Phatr_bicluster_0181 Residual: 0.26
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_0181 0.26 Phaeodactylum tricornutum
Displaying 1 - 20 of 20
PHATRDRAFT_14996 yggt family membrane protein (YGGT)

PHATRDRAFT_14996 - yggt family membrane protein (YGGT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14996
PHATRDRAFT_16911 yad7_schpo uncharacterized rna methyltransferase (TrmA)

PHATRDRAFT_16911 - yad7_schpo uncharacterized rna methyltransferase (TrmA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16911
PHATRDRAFT_22955 pantoate--beta-alanine ligase (PanC)

PHATRDRAFT_22955 - pantoate--beta-alanine ligase (PanC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22955
PHATRDRAFT_23798 kelch repeat-containing protein (DUF4110)

PHATRDRAFT_23798 - kelch repeat-containing protein (DUF4110)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23798
PHATRDRAFT_30585 transcription-repair coupling factor (HELICc)

PHATRDRAFT_30585 - transcription-repair coupling factor (HELICc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30585
PHATRDRAFT_33633 dna gyrase subunit a (PRK05560)

PHATRDRAFT_33633 - dna gyrase subunit a (PRK05560)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33633
PHATRDRAFT_39247 d-amino acid dehydrogenase (DadA)

PHATRDRAFT_39247 - d-amino acid dehydrogenase (DadA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39247
PHATRDRAFT_39419 mitochondrial outer membrane beta-barrel protein tob55 omp85 sam50 (Bac_surface_Ag superfamily)

PHATRDRAFT_39419 - mitochondrial outer membrane beta-barrel protein tob55 omp85 sam50 (Bac_surface_Ag superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39419
PHATRDRAFT_39648

PHATRDRAFT_39648 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39648
PHATRDRAFT_42151 dnaj protein homolog atj3 (PTZ00037)

PHATRDRAFT_42151 - dnaj protein homolog atj3 (PTZ00037)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42151
PHATRDRAFT_4402 methylene tetrahydrofolate dehydrogenase (NAD_bind_amino_acid_DH superfamily)

PHATRDRAFT_4402 - methylene tetrahydrofolate dehydrogenase (NAD_bind_amino_acid_DH superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_4402
PHATRDRAFT_47627

PHATRDRAFT_47627 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47627
PHATRDRAFT_47943 (MIF4G)

PHATRDRAFT_47943 - (MIF4G)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47943
PHATRDRAFT_48118

PHATRDRAFT_48118 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48118
PHATRDRAFT_50058 (vWFA superfamily)

PHATRDRAFT_50058 - (vWFA superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50058
PHATRDRAFT_50067 domain protein (DnaJ)

PHATRDRAFT_50067 - domain protein (DnaJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50067
PHATRDRAFT_50071 amino acid transporter-like protein (Aa_trans superfamily)

PHATRDRAFT_50071 - amino acid transporter-like protein (Aa_trans superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50071
PHATRDRAFT_50302 spermatogenesis associated

PHATRDRAFT_50302 - spermatogenesis associated

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50302
PHATRDRAFT_51232 phf5_arath uncharacterized protein at1g07170 at2g30000 (PHF5)

PHATRDRAFT_51232 - phf5_arath uncharacterized protein at1g07170 at2g30000 (PHF5)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51232
PHATRDRAFT_51630 calcitonin gene-related peptide-receptor component protein (RNA_pol_Rpb4)

PHATRDRAFT_51630 - calcitonin gene-related peptide-receptor component protein (RNA_pol_Rpb4)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51630
GO ID Go Term p-value q-value Cluster
GO:0015940 pantothenate biosynthesis 0.00591934 1 Phatr_bicluster_0181
GO:0006268 DNA unwinding 0.0147381 1 Phatr_bicluster_0181
GO:0051336 regulation of hydrolase activity 0.0176618 1 Phatr_bicluster_0181
GO:0009396 folic acid and derivative biosynthesis 0.0234852 1 Phatr_bicluster_0181
GO:0006265 DNA topological change 0.026385 1 Phatr_bicluster_0181
GO:0006259 DNA metabolism 0.0350372 1 Phatr_bicluster_0181
GO:0006457 protein folding 0.0452262 1 Phatr_bicluster_0181
GO:0006865 amino acid transport 0.0800035 1 Phatr_bicluster_0181
GO:0006396 RNA processing 0.1541 1 Phatr_bicluster_0181
GO:0006355 regulation of transcription, DNA-dependent 0.487367 1 Phatr_bicluster_0181
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