Phatr_bicluster_0209 Residual: 0.23
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_0209 0.23 Phaeodactylum tricornutum
Displaying 1 - 19 of 19
PHATRDRAFT_12355 prpl12 chloroplast ribosomal protein l12 (Ribosomal_L7_L12)

PHATRDRAFT_12355 - prpl12 chloroplast ribosomal protein l12 (Ribosomal_L7_L12)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12355
PHATRDRAFT_12737 glycine-rich protein 2 (CSP_CDS)

PHATRDRAFT_12737 - glycine-rich protein 2 (CSP_CDS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12737
PHATRDRAFT_13361 60s ribosomal protein l3 (PTZ00103)

PHATRDRAFT_13361 - 60s ribosomal protein l3 (PTZ00103)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13361
PHATRDRAFT_18087 adenylosuccinate lyase (Adenylsuccinate_lyase_2)

PHATRDRAFT_18087 - adenylosuccinate lyase (Adenylsuccinate_lyase_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18087
PHATRDRAFT_23959 poly a bindingcytoplasmic 1 (PABP-1234)

PHATRDRAFT_23959 - poly a bindingcytoplasmic 1 (PABP-1234)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23959
PHATRDRAFT_25743 cell cycle control (PTZ00424)

PHATRDRAFT_25743 - cell cycle control (PTZ00424)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25743
PHATRDRAFT_26176 elongation factor 1 gamma (GST_C_EF1Bgamma_like)

PHATRDRAFT_26176 - elongation factor 1 gamma (GST_C_EF1Bgamma_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_26176
PHATRDRAFT_26975 eukaryotic translation initiation factorsubunit 9 (COG5354)

PHATRDRAFT_26975 - eukaryotic translation initiation factorsubunit 9 (COG5354)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_26975
PHATRDRAFT_27118 ubiquitin extension protein (Ubiquitin)

PHATRDRAFT_27118 - ubiquitin extension protein (Ubiquitin)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27118
PHATRDRAFT_30967 acetohydroxy acid isomeroreductase (ilvC)

PHATRDRAFT_30967 - acetohydroxy acid isomeroreductase (ilvC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30967
PHATRDRAFT_32326 phosphoribosylpyrophosphate synthetase (PLN02369)

PHATRDRAFT_32326 - phosphoribosylpyrophosphate synthetase (PLN02369)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32326
PHATRDRAFT_32531 translation elongation factor (EF1_GNE)

PHATRDRAFT_32531 - translation elongation factor (EF1_GNE)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32531
PHATRDRAFT_34538 eukaryotic translation initiation factor 2 alpha subunit (eif-2-alpha) (PTZ00248)

PHATRDRAFT_34538 - eukaryotic translation initiation factor 2 alpha subunit (eif-2-alpha) (PTZ00248)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34538
PHATRDRAFT_43428 syk_crigrlysyl-trna synthetase (lysine--trna ligase) (PLN02502)

PHATRDRAFT_42289 - syk_crigrlysyl-trna synthetase (lysine--trna ligase) (PLN02502)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42289
PHATRDRAFT_43431

PHATRDRAFT_43428 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43428
PHATRDRAFT_46897 im:6900357 protein (WD40 superfamily)

PHATRDRAFT_43431 - im:6900357 protein (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43431
PHATRDRAFT_48010 histamine-releasing factor (TCTP superfamily)

PHATRDRAFT_46897 - histamine-releasing factor (TCTP superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46897
PHATRDRAFT_5236 mpt family transporter: outer membrane translocasetom40 (Porin3_Tom40)

PHATRDRAFT_48010 - mpt family transporter: outer membrane translocasetom40 (Porin3_Tom40)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48010

PHATRDRAFT_5236 - diphthine synthase family protein (Diphthine_synthase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5236
GO ID Go Term p-value q-value Cluster
GO:0006412 protein biosynthesis 0.00069037 1 Phatr_bicluster_0209
GO:0006414 translational elongation 0.00183602 1 Phatr_bicluster_0209
GO:0017183 peptidyl-diphthamide biosynthesis from peptidyl-histidine 0.00469252 1 Phatr_bicluster_0209
GO:0009152 purine ribonucleotide biosynthesis 0.00469252 1 Phatr_bicluster_0209
GO:0009082 branched chain family amino acid biosynthesis 0.00936417 1 Phatr_bicluster_0209
GO:0006430 lysyl-tRNA aminoacylation 0.00936417 1 Phatr_bicluster_0209
GO:0009165 nucleotide biosynthesis 0.0186452 1 Phatr_bicluster_0209
GO:0006422 aspartyl-tRNA aminoacylation 0.0278439 1 Phatr_bicluster_0209
GO:0009116 nucleoside metabolism 0.0414888 1 Phatr_bicluster_0209
GO:0006820 anion transport 0.0549522 1 Phatr_bicluster_0209
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