Phatr_bicluster_0126 Residual: 0.29
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_0126 0.29 Phaeodactylum tricornutum
Displaying 1 - 26 of 26
PHATRDRAFT_10367 non-transporter abc protein (Uup)

PHATRDRAFT_10367 - non-transporter abc protein (Uup)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10367
PHATRDRAFT_14618 atph+mitochondrial f1alpha subunitcardiac muscle (PRK09281)

PHATRDRAFT_14618 - atph+mitochondrial f1alpha subunitcardiac muscle (PRK09281)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14618
PHATRDRAFT_14756 peptidase a22b family protein (Peptidase_A22B superfamily)

PHATRDRAFT_14756 - peptidase a22b family protein (Peptidase_A22B superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14756
PHATRDRAFT_16376 fatty-acyl elongase (ELO)

PHATRDRAFT_16376 - fatty-acyl elongase (ELO)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16376
PHATRDRAFT_18745 udp-glucose 6-expressed (PLN02353)

PHATRDRAFT_18745 - udp-glucose 6-expressed (PLN02353)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18745
PHATRDRAFT_22774 ribosomal proteinisoform cra_a (L7)

PHATRDRAFT_22774 - ribosomal proteinisoform cra_a (L7)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22774
PHATRDRAFT_22797 duf850 domain protein (DUF106)

PHATRDRAFT_22797 - duf850 domain protein (DUF106)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22797
PHATRDRAFT_23059 aspartatemitochondrial precursor (Aminotran_1_2)

PHATRDRAFT_23059 - aspartatemitochondrial precursor (Aminotran_1_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23059
PHATRDRAFT_23079 rl8_schpo 60s ribosomal protein l8 (Ribosomal_L7Ae superfamily)

PHATRDRAFT_23079 - rl8_schpo 60s ribosomal protein l8 (Ribosomal_L7Ae superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23079
PHATRDRAFT_31440 acyl carrier (PP-binding superfamily)

PHATRDRAFT_31440 - acyl carrier (PP-binding superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31440
PHATRDRAFT_39687 ribosomal protein l22 (Ribosomal_L22e)

PHATRDRAFT_39687 - ribosomal protein l22 (Ribosomal_L22e)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39687
PHATRDRAFT_40052 polysaccharide deacetylase family protein (uraD_N-term-dom)

PHATRDRAFT_40052 - polysaccharide deacetylase family protein (uraD_N-term-dom)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40052
PHATRDRAFT_40492 dmt family transporter: phosphate phosphoenolpyruvate

PHATRDRAFT_40492 - dmt family transporter: phosphate phosphoenolpyruvate

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40492
PHATRDRAFT_43824 diphosphomevalonate decarboxylase (mevalonate pyrophosphate decarboxylase)

PHATRDRAFT_43824 - diphosphomevalonate decarboxylase (mevalonate pyrophosphate decarboxylase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43824
PHATRDRAFT_46969 cytoplasmicintermediate chain 2 (WD40 superfamily)

PHATRDRAFT_46969 - cytoplasmicintermediate chain 2 (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46969
PHATRDRAFT_47104 (A_NRPS)

PHATRDRAFT_47104 - (A_NRPS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47104
PHATRDRAFT_47675 rcc1-like g exchanging factor rlg

PHATRDRAFT_47675 - rcc1-like g exchanging factor rlg

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47675
PHATRDRAFT_47749 chaperone protein (DnaJ)

PHATRDRAFT_47749 - chaperone protein (DnaJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47749
PHATRDRAFT_48411 ribosomal protein s2 (rpsE_arch)

PHATRDRAFT_48411 - ribosomal protein s2 (rpsE_arch)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48411
PHATRDRAFT_48457 transcriptional regulator (DUF179 superfamily)

PHATRDRAFT_48457 - transcriptional regulator (DUF179 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48457
PHATRDRAFT_49114 chaperonin containingsubunit 2 (TCP1_beta)

PHATRDRAFT_49114 - chaperonin containingsubunit 2 (TCP1_beta)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49114
PHATRDRAFT_49608 assembly protein (UPF0051)

PHATRDRAFT_49608 - assembly protein (UPF0051)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49608
PHATRDRAFT_51026 histone deacetylase 1 (PTZ00063)

PHATRDRAFT_51026 - histone deacetylase 1 (PTZ00063)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51026
PHATRDRAFT_51169 gtp-binding nuclear protein ran (PTZ00132)

PHATRDRAFT_51169 - gtp-binding nuclear protein ran (PTZ00132)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51169
PHATRDRAFT_54805 cation-transporting atpase (MgtA)

PHATRDRAFT_54805 - cation-transporting atpase (MgtA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54805
PHATRDRAFT_6847 40s ribosomal proteinexpressed (PTZ00155)

PHATRDRAFT_6847 - 40s ribosomal proteinexpressed (PTZ00155)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6847
GO ID Go Term p-value q-value Cluster
GO:0006412 protein biosynthesis 0.00113258 1 Phatr_bicluster_0126
GO:0016575 histone deacetylation 0.0103473 1 Phatr_bicluster_0126
GO:0006754 ATP biosynthesis 0.0154826 1 Phatr_bicluster_0126
GO:0042254 ribosome biogenesis and assembly 0.0307368 1 Phatr_bicluster_0126
GO:0044267 cellular protein metabolism 0.0507259 1 Phatr_bicluster_0126
GO:0006633 fatty acid biosynthesis 0.0654593 1 Phatr_bicluster_0126
GO:0007264 small GTPase mediated signal transduction 0.103691 1 Phatr_bicluster_0126
GO:0006520 amino acid metabolism 0.117641 1 Phatr_bicluster_0126
GO:0015031 protein transport 0.149389 1 Phatr_bicluster_0126
GO:0015986 ATP synthesis coupled proton transport 0.175733 1 Phatr_bicluster_0126
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