Phatr_bicluster_0075 Residual: 0.22
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_0075 0.22 Phaeodactylum tricornutum
Displaying 1 - 25 of 25
PHATRDRAFT_13664 mgc53781 protein (DUS_like_FMN)

PHATRDRAFT_13664 - mgc53781 protein (DUS_like_FMN)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13664
PHATRDRAFT_14161 novel protein (SrmB)

PHATRDRAFT_14161 - novel protein (SrmB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14161
PHATRDRAFT_16162 ribonuclease z (Lactamase_B superfamily)

PHATRDRAFT_16162 - ribonuclease z (Lactamase_B superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16162
PHATRDRAFT_21682 tyw1_oryswybutosine-synthesizing protein 1 homolog (PRK13762)

PHATRDRAFT_21682 - tyw1_oryswybutosine-synthesizing protein 1 homolog (PRK13762)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21682
PHATRDRAFT_28689 dead (asp-glu-ala-asp) box polypeptide 51 (DEXDc superfamily)

PHATRDRAFT_28689 - dead (asp-glu-ala-asp) box polypeptide 51 (DEXDc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28689
PHATRDRAFT_30019 rio kinase 2 (COG0478)

PHATRDRAFT_30019 - rio kinase 2 (COG0478)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30019
PHATRDRAFT_35961

PHATRDRAFT_35961 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35961
PHATRDRAFT_40070 nucleolar protein with mif4g domain 1 (MIF4G)

PHATRDRAFT_40070 - nucleolar protein with mif4g domain 1 (MIF4G)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40070
PHATRDRAFT_40209

PHATRDRAFT_40209 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40209
PHATRDRAFT_43859 (THUMP_THUMPD1_like)

PHATRDRAFT_43859 - (THUMP_THUMPD1_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43859
PHATRDRAFT_43865

PHATRDRAFT_43865 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43865
PHATRDRAFT_43870 domain protein (Cupin_8 superfamily)

PHATRDRAFT_43870 - domain protein (Cupin_8 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43870
PHATRDRAFT_4708 pp-loop family protein (Alpha_ANH_like_II)

PHATRDRAFT_4708 - pp-loop family protein (Alpha_ANH_like_II)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_4708
PHATRDRAFT_47280

PHATRDRAFT_47280 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47280
PHATRDRAFT_47290 23s rrna (uracil-5-)-methyltransferase (rumA)

PHATRDRAFT_47290 - 23s rrna (uracil-5-)-methyltransferase (rumA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47290
PHATRDRAFT_47345 trna pseudouridine synthase a (PseudoU_synth superfamily)

PHATRDRAFT_47345 - trna pseudouridine synthase a (PseudoU_synth superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47345
PHATRDRAFT_47967 trm5 trna methyltransferase 5 homolog (Met_10)

PHATRDRAFT_47967 - trm5 trna methyltransferase 5 homolog (Met_10)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47967
PHATRDRAFT_47986 salt-inducible protein (PPR_2)

PHATRDRAFT_47986 - salt-inducible protein (PPR_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47986
PHATRDRAFT_48602 phospholipase carboxylesterase familyexpressed (PRK00142)

PHATRDRAFT_48602 - phospholipase carboxylesterase familyexpressed (PRK00142)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48602
PHATRDRAFT_48919

PHATRDRAFT_48919 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48919
PHATRDRAFT_49149 helix-hairpin-helix motif family protein (NT_POLXc)

PHATRDRAFT_49149 - helix-hairpin-helix motif family protein (NT_POLXc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49149
PHATRDRAFT_49177 (NT_PAP_TUTase)

PHATRDRAFT_49177 - (NT_PAP_TUTase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49177
PHATRDRAFT_49210 (Syo1_like superfamily)

PHATRDRAFT_49210 - (Syo1_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49210
PHATRDRAFT_49436

PHATRDRAFT_49436 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49436
PHATRDRAFT_55067 programmed cell death 2 (PDCD2_C superfamily)

PHATRDRAFT_55067 - programmed cell death 2 (PDCD2_C superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55067
GO ID Go Term p-value q-value Cluster
GO:0008033 tRNA processing 0.000637704 1 Phatr_bicluster_0075
GO:0006298 mismatch repair 0.0118036 1 Phatr_bicluster_0075
GO:0051341 regulation of oxidoreductase activity 0.0312056 1 Phatr_bicluster_0075
GO:0006260 DNA replication 0.0502734 1 Phatr_bicluster_0075
GO:0006281 DNA repair 0.0652904 1 Phatr_bicluster_0075
GO:0006412 protein biosynthesis 0.277391 1 Phatr_bicluster_0075
GO:0006468 protein amino acid phosphorylation 0.2936 1 Phatr_bicluster_0075
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