Phatr_bicluster_0076 Residual: 0.38
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_0076 0.38 Phaeodactylum tricornutum
Displaying 1 - 23 of 23
PHATRDRAFT_10350 peptidyl-prolyl cis-transcyclophilin-type (cyclophilin superfamily)

PHATRDRAFT_10350 - peptidyl-prolyl cis-transcyclophilin-type (cyclophilin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10350
PHATRDRAFT_11527 anthranilate synthase (IGPS)

PHATRDRAFT_11527 - anthranilate synthase (IGPS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11527
PHATRDRAFT_16295 short chain dehydrogenase (NADB_Rossmann superfamily)

PHATRDRAFT_16295 - short chain dehydrogenase (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16295
PHATRDRAFT_2542 afg1-family atpase

PHATRDRAFT_2542 - afg1-family atpase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_2542
PHATRDRAFT_29821 loc432087 protein (Alpha_L_fucos)

PHATRDRAFT_29821 - loc432087 protein (Alpha_L_fucos)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29821
PHATRDRAFT_32809

PHATRDRAFT_32809 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32809
PHATRDRAFT_34898 uracil phosphoribosyltransferase

PHATRDRAFT_34898 - uracil phosphoribosyltransferase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34898
PHATRDRAFT_35406 uncharacterized acr (DUF501 superfamily)

PHATRDRAFT_35406 - uncharacterized acr (DUF501 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35406
PHATRDRAFT_35464 (DSPc superfamily)

PHATRDRAFT_35464 - (DSPc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35464
PHATRDRAFT_35595 3-5 exonuclease

PHATRDRAFT_35595 - 3-5 exonuclease

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35595
PHATRDRAFT_35746

PHATRDRAFT_35746 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35746
PHATRDRAFT_36180

PHATRDRAFT_36180 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36180
PHATRDRAFT_38066

PHATRDRAFT_38066 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38066
PHATRDRAFT_40603

PHATRDRAFT_40603 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40603
PHATRDRAFT_42613 (ANK)

PHATRDRAFT_42613 - (ANK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42613
PHATRDRAFT_44703

PHATRDRAFT_44703 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44703
PHATRDRAFT_45413 (hot_dog superfamily)

PHATRDRAFT_45413 - (hot_dog superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45413
PHATRDRAFT_48986

PHATRDRAFT_48986 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48986
PHATRDRAFT_49418 mitochondrial rna splicing protein (Mrs2_Mfm1p-like)

PHATRDRAFT_49418 - mitochondrial rna splicing protein (Mrs2_Mfm1p-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49418
PHATRDRAFT_49936 myosin light polypeptide 5 regulatory (MFS)

PHATRDRAFT_49936 - myosin light polypeptide 5 regulatory (MFS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49936
PHATRDRAFT_50441

PHATRDRAFT_50441 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50441
PHATRDRAFT_7666 methionine sulfoxide reductase b (SelR superfamily)

PHATRDRAFT_7666 - methionine sulfoxide reductase b (SelR superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7666
PHATRDRAFT_8866 protein kinase domain containing protein (S_TKc)

PHATRDRAFT_8866 - protein kinase domain containing protein (S_TKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8866
GO ID Go Term p-value q-value Cluster
GO:0009399 nitrogen fixation 0.00394818 1 Phatr_bicluster_0076
GO:0006568 tryptophan metabolism 0.0118036 1 Phatr_bicluster_0076
GO:0030001 metal ion transport 0.0312056 1 Phatr_bicluster_0076
GO:0006470 protein amino acid dephosphorylation 0.0369608 1 Phatr_bicluster_0076
GO:0005975 carbohydrate metabolism 0.118 1 Phatr_bicluster_0076
GO:0006457 protein folding 0.209255 1 Phatr_bicluster_0076
GO:0006468 protein amino acid phosphorylation 0.2936 1 Phatr_bicluster_0076
GO:0008152 metabolism 0.453158 1 Phatr_bicluster_0076
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