Phatr_bicluster_0123 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_0123 0.20 Phaeodactylum tricornutum
Displaying 1 - 22 of 22
PHATRDRAFT_10025 atp phosphoribosyltransferase (hisG)

PHATRDRAFT_10025 - atp phosphoribosyltransferase (hisG)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10025
PHATRDRAFT_10148 dna-directed rna polymerase subunit rpb6 (PLN00152)

PHATRDRAFT_10148 - dna-directed rna polymerase subunit rpb6 (PLN00152)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10148
PHATRDRAFT_14230 anthranilatechloroplast precursor (PLN02641)

PHATRDRAFT_14230 - anthranilatechloroplast precursor (PLN02641)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14230
PHATRDRAFT_17862 p68-like protein (DEADc)

PHATRDRAFT_17862 - p68-like protein (DEADc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17862
PHATRDRAFT_20470 gamma-tocopherol methyltransferase (PLN02244)

PHATRDRAFT_20470 - gamma-tocopherol methyltransferase (PLN02244)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20470
PHATRDRAFT_21290 initiation factor 2 subunit familyexpressed (GCD2)

PHATRDRAFT_21290 - initiation factor 2 subunit familyexpressed (GCD2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21290
PHATRDRAFT_2738 homogentisate solanesyltransferase (PT_UbiA superfamily)

PHATRDRAFT_2738 - homogentisate solanesyltransferase (PT_UbiA superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_2738
PHATRDRAFT_27821 dead (asp-glu-ala-asp) box polypeptide 21 (DEADc)

PHATRDRAFT_27821 - dead (asp-glu-ala-asp) box polypeptide 21 (DEADc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27821
PHATRDRAFT_28937 anthranilatechloroplast precursor (PLN02641)

PHATRDRAFT_28937 - anthranilatechloroplast precursor (PLN02641)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28937
PHATRDRAFT_31731 low-co2-inducible membrane protein (MtN3_slv superfamily)

PHATRDRAFT_31731 - low-co2-inducible membrane protein (MtN3_slv superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31731
PHATRDRAFT_34582 diaminopimelate epimerase (PLN02536)

PHATRDRAFT_34582 - diaminopimelate epimerase (PLN02536)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34582
PHATRDRAFT_35311 (Nucleoporin_C superfamily)

PHATRDRAFT_35311 - (Nucleoporin_C superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35311
PHATRDRAFT_41601 y-box protein 1 2 3 (CSP_CDS)

PHATRDRAFT_41601 - y-box protein 1 2 3 (CSP_CDS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41601
PHATRDRAFT_42768 n-ethylmaleimide-sensitive factor nsf sec18p (AAA)

PHATRDRAFT_42768 - n-ethylmaleimide-sensitive factor nsf sec18p (AAA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42768
PHATRDRAFT_43336 (DUF3414 superfamily)

PHATRDRAFT_43336 - (DUF3414 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43336
PHATRDRAFT_43701 (TPR)

PHATRDRAFT_43701 - (TPR)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43701
PHATRDRAFT_46595 lag1ceramide synthase 2 (TRAM_LAG1_CLN8)

PHATRDRAFT_46595 - lag1ceramide synthase 2 (TRAM_LAG1_CLN8)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46595
PHATRDRAFT_49098 pyruvate kinase (PLN02461)

PHATRDRAFT_49098 - pyruvate kinase (PLN02461)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49098
PHATRDRAFT_52316 aspartate kinase (PLN02551)

PHATRDRAFT_52316 - aspartate kinase (PLN02551)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52316
PHATRDRAFT_54080 (RusA)

PHATRDRAFT_54080 - (RusA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54080
PHATRDRAFT_7173 (Lumazine_synthase-I)

PHATRDRAFT_7173 - (Lumazine_synthase-I)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7173
PHATRDRAFT_9706 (COG2042)

PHATRDRAFT_9706 - (COG2042)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9706
GO ID Go Term p-value q-value Cluster
GO:0000162 tryptophan biosynthesis 0.0000285 0.0658673 Phatr_bicluster_0123
GO:0006206 pyrimidine base metabolism 0.0000569 0.131325 Phatr_bicluster_0123
GO:0006351 transcription, DNA-dependent 0.00321067 1 Phatr_bicluster_0123
GO:0009089 lysine biosynthesis via diaminopimelate 0.00960348 1 Phatr_bicluster_0123
GO:0009231 riboflavin biosynthesis 0.0191218 1 Phatr_bicluster_0123
GO:0000105 histidine biosynthesis 0.0285555 1 Phatr_bicluster_0123
GO:0006413 translational initiation 0.0744808 1 Phatr_bicluster_0123
GO:0006096 glycolysis 0.106876 1 Phatr_bicluster_0123
GO:0008152 metabolism 0.242573 1 Phatr_bicluster_0123
GO:0006355 regulation of transcription, DNA-dependent 0.515177 1 Phatr_bicluster_0123
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