Phatr_bicluster_0143 Residual: 0.35
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_0143 0.35 Phaeodactylum tricornutum
Displaying 1 - 29 of 29
PHATRDRAFT_13253 (DUF1825 superfamily)

PHATRDRAFT_13253 - (DUF1825 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13253
PHATRDRAFT_22713 ypt1_phyinras-like gtp-binding protein ypt1 (Rab1_Ypt1)

PHATRDRAFT_22713 - ypt1_phyinras-like gtp-binding protein ypt1 (Rab1_Ypt1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22713
PHATRDRAFT_23467 aldehyde dehydrogenase 6member a1 (ALDH_F6_MMSDH)

PHATRDRAFT_23467 - aldehyde dehydrogenase 6member a1 (ALDH_F6_MMSDH)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23467
PHATRDRAFT_23658 long chain (PRK09267)

PHATRDRAFT_23658 - long chain (PRK09267)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23658
PHATRDRAFT_29340 ubiquitin-specific protease 6 (Peptidase_C19 superfamily)

PHATRDRAFT_29340 - ubiquitin-specific protease 6 (Peptidase_C19 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29340
PHATRDRAFT_35869 histone deacetylase 6 (HDAC_classII)

PHATRDRAFT_35869 - histone deacetylase 6 (HDAC_classII)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35869
PHATRDRAFT_36084 (FlaRed superfamily)

PHATRDRAFT_36084 - (FlaRed superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36084
PHATRDRAFT_38671 poly-glutamine tract-binding protein

PHATRDRAFT_38671 - poly-glutamine tract-binding protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38671
PHATRDRAFT_38849

PHATRDRAFT_38849 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38849
PHATRDRAFT_40017 domain containing protein (Tyrosinase superfamily)

PHATRDRAFT_40017 - domain containing protein (Tyrosinase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40017
PHATRDRAFT_41423 fructose--bisphosphate aldolase (FBP_aldolase_I_a)

PHATRDRAFT_41423 - fructose--bisphosphate aldolase (FBP_aldolase_I_a)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41423
PHATRDRAFT_43472 (DnaJ)

PHATRDRAFT_43472 - (DnaJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43472
PHATRDRAFT_43772 conserved protein (DUF221 superfamily)

PHATRDRAFT_43772 - conserved protein (DUF221 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43772
PHATRDRAFT_46444

PHATRDRAFT_46444 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46444
PHATRDRAFT_46889

PHATRDRAFT_46889 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46889
PHATRDRAFT_47674 (DUF305 superfamily)

PHATRDRAFT_47674 - (DUF305 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47674
PHATRDRAFT_47937

PHATRDRAFT_47937 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47937
PHATRDRAFT_48103 napb-prov protein (SNAP)

PHATRDRAFT_48103 - napb-prov protein (SNAP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48103
PHATRDRAFT_49101 nudix (Nudix_Hydrolase_19)

PHATRDRAFT_49101 - nudix (Nudix_Hydrolase_19)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49101
PHATRDRAFT_49272

PHATRDRAFT_49272 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49272
PHATRDRAFT_51183 cellular repressor of e1a-stimulated genesfamily (Pyrid_oxidase_2)

PHATRDRAFT_51183 - cellular repressor of e1a-stimulated genesfamily (Pyrid_oxidase_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51183
PHATRDRAFT_52498

PHATRDRAFT_52498 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52498
PHATRDRAFT_52684 ncair mutase-related protein (COG1691)

PHATRDRAFT_52684 - ncair mutase-related protein (COG1691)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52684
PHATRDRAFT_54412 ncair mutase-related protein (COG1691)

PHATRDRAFT_54412 - ncair mutase-related protein (COG1691)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54412
PHATRDRAFT_54494 enoyl-hydratase carnithine racemase (CaiD)

PHATRDRAFT_54494 - enoyl-hydratase carnithine racemase (CaiD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54494
PHATRDRAFT_54528 3-hydroxyisobutyryl-coenzyme a hydrolase (PRK05617)

PHATRDRAFT_54528 - 3-hydroxyisobutyryl-coenzyme a hydrolase (PRK05617)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54528
PHATRDRAFT_54986

PHATRDRAFT_54986 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54986
PHATRDRAFT_54987

PHATRDRAFT_54987 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54987
PHATRDRAFT_55031

PHATRDRAFT_55031 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55031
GO ID Go Term p-value q-value Cluster
GO:0006886 intracellular protein transport 0.00921303 1 Phatr_bicluster_0143
GO:0006573 valine metabolism 0.0110755 1 Phatr_bicluster_0143
GO:0007264 small GTPase mediated signal transduction 0.0751604 1 Phatr_bicluster_0143
GO:0000160 two-component signal transduction system (phosphorelay) 0.0922612 1 Phatr_bicluster_0143
GO:0015031 protein transport 0.109067 1 Phatr_bicluster_0143
GO:0006096 glycolysis 0.122301 1 Phatr_bicluster_0143
GO:0006511 ubiquitin-dependent protein catabolism 0.15459 1 Phatr_bicluster_0143
GO:0006118 electron transport 0.206793 1 Phatr_bicluster_0143
GO:0006464 protein modification 0.209932 1 Phatr_bicluster_0143
GO:0008152 metabolism 0.298106 1 Phatr_bicluster_0143
Log in to post comments