Phatr_bicluster_0256 Residual: 0.28
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_0256 0.28 Phaeodactylum tricornutum
Displaying 1 - 27 of 27
PHATRDRAFT_16074 non-specific dna-binding protein (HU)

PHATRDRAFT_16074 - non-specific dna-binding protein (HU)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16074
PHATRDRAFT_17198 isoleucyl-trna synthetase (PLN02843)

PHATRDRAFT_17198 - isoleucyl-trna synthetase (PLN02843)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17198
PHATRDRAFT_17332 band 7 protein (SPFH_paraslipin)

PHATRDRAFT_17332 - band 7 protein (SPFH_paraslipin)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17332
PHATRDRAFT_19690 fkbp-type peptidyl-prolyl cis-trans isomerase (FKBP_C)

PHATRDRAFT_19690 - fkbp-type peptidyl-prolyl cis-trans isomerase (FKBP_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19690
PHATRDRAFT_21116 argininosuccinate synthetase (Argininosuccinate_Synthase)

PHATRDRAFT_21116 - argininosuccinate synthetase (Argininosuccinate_Synthase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21116
PHATRDRAFT_25420 rna polymeraseii and iia subunit (PLN03111)

PHATRDRAFT_25420 - rna polymeraseii and iia subunit (PLN03111)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25420
PHATRDRAFT_26346 cysteinyl-trna synthetase (PTZ00399)

PHATRDRAFT_26346 - cysteinyl-trna synthetase (PTZ00399)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_26346
PHATRDRAFT_31768 elongation factor ts (tsf)

PHATRDRAFT_31768 - elongation factor ts (tsf)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31768
PHATRDRAFT_32846 (Methyltrans_RNA superfamily)

PHATRDRAFT_32846 - (Methyltrans_RNA superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32846
PHATRDRAFT_34564

PHATRDRAFT_34564 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34564
PHATRDRAFT_37579 mitochondrial ribosomal (Nudix_Hydrolase superfamily)

PHATRDRAFT_37579 - mitochondrial ribosomal (Nudix_Hydrolase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37579
PHATRDRAFT_42754 (RRM_SF)

PHATRDRAFT_42754 - (RRM_SF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42754
PHATRDRAFT_45039 glycosyl transferase (Gly_transf_sug superfamily)

PHATRDRAFT_45039 - glycosyl transferase (Gly_transf_sug superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45039
PHATRDRAFT_46163 phytanoyl-dioxygenase family protein (PhyH superfamily)

PHATRDRAFT_46163 - phytanoyl-dioxygenase family protein (PhyH superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46163
PHATRDRAFT_46320 eif3a (eukaryotic translation initiation factor 3a)

PHATRDRAFT_46320 - eif3a (eukaryotic translation initiation factor 3a)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46320
PHATRDRAFT_46461 homoserine (PTZ00299)

PHATRDRAFT_46461 - homoserine (PTZ00299)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46461
PHATRDRAFT_46522 (NTF2)

PHATRDRAFT_46522 - (NTF2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46522
PHATRDRAFT_47116 polymeraseiii (dna directed) polypeptide c

PHATRDRAFT_47116 - polymeraseiii (dna directed) polypeptide c

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47116
PHATRDRAFT_47412 (DEXDc)

PHATRDRAFT_47412 - (DEXDc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47412
PHATRDRAFT_47492 mgc68780 protein (TPR)

PHATRDRAFT_47492 - mgc68780 protein (TPR)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47492
PHATRDRAFT_47999 ac007980_9cytosolic trna-ala synthetase (PLN02900)

PHATRDRAFT_47999 - ac007980_9cytosolic trna-ala synthetase (PLN02900)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47999
PHATRDRAFT_48686

PHATRDRAFT_48686 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48686
PHATRDRAFT_49738

PHATRDRAFT_49738 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49738
PHATRDRAFT_51005 ligase i (PRK01109)

PHATRDRAFT_51005 - ligase i (PRK01109)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51005
PHATRDRAFT_51868 amine oxidase (NAD_binding_8 superfamily)

PHATRDRAFT_51868 - amine oxidase (NAD_binding_8 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51868
PHATRDRAFT_8720 50s ribosomal protein l17 (rplQ)

PHATRDRAFT_8720 - 50s ribosomal protein l17 (rplQ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8720
PHATRDRAFT_9197 h aca ribonucleoprotein complex subunit 3 (Nop10p)

PHATRDRAFT_9197 - h aca ribonucleoprotein complex subunit 3 (Nop10p)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9197
GO ID Go Term p-value q-value Cluster
GO:0006423 cysteinyl-tRNA aminoacylation 0.012546 1 Phatr_bicluster_0256
GO:0006606 protein-nucleus import 0.012546 1 Phatr_bicluster_0256
GO:0006419 alanyl-tRNA aminoacylation 0.012546 1 Phatr_bicluster_0256
GO:0006526 arginine biosynthesis 0.0290436 1 Phatr_bicluster_0256
GO:0016310 phosphorylation 0.057292 1 Phatr_bicluster_0256
GO:0006414 translational elongation 0.057292 1 Phatr_bicluster_0256
GO:0006260 DNA replication 0.103926 1 Phatr_bicluster_0256
GO:0006281 DNA repair 0.1338 1 Phatr_bicluster_0256
GO:0006310 DNA recombination 0.144759 1 Phatr_bicluster_0256
GO:0006418 tRNA aminoacylation for protein translation 0.197624 1 Phatr_bicluster_0256
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