Phatr_bicluster_0044 Residual: 0.37
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_0044 0.37 Phaeodactylum tricornutum
Displaying 1 - 36 of 36
PHATRDRAFT_1103 calcium-dependent protein kinase (S_TKc)

PHATRDRAFT_1103 - calcium-dependent protein kinase (S_TKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_1103
PHATRDRAFT_13320 (COG0412)

PHATRDRAFT_13320 - (COG0412)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13320
PHATRDRAFT_17720 long chain acyl-coa synthetase (PLN02736)

PHATRDRAFT_17720 - long chain acyl-coa synthetase (PLN02736)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17720
PHATRDRAFT_19333 fas2 (fasciata 2) nucleotide binding (WD40 superfamily)

PHATRDRAFT_19333 - fas2 (fasciata 2) nucleotide binding (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19333
PHATRDRAFT_31980 trna-specific adenosine deaminase (A_deamin superfamily)

PHATRDRAFT_31980 - trna-specific adenosine deaminase (A_deamin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31980
PHATRDRAFT_32772 f119b_bovin protein fam119b (Methyltransf_16 superfamily)

PHATRDRAFT_32772 - f119b_bovin protein fam119b (Methyltransf_16 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32772
PHATRDRAFT_33705 basic-leucine zippertranscription factor

PHATRDRAFT_33705 - basic-leucine zippertranscription factor

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33705
PHATRDRAFT_34923 glutamineclass i (GATase1_1)

PHATRDRAFT_34923 - glutamineclass i (GATase1_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34923
PHATRDRAFT_38937

PHATRDRAFT_36877 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36877
PHATRDRAFT_42689

PHATRDRAFT_38937 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38937
PHATRDRAFT_42949

PHATRDRAFT_42689 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42689
PHATRDRAFT_42960

PHATRDRAFT_42949 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42949
PHATRDRAFT_43160

PHATRDRAFT_42960 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42960
PHATRDRAFT_43746 (ATP-grasp_4 superfamily)

PHATRDRAFT_43160 - (ATP-grasp_4 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43160
PHATRDRAFT_44961

PHATRDRAFT_43746 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43746
PHATRDRAFT_45017 molybdenum cofactor biosynthesis protein (MoeA)

PHATRDRAFT_44961 - molybdenum cofactor biosynthesis protein (MoeA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44961
PHATRDRAFT_45353 isocitrate dehydrogenase nadp-monomeric type (IDH superfamily)

PHATRDRAFT_45017 - isocitrate dehydrogenase nadp-monomeric type (IDH superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45017
PHATRDRAFT_45622

PHATRDRAFT_45353 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45353
PHATRDRAFT_45623 hypothetical conserved protein (AIM24)

PHATRDRAFT_45622 - hypothetical conserved protein (AIM24)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45622
PHATRDRAFT_46131 (AIM24)

PHATRDRAFT_45623 - (AIM24)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45623
PHATRDRAFT_46709 vacuolar sorting receptor-like protein (PA)

PHATRDRAFT_46131 - vacuolar sorting receptor-like protein (PA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46131
PHATRDRAFT_47036

PHATRDRAFT_46709 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46709
PHATRDRAFT_47531 protein serine threonine (S_TKc)

PHATRDRAFT_47036 - protein serine threonine (S_TKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47036
PHATRDRAFT_48136

PHATRDRAFT_47531 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47531
PHATRDRAFT_48675 (CAF1A)

PHATRDRAFT_48136 - (CAF1A)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48136
PHATRDRAFT_48878

PHATRDRAFT_48675 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48675
PHATRDRAFT_48992

PHATRDRAFT_48878 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48878
PHATRDRAFT_48993

PHATRDRAFT_48992 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48992
PHATRDRAFT_49832

PHATRDRAFT_48993 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48993
PHATRDRAFT_49931

PHATRDRAFT_49832 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49832
PHATRDRAFT_49956

PHATRDRAFT_49931 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49931
PHATRDRAFT_50241 cip1 (cop1-interactive protein 1)

PHATRDRAFT_49956 - cip1 (cop1-interactive protein 1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49956
PHATRDRAFT_54251

PHATRDRAFT_50241 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50241
PHATRDRAFT_54863 (alpha_CA superfamily)

PHATRDRAFT_54251 - (alpha_CA superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54251
PHATRDRAFT_9413 epsilon frustilin

PHATRDRAFT_54863 - epsilon frustilin

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54863

PHATRDRAFT_9413 - camp-dependent protein kinase (PKc_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9413
GO ID Go Term p-value q-value Cluster
GO:0008152 metabolism 0.453158 1 Phatr_bicluster_0044
GO:0006777 Mo-molybdopterin cofactor biosynthesis 0.0118036 1 Phatr_bicluster_0044
GO:0006468 protein amino acid phosphorylation 0.00360249 1 Phatr_bicluster_0044
GO:0016567 protein ubiquitination 0.13382 1 Phatr_bicluster_0044
GO:0006396 RNA processing 0.105521 1 Phatr_bicluster_0044
GO:0006099 tricarboxylic acid cycle 0.015711 1 Phatr_bicluster_0044
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