Phatr_bicluster_0253 Residual: 0.20
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_0253 0.20 Phaeodactylum tricornutum
Displaying 1 - 23 of 23
PHATRDRAFT_25379 pyrroline-5-carboxylate reductase (PLN02688)

PHATRDRAFT_25379 - pyrroline-5-carboxylate reductase (PLN02688)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25379
PHATRDRAFT_31539

PHATRDRAFT_31539 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31539
PHATRDRAFT_32833 gcn5-related n-acetyltransferase (RimI)

PHATRDRAFT_32833 - gcn5-related n-acetyltransferase (RimI)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32833
PHATRDRAFT_33075

PHATRDRAFT_33075 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33075
PHATRDRAFT_34536 chloroplast light harvesting protein isoform 5 (Chloroa_b-bind superfamily)

PHATRDRAFT_34536 - chloroplast light harvesting protein isoform 5 (Chloroa_b-bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34536
PHATRDRAFT_42529

PHATRDRAFT_42529 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42529
PHATRDRAFT_42535

PHATRDRAFT_42535 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42535
PHATRDRAFT_42612

PHATRDRAFT_42612 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42612
PHATRDRAFT_42850 protein kinase 6-like (S_TKc)

PHATRDRAFT_42850 - protein kinase 6-like (S_TKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42850
PHATRDRAFT_43131

PHATRDRAFT_43131 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43131
PHATRDRAFT_43280 solute carrier familymember 1 (Aa_trans superfamily)

PHATRDRAFT_43280 - solute carrier familymember 1 (Aa_trans superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43280
PHATRDRAFT_43383

PHATRDRAFT_43383 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43383
PHATRDRAFT_43470 interferon gamma-inducible protein 30 (GILT superfamily)

PHATRDRAFT_43470 - interferon gamma-inducible protein 30 (GILT superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43470
PHATRDRAFT_43581

PHATRDRAFT_43581 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43581
PHATRDRAFT_43716

PHATRDRAFT_43716 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43716
PHATRDRAFT_44437

PHATRDRAFT_44437 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44437
PHATRDRAFT_44512 ampk-activated protein kinase gamma-1 subunit (CBS_pair superfamily)

PHATRDRAFT_44512 - ampk-activated protein kinase gamma-1 subunit (CBS_pair superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44512
PHATRDRAFT_46662

PHATRDRAFT_46662 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46662
PHATRDRAFT_47006

PHATRDRAFT_47006 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47006
PHATRDRAFT_50411 pentatricopeptiderepeat-containing protein (PPR_2)

PHATRDRAFT_50411 - pentatricopeptiderepeat-containing protein (PPR_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50411
PHATRDRAFT_6288 haloacid dehalogenasesuperfamily protein (HAD_like)

PHATRDRAFT_6288 - haloacid dehalogenasesuperfamily protein (HAD_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6288
PHATRDRAFT_8091 ahe high-resolution three-dimensional solution structures of the oxidized and reduced states of human thioredoxin (TRX_family)

PHATRDRAFT_8091 - ahe high-resolution three-dimensional solution structures of the oxidized and reduced states of human thioredoxin (TRX_family)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8091
PHATRDRAFT_9258 1-deoxy-d-xylulose 5-phosphate reductoisomerase (PRK05447)

PHATRDRAFT_9258 - 1-deoxy-d-xylulose 5-phosphate reductoisomerase (PRK05447)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9258
GO ID Go Term p-value q-value Cluster
GO:0006561 proline biosynthesis 0.00739095 1 Phatr_bicluster_0253
GO:0008299 isoprenoid biosynthesis 0.0132709 1 Phatr_bicluster_0253
GO:0006865 amino acid transport 0.0408058 1 Phatr_bicluster_0253
GO:0009765 photosynthesis light harvesting 0.0564522 1 Phatr_bicluster_0253
GO:0006468 protein amino acid phosphorylation 0.229422 1 Phatr_bicluster_0253
GO:0006118 electron transport 0.294987 1 Phatr_bicluster_0253
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