Phatr_bicluster_0005 Residual: 0.48
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_0005 0.48 Phaeodactylum tricornutum
" class="views-fluidgrid-wrapper clear-block">
Displaying 1 - 37 of 37
" class="views-fluidgrid-wrapper clear-block">
PHATRDRAFT_15563 nli interacting factorfamily protein (NIF)

PHATRDRAFT_15563 - nli interacting factorfamily protein (NIF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15563
PHATRDRAFT_16875 kinesin family member 9 (SET)

PHATRDRAFT_16875 - kinesin family member 9 (SET)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16875
PHATRDRAFT_25876 glutathione synthetase (PLN02977)

PHATRDRAFT_25876 - glutathione synthetase (PLN02977)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25876
PHATRDRAFT_30040 glucose-6-phosphate dehydrogenase (PTZ00309)

PHATRDRAFT_30040 - glucose-6-phosphate dehydrogenase (PTZ00309)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30040
PHATRDRAFT_3267 p-protein: chorismateprephenate dehydratase (PheA)

PHATRDRAFT_3267 - p-protein: chorismateprephenate dehydratase (PheA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3267
PHATRDRAFT_33082

PHATRDRAFT_33082 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33082
PHATRDRAFT_33504

PHATRDRAFT_33504 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33504
PHATRDRAFT_33555

PHATRDRAFT_33555 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33555
PHATRDRAFT_3388 rna polymerase sigma factor (Sig70-cyanoRpoD)

PHATRDRAFT_3388 - rna polymerase sigma factor (Sig70-cyanoRpoD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3388
PHATRDRAFT_37482 (EFh)

PHATRDRAFT_37482 - (EFh)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37482
PHATRDRAFT_37636 zinc finger protein (CTH1)

PHATRDRAFT_37636 - zinc finger protein (CTH1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37636
PHATRDRAFT_38662 cog0457: fog: tpr repeat

PHATRDRAFT_38662 - cog0457: fog: tpr repeat

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38662
PHATRDRAFT_39109

PHATRDRAFT_39109 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39109
PHATRDRAFT_39174 mitochondrial uncoupling protein

PHATRDRAFT_39174 - mitochondrial uncoupling protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39174
PHATRDRAFT_39237 zinc-binding dehydrogenase family protein (MDR superfamily)

PHATRDRAFT_39237 - zinc-binding dehydrogenase family protein (MDR superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39237
PHATRDRAFT_39465

PHATRDRAFT_39465 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39465
PHATRDRAFT_39515 general substrate transporter (2A0109)

PHATRDRAFT_39515 - general substrate transporter (2A0109)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39515
PHATRDRAFT_39901

PHATRDRAFT_39901 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39901
PHATRDRAFT_40895

PHATRDRAFT_40895 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40895
PHATRDRAFT_40994 heat shock factor 3 (HSF_DNA-bind superfamily)

PHATRDRAFT_40994 - heat shock factor 3 (HSF_DNA-bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40994
PHATRDRAFT_41478 (O-FucT_like superfamily)

PHATRDRAFT_41478 - (O-FucT_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41478
PHATRDRAFT_47666 solute carrier family 34 (sodium phosphate)member 3 (Na_Pi_cotrans)

PHATRDRAFT_47666 - solute carrier family 34 (sodium phosphate)member 3 (Na_Pi_cotrans)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47666
PHATRDRAFT_47851 soul3-like protein

PHATRDRAFT_47851 - soul3-like protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47851
PHATRDRAFT_48096 (Hydrolase_4 superfamily)

PHATRDRAFT_48096 - (Hydrolase_4 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48096
PHATRDRAFT_48636 glutathione peroxidase (Thioredoxin_like superfamily)

PHATRDRAFT_48636 - glutathione peroxidase (Thioredoxin_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48636
PHATRDRAFT_48666 (AFD_class_I superfamily)

PHATRDRAFT_48666 - (AFD_class_I superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48666
PHATRDRAFT_48994

PHATRDRAFT_48994 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48994
PHATRDRAFT_49236

PHATRDRAFT_49236 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49236
PHATRDRAFT_49323

PHATRDRAFT_49323 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49323
PHATRDRAFT_49343 major facilitator superfamily mfs_1 (MFS_1)

PHATRDRAFT_49343 - major facilitator superfamily mfs_1 (MFS_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49343
PHATRDRAFT_49496 g protein-coupled inwardly rectifying potassium channel (IRK superfamily)

PHATRDRAFT_49496 - g protein-coupled inwardly rectifying potassium channel (IRK superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49496
PHATRDRAFT_49917

PHATRDRAFT_49917 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49917
PHATRDRAFT_49922

PHATRDRAFT_49922 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49922
PHATRDRAFT_50004 s-layer domain protein

PHATRDRAFT_50004 - s-layer domain protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50004
PHATRDRAFT_50602 (COG3899)

PHATRDRAFT_50602 - (COG3899)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50602
PHATRDRAFT_7848 glycine rich (LSm4)

PHATRDRAFT_7848 - glycine rich (LSm4)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7848
PHATRDRAFT_8293 nhp6_ashgo non-histone chromosomal protein 6 (HMGB-UBF_HMG-box)

PHATRDRAFT_8293 - nhp6_ashgo non-histone chromosomal protein 6 (HMGB-UBF_HMG-box)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8293
GO ID Go Term p-value q-value Cluster
GO:0006813 potassium ion transport 0.0670802 1 Phatr_bicluster_0005
GO:0006397 mRNA processing 0.076774 1 Phatr_bicluster_0005
GO:0006979 response to oxidative stress 0.0799844 1 Phatr_bicluster_0005
GO:0006810 transport 0.492171 1 Phatr_bicluster_0005
GO:0006508 proteolysis and peptidolysis 0.549807 1 Phatr_bicluster_0005
GO:0008152 metabolism 0.65254 1 Phatr_bicluster_0005
GO:0009094 L-phenylalanine biosynthesis 0.00345764 1 Phatr_bicluster_0005
GO:0006750 glutathione biosynthesis 0.00690418 1 Phatr_bicluster_0005
GO:0006006 glucose metabolism 0.0239715 1 Phatr_bicluster_0005
GO:0006817 phosphate transport 0.0239715 1 Phatr_bicluster_0005
Log in to post comments