-type dna-binding domain containing protein (HSF_DNA-bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47952
PHATRDRAFT_48159 solute carrier familymember 2 isoform 2 (MATE_eukaryotic)

PHATRDRAFT_48159 - solute carrier familymember 2 isoform 2 (MATE_eukaryotic)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48159
PHATRDRAFT_48223

PHATRDRAFT_48223 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48223
PHATRDRAFT_48362 leucine-rich repeat transmembrane protein kinase 1

PHATRDRAFT_48362 - leucine-rich repeat transmembrane protein kinase 1

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48362
PHATRDRAFT_48711

PHATRDRAFT_48711 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48711
PHATRDRAFT_49559 (ANK)

PHATRDRAFT_49559 - (ANK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49559
PHATRDRAFT_49600

PHATRDRAFT_49600 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49600
PHATRDRAFT_50077 (Beta_helix)

PHATRDRAFT_50077 - (Beta_helix)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50077
PHATRDRAFT_50235 at1g69520 f10d13_17

PHATRDRAFT_50235 - at1g69520 f10d13_17

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50235
PHATRDRAFT_50619

PHATRDRAFT_50619 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50619
PHATRDRAFT_51931 plasmodium falciparum polyubiquitin (Ubiquitin)

PHATRDRAFT_51931 - plasmodium falciparum polyubiquitin (Ubiquitin)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51931
PHATRDRAFT_52750 hect (homologous to the e6-apcarboxyl terminus) domain and rcc1-like domain2 (HECTc superfamily)

PHATRDRAFT_52750 - hect (homologous to the e6-apcarboxyl terminus) domain and rcc1-like domain2 (HECTc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52750
GO ID Go Term p-value q-value Cluster
GO:0006508 proteolysis and peptidolysis 0.0253471 1 Phatr_bicluster_0055
GO:0015992 proton transport 0.0407661 1 Phatr_bicluster_0055
GO:0006470 protein amino acid dephosphorylation 0.0549522 1 Phatr_bicluster_0055
GO:0006512 ubiquitin cycle 0.107123 1 Phatr_bicluster_0055
GO:0006464 protein modification 0.171749 1 Phatr_bicluster_0055
GO:0006468 protein amino acid phosphorylation 0.406444 1 Phatr_bicluster_0055
GO:0006810 transport 0.440472 1 Phatr_bicluster_0055
GO:0006355 regulation of transcription, DNA-dependent 0.487367 1 Phatr_bicluster_0055
GO:0006118 electron transport 0.503223 1 Phatr_bicluster_0055
GO:0008152 metabolism 0.595805 1 Phatr_bicluster_0055
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