Phatr_bicluster_0235 Residual: 0.24
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_0235 0.24 Phaeodactylum tricornutum
Displaying 1 - 23 of 23
PHATRDRAFT_11403 mitogen-activated protein kinase (PKc_like superfamily)

PHATRDRAFT_11403 - mitogen-activated protein kinase (PKc_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11403
PHATRDRAFT_12221 loc100125006 protein (DnaJ)

PHATRDRAFT_12221 - loc100125006 protein (DnaJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12221
PHATRDRAFT_13057 transcriptional co-repressor sin3a isoform 5 (PAH)

PHATRDRAFT_13057 - transcriptional co-repressor sin3a isoform 5 (PAH)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13057
PHATRDRAFT_13114 ubiquitin-conjugating enzymej1 (UBCc)

PHATRDRAFT_13114 - ubiquitin-conjugating enzymej1 (UBCc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13114
PHATRDRAFT_19586 spx (syg1 pho81 xpr1) domain-containing protein (SPX)

PHATRDRAFT_19586 - spx (syg1 pho81 xpr1) domain-containing protein (SPX)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19586
PHATRDRAFT_3046 bass family transporter: sodium ion bile acid (COG0385)

PHATRDRAFT_3046 - bass family transporter: sodium ion bile acid (COG0385)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3046
PHATRDRAFT_32539 sjchgc07023 protein (Mod_r superfamily)

PHATRDRAFT_32539 - sjchgc07023 protein (Mod_r superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32539
PHATRDRAFT_3296 glycine d-amino acid oxidases-like

PHATRDRAFT_3296 - glycine d-amino acid oxidases-like

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3296
PHATRDRAFT_36058

PHATRDRAFT_35081 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35081
PHATRDRAFT_36386

PHATRDRAFT_36058 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36058
PHATRDRAFT_36976

PHATRDRAFT_36386 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36386
PHATRDRAFT_42051 tyrosine transport protein (Trp_Tyr_perm superfamily)

PHATRDRAFT_36976 - tyrosine transport protein (Trp_Tyr_perm superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36976
PHATRDRAFT_45559 gene product (PLN02850)

PHATRDRAFT_42051 - gene product (PLN02850)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42051
PHATRDRAFT_46063 heat shock protein (HSF_DNA-bind superfamily)

PHATRDRAFT_45559 - heat shock protein (HSF_DNA-bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45559
PHATRDRAFT_46170 ygi2_yeast uncharacterized protein ygl082w (DUF544 superfamily)

PHATRDRAFT_46063 - ygi2_yeast uncharacterized protein ygl082w (DUF544 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46063
PHATRDRAFT_46435 cell wall surface anchor family protein

PHATRDRAFT_46170 - cell wall surface anchor family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46170
PHATRDRAFT_47082

PHATRDRAFT_46435 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46435
PHATRDRAFT_47461

PHATRDRAFT_47082 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47082
PHATRDRAFT_50804

PHATRDRAFT_47461 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47461
PHATRDRAFT_5954 l-lactate dehydrogenase (FMN_dh)

PHATRDRAFT_50804 - l-lactate dehydrogenase (FMN_dh)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50804

PHATRDRAFT_5954 - abc transporter related (ABC_ATPase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5954

PHATRDRAFT_9070 - peptidyl-prolyl cis-transcyclophilin-type (cyclophilin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9070

PHATRDRAFT_9255 - polyunsaturated fatty acid elongase 2 (ELO)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9255
GO ID Go Term p-value q-value Cluster
GO:0007160 cell-matrix adhesion 0.0118109 1 Phatr_bicluster_0235
GO:0006422 aspartyl-tRNA aminoacylation 0.0234909 1 Phatr_bicluster_0235
GO:0006814 sodium ion transport 0.0426705 1 Phatr_bicluster_0235
GO:0007155 cell adhesion 0.0502429 1 Phatr_bicluster_0235
GO:0006457 protein folding 0.0763282 1 Phatr_bicluster_0235
GO:0006865 amino acid transport 0.105272 1 Phatr_bicluster_0235
GO:0007018 microtubule-based movement 0.112379 1 Phatr_bicluster_0235
GO:0006512 ubiquitin cycle 0.140282 1 Phatr_bicluster_0235
GO:0006418 tRNA aminoacylation for protein translation 0.187143 1 Phatr_bicluster_0235
GO:0006355 regulation of transcription, DNA-dependent 0.213253 1 Phatr_bicluster_0235
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