Phatr_bicluster_0246 Residual: 0.27
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_0246 0.27 Phaeodactylum tricornutum
Displaying 1 - 25 of 25
PHATRDRAFT_11458 26s proteasome regulatory subunit (MPN_eIF3f)

PHATRDRAFT_11458 - 26s proteasome regulatory subunit (MPN_eIF3f)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11458
PHATRDRAFT_11850 elac homolog 1 (Lactamase_B superfamily)

PHATRDRAFT_11850 - elac homolog 1 (Lactamase_B superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11850
PHATRDRAFT_12238 50s ribosomal protein l4 (Ribosomal_L4 superfamily)

PHATRDRAFT_12238 - 50s ribosomal protein l4 (Ribosomal_L4 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12238
PHATRDRAFT_13088 eukaryotic translation initiation factorsubunit 7 (eIF-3_zeta)

PHATRDRAFT_13088 - eukaryotic translation initiation factorsubunit 7 (eIF-3_zeta)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13088
PHATRDRAFT_17545 cyc07-like protein (Ribosomal_S3Ae)

PHATRDRAFT_17545 - cyc07-like protein (Ribosomal_S3Ae)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17545
PHATRDRAFT_18246 5-enolpyruvylshikimate-3-phosphate synthase (PLN02338)

PHATRDRAFT_18246 - 5-enolpyruvylshikimate-3-phosphate synthase (PLN02338)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18246
PHATRDRAFT_21181 quinoid dihydropteridine reductase (NADB_Rossmann superfamily)

PHATRDRAFT_21181 - quinoid dihydropteridine reductase (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21181
PHATRDRAFT_21485 eukaryotic translation initiation factorsubunit 6 (eIF3_N)

PHATRDRAFT_21485 - eukaryotic translation initiation factorsubunit 6 (eIF3_N)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21485
PHATRDRAFT_21592 diaminopimelate decarboxylase (PLPDE_III_DapDC)

PHATRDRAFT_21592 - diaminopimelate decarboxylase (PLPDE_III_DapDC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21592
PHATRDRAFT_22525 ubiquitin conjugating enzyme (UBCc)

PHATRDRAFT_22525 - ubiquitin conjugating enzyme (UBCc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22525
PHATRDRAFT_22666 chaperonin subunit 6a (TCP1_zeta)

PHATRDRAFT_22666 - chaperonin subunit 6a (TCP1_zeta)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22666
PHATRDRAFT_23371 gtp-binding protein (odn superfamily) (PTZ00258)

PHATRDRAFT_23371 - gtp-binding protein (odn superfamily) (PTZ00258)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23371
PHATRDRAFT_27385 glutamine-trna ligase (PRK05347)

PHATRDRAFT_27385 - glutamine-trna ligase (PRK05347)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27385
PHATRDRAFT_27838 elongation factor 3 (Uup)

PHATRDRAFT_27838 - elongation factor 3 (Uup)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27838
PHATRDRAFT_31811

PHATRDRAFT_31811 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31811
PHATRDRAFT_35513 prpl12 chloroplast ribosomal protein l12 (Ribosomal_L7_L12)

PHATRDRAFT_35513 - prpl12 chloroplast ribosomal protein l12 (Ribosomal_L7_L12)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35513
PHATRDRAFT_37131 at3g11830 f26k24_12 (TCP1_eta)

PHATRDRAFT_37131 - at3g11830 f26k24_12 (TCP1_eta)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37131
PHATRDRAFT_40621 gtp-binding protein (TypA)

PHATRDRAFT_40621 - gtp-binding protein (TypA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40621
PHATRDRAFT_43732 (CLU)

PHATRDRAFT_43732 - (CLU)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43732
PHATRDRAFT_45641

PHATRDRAFT_45641 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45641
PHATRDRAFT_46766

PHATRDRAFT_46766 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46766
PHATRDRAFT_46847 riken cdnaisoform cra_b (CTD_bind)

PHATRDRAFT_46847 - riken cdnaisoform cra_b (CTD_bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46847
PHATRDRAFT_47027 proteasome family protein (PCI)

PHATRDRAFT_47027 - proteasome family protein (PCI)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47027
PHATRDRAFT_48822 translation elongation factor (GST_C_eEF1b_like)

PHATRDRAFT_48822 - translation elongation factor (GST_C_eEF1b_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48822
PHATRDRAFT_54376 (DnaJ)

PHATRDRAFT_54376 - (DnaJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54376
GO ID Go Term p-value q-value Cluster
GO:0044267 cellular protein metabolism 0.000646869 1 Phatr_bicluster_0246
GO:0006412 protein biosynthesis 0.00301306 1 Phatr_bicluster_0246
GO:0016089 aromatic amino acid family biosynthesis, shikimate pathway 0.00395159 1 Phatr_bicluster_0246
GO:0006424 glutamyl-tRNA aminoacylation 0.00788854 1 Phatr_bicluster_0246
GO:0009089 lysine biosynthesis via diaminopimelate 0.0118109 1 Phatr_bicluster_0246
GO:0007186 G-protein coupled receptor protein signaling pathway 0.0502429 1 Phatr_bicluster_0246
GO:0006414 translational elongation 0.0540081 1 Phatr_bicluster_0246
GO:0006413 translational initiation 0.0908976 1 Phatr_bicluster_0246
GO:0006512 ubiquitin cycle 0.140282 1 Phatr_bicluster_0246
GO:0006418 tRNA aminoacylation for protein translation 0.187143 1 Phatr_bicluster_0246
Log in to post comments