Phatr_bicluster_0101 Residual: 0.21
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_0101 0.21 Phaeodactylum tricornutum
Displaying 1 - 17 of 17
PHATRDRAFT_10628 polo-like kinase 1 (S_TKc)

PHATRDRAFT_10628 - polo-like kinase 1 (S_TKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10628
PHATRDRAFT_22921 cmp-sialic acid transporter (Nuc_sug_transp)

PHATRDRAFT_22921 - cmp-sialic acid transporter (Nuc_sug_transp)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22921
PHATRDRAFT_36499

PHATRDRAFT_36499 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36499
PHATRDRAFT_37268 (SMC_prok_B)

PHATRDRAFT_37268 - (SMC_prok_B)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37268
PHATRDRAFT_42793

PHATRDRAFT_42793 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42793
PHATRDRAFT_43122 protein regulator of cytokinesis 1 isoform 2 (MAP65_ASE1)

PHATRDRAFT_43122 - protein regulator of cytokinesis 1 isoform 2 (MAP65_ASE1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43122
PHATRDRAFT_43718

PHATRDRAFT_43718 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43718
PHATRDRAFT_43936 at hook motif familyexpressed (AAA)

PHATRDRAFT_43936 - at hook motif familyexpressed (AAA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43936
PHATRDRAFT_44821

PHATRDRAFT_44821 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44821
PHATRDRAFT_46020 histone h2a (PLN00157)

PHATRDRAFT_46020 - histone h2a (PLN00157)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46020
PHATRDRAFT_47734 proteophosphoglycan ppg4

PHATRDRAFT_47734 - proteophosphoglycan ppg4

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47734
PHATRDRAFT_48333

PHATRDRAFT_48333 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48333
PHATRDRAFT_48735 chu large protein

PHATRDRAFT_48735 - chu large protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48735
PHATRDRAFT_49354

PHATRDRAFT_49354 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49354
PHATRDRAFT_49976

PHATRDRAFT_49976 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49976
PHATRDRAFT_51024 dna-binding horma domain-containing protein (HORMA)

PHATRDRAFT_51024 - dna-binding horma domain-containing protein (HORMA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51024
PHATRDRAFT_54677 dpod1_orysj dna polymerase delta catalytic subunit (PTZ00166)

PHATRDRAFT_54677 - dpod1_orysj dna polymerase delta catalytic subunit (PTZ00166)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54677
GO ID Go Term p-value q-value Cluster
GO:0015780 nucleotide-sugar transport 0.00689992 1 Phatr_bicluster_0101
GO:0008643 carbohydrate transport 0.0273554 1 Phatr_bicluster_0101
GO:0006334 nucleosome assembly 0.0273554 1 Phatr_bicluster_0101
GO:0007001 chromosome organization and biogenesis (sensu Eukaryota) 0.0290436 1 Phatr_bicluster_0101
GO:0006979 response to oxidative stress 0.0407909 1 Phatr_bicluster_0101
GO:0006468 protein amino acid phosphorylation 0.262204 1 Phatr_bicluster_0101
GO:0006508 proteolysis and peptidolysis 0.328797 1 Phatr_bicluster_0101
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