Phatr_bicluster_0097 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_0097 0.27 Phaeodactylum tricornutum
Displaying 1 - 25 of 25
PHATRDRAFT_11441 rna polymerase ii second largest subunit (PRK08565)

PHATRDRAFT_11441 - rna polymerase ii second largest subunit (PRK08565)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11441
PHATRDRAFT_12239 adenylate kinase (adk)

PHATRDRAFT_12239 - adenylate kinase (adk)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12239
PHATRDRAFT_14995 cell division protein (FtsZ_type1)

PHATRDRAFT_14995 - cell division protein (FtsZ_type1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14995
PHATRDRAFT_15764 glutathione s-transferase (Gst)

PHATRDRAFT_15764 - glutathione s-transferase (Gst)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15764
PHATRDRAFT_20708 aspartyl aminopeptidase (M18_DAP)

PHATRDRAFT_20708 - aspartyl aminopeptidase (M18_DAP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20708
PHATRDRAFT_22388 membrane protein (PRX5_like)

PHATRDRAFT_22388 - membrane protein (PRX5_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22388
PHATRDRAFT_22459 delta-5 fatty acid desaturase (Delta6-FADS-like)

PHATRDRAFT_22459 - delta-5 fatty acid desaturase (Delta6-FADS-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22459
PHATRDRAFT_35819 glutathione reductase (PRK06116)

PHATRDRAFT_35819 - glutathione reductase (PRK06116)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35819
PHATRDRAFT_40952 (PUB)

PHATRDRAFT_40952 - (PUB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40952
PHATRDRAFT_41676 nucleoside diphosphate kinase family protein (NDPk_I)

PHATRDRAFT_41676 - nucleoside diphosphate kinase family protein (NDPk_I)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41676
PHATRDRAFT_42018 chloroplast ferredoxin nadp(+) reductase (PLN03116)

PHATRDRAFT_42018 - chloroplast ferredoxin nadp(+) reductase (PLN03116)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42018
PHATRDRAFT_42503

PHATRDRAFT_42503 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42503
PHATRDRAFT_43320

PHATRDRAFT_43320 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43320
PHATRDRAFT_44172 acid phosphataselysophosphatidic (HP_HAP_like)

PHATRDRAFT_44172 - acid phosphataselysophosphatidic (HP_HAP_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44172
PHATRDRAFT_45692 nuclear exosome component rrp6p (DnaQ_like_exo superfamily)

PHATRDRAFT_45692 - nuclear exosome component rrp6p (DnaQ_like_exo superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45692
PHATRDRAFT_46917

PHATRDRAFT_46917 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46917
PHATRDRAFT_47624

PHATRDRAFT_47624 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47624
PHATRDRAFT_47811

PHATRDRAFT_47811 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47811
PHATRDRAFT_47954 mitochondrial phosphate carrier protein (Mito_carr)

PHATRDRAFT_47954 - mitochondrial phosphate carrier protein (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47954
PHATRDRAFT_48879

PHATRDRAFT_48879 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48879
PHATRDRAFT_50464

PHATRDRAFT_50464 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50464
PHATRDRAFT_51100 lsm (like-sm) domain-containing protein (Sm_like superfamily)

PHATRDRAFT_51100 - lsm (like-sm) domain-containing protein (Sm_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51100
PHATRDRAFT_54285 p-atpase family transporter: cation (P-ATPase-V)

PHATRDRAFT_54285 - p-atpase family transporter: cation (P-ATPase-V)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54285
PHATRDRAFT_6834 adenine phosphoribosyltransferase (PRTases_typeI)

PHATRDRAFT_6834 - adenine phosphoribosyltransferase (PRTases_typeI)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6834
PHATRDRAFT_7784 uncharacterized conserved membrane protein

PHATRDRAFT_7784 - uncharacterized conserved membrane protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7784
GO ID Go Term p-value q-value Cluster
GO:0006749 glutathione metabolism 0.00419857 1 Phatr_bicluster_0097
GO:0006241 CTP biosynthesis 0.012546 1 Phatr_bicluster_0097
GO:0006183 GTP biosynthesis 0.012546 1 Phatr_bicluster_0097
GO:0006228 UTP biosynthesis 0.012546 1 Phatr_bicluster_0097
GO:0006118 electron transport 0.0132312 1 Phatr_bicluster_0097
GO:0051258 protein polymerization 0.0208275 1 Phatr_bicluster_0097
GO:0009116 nucleoside metabolism 0.0371948 1 Phatr_bicluster_0097
GO:0006636 fatty acid desaturation 0.0412462 1 Phatr_bicluster_0097
GO:0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolism 0.0452816 1 Phatr_bicluster_0097
GO:0006350 transcription 0.0847655 1 Phatr_bicluster_0097
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