Phatr_bicluster_0133 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_0133 0.27 Phaeodactylum tricornutum
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Displaying 1 - 28 of 28
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PHATRDRAFT_10769 ubiquitin-like protein ribosomal protein (Ribosomal_S30)

PHATRDRAFT_10769 - ubiquitin-like protein ribosomal protein (Ribosomal_S30)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10769
PHATRDRAFT_14713 ribosomal protein l13 (Ribosomal_L13)

PHATRDRAFT_14713 - ribosomal protein l13 (Ribosomal_L13)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14713
PHATRDRAFT_18559 s6 ribosomal protein (Ribosomal_S6e superfamily)

PHATRDRAFT_18559 - s6 ribosomal protein (Ribosomal_S6e superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18559
PHATRDRAFT_19025 ribosomal proteincytosolic (PTZ00027)

PHATRDRAFT_19025 - ribosomal proteincytosolic (PTZ00027)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19025
PHATRDRAFT_19152 rl24a_schpo 60s ribosomal protein l24-a (Ribosomal_L24e_L24 superfamily)

PHATRDRAFT_19152 - rl24a_schpo 60s ribosomal protein l24-a (Ribosomal_L24e_L24 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19152
PHATRDRAFT_20167 snrnp sm protein f-like (Sm_F)

PHATRDRAFT_20167 - snrnp sm protein f-like (Sm_F)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20167
PHATRDRAFT_20787 af297643_1mitochondrial processing peptidase beta subunit (PqqL)

PHATRDRAFT_20787 - af297643_1mitochondrial processing peptidase beta subunit (PqqL)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20787
PHATRDRAFT_22597 rna polymeraseii and iia subunit (RNA_pol_Rpb8 superfamily)

PHATRDRAFT_22597 - rna polymeraseii and iia subunit (RNA_pol_Rpb8 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22597
PHATRDRAFT_23083 translation elongation factor tu (PLN03127)

PHATRDRAFT_23083 - translation elongation factor tu (PLN03127)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23083
PHATRDRAFT_24238 carbamate kinase (AAK_CK)

PHATRDRAFT_24238 - carbamate kinase (AAK_CK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_24238
PHATRDRAFT_28694 receptor of activated protein kinase ccomponent of 40s small ribosomal subunit (WD40)

PHATRDRAFT_28694 - receptor of activated protein kinase ccomponent of 40s small ribosomal subunit (WD40)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28694
PHATRDRAFT_28737 translation elongation factor 1 alpha (PTZ00141)

PHATRDRAFT_28737 - translation elongation factor 1 alpha (PTZ00141)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28737
PHATRDRAFT_29177 rl17_podca60s ribosomal protein l17 (Ribosomal_L22)

PHATRDRAFT_29177 - rl17_podca60s ribosomal protein l17 (Ribosomal_L22)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29177
PHATRDRAFT_30572 seryl-trna synthetase (PLN02678)

PHATRDRAFT_30572 - seryl-trna synthetase (PLN02678)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30572
PHATRDRAFT_30670 40s ribosomal protein (Ribosomal_S21e)

PHATRDRAFT_30670 - 40s ribosomal protein (Ribosomal_S21e)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30670
PHATRDRAFT_38678

PHATRDRAFT_38678 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38678
PHATRDRAFT_40626 nuclear rna binding (HABP4_PAI-RBP1)

PHATRDRAFT_40626 - nuclear rna binding (HABP4_PAI-RBP1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40626
PHATRDRAFT_41287 nuclear rna binding (HABP4_PAI-RBP1)

PHATRDRAFT_41287 - nuclear rna binding (HABP4_PAI-RBP1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41287
PHATRDRAFT_42774 nuclear protein set (SET)

PHATRDRAFT_42774 - nuclear protein set (SET)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42774
PHATRDRAFT_43222 carbamoyltransferase (BcrAD_BadFG superfamily)

PHATRDRAFT_43222 - carbamoyltransferase (BcrAD_BadFG superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43222
PHATRDRAFT_45880 mitochondrial ribosomal protein l51 s25 ci-b8 familyexpressed (L51_S25_CI-B8 superfamily)

PHATRDRAFT_45880 - mitochondrial ribosomal protein l51 s25 ci-b8 familyexpressed (L51_S25_CI-B8 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45880
PHATRDRAFT_47494

PHATRDRAFT_47494 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47494
PHATRDRAFT_48371 binding protein binding (LPA1)

PHATRDRAFT_48371 - binding protein binding (LPA1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48371
PHATRDRAFT_48728 nascent polypeptide associated complex alpha chain (NAC)

PHATRDRAFT_48728 - nascent polypeptide associated complex alpha chain (NAC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48728
PHATRDRAFT_49307

PHATRDRAFT_49307 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49307
PHATRDRAFT_50520 regulator of chromosome condensation (RCC1)

PHATRDRAFT_50520 - regulator of chromosome condensation (RCC1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50520
PHATRDRAFT_51291 ribosomal protein s20 (Ribosomal_S10 superfamily)

PHATRDRAFT_51291 - ribosomal protein s20 (Ribosomal_S10 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51291
PHATRDRAFT_54375 mu1 adaptin (AP-1_Mu1_Cterm)

PHATRDRAFT_54375 - mu1 adaptin (AP-1_Mu1_Cterm)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54375
GO ID Go Term p-value q-value Cluster
GO:0006412 protein biosynthesis 0.00000000181 0.00000421 Phatr_bicluster_0133
GO:0006414 translational elongation 0.00224587 1 Phatr_bicluster_0133
GO:0006434 seryl-tRNA aminoacylation 0.0103473 1 Phatr_bicluster_0133
GO:0006525 arginine metabolism 0.0103473 1 Phatr_bicluster_0133
GO:0008652 amino acid biosynthesis 0.0357713 1 Phatr_bicluster_0133
GO:0006350 transcription 0.103691 1 Phatr_bicluster_0133
GO:0006397 mRNA processing 0.113014 1 Phatr_bicluster_0133
GO:0009058 biosynthesis 0.209652 1 Phatr_bicluster_0133
GO:0006418 tRNA aminoacylation for protein translation 0.238237 1 Phatr_bicluster_0133
GO:0006508 proteolysis and peptidolysis 0.325228 1 Phatr_bicluster_0133
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