Phatr_bicluster_0221 Residual: 0.32
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_0221 0.32 Phaeodactylum tricornutum
Displaying 1 - 29 of 29
PHATRDRAFT_17265 proton phosphate symporter (MFS)

PHATRDRAFT_17265 - proton phosphate symporter (MFS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17265
PHATRDRAFT_31257 dihydrokaempferol 4-reductase (NADB_Rossmann superfamily)

PHATRDRAFT_31257 - dihydrokaempferol 4-reductase (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31257
PHATRDRAFT_31535

PHATRDRAFT_31535 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31535
PHATRDRAFT_35445

PHATRDRAFT_35445 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35445
PHATRDRAFT_35741

PHATRDRAFT_35741 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35741
PHATRDRAFT_36256 acetate kinase (Acetate_kinase superfamily)

PHATRDRAFT_36256 - acetate kinase (Acetate_kinase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36256
PHATRDRAFT_42561 histidine acid phosphatase family protein (HP_HAP_like)

PHATRDRAFT_42561 - histidine acid phosphatase family protein (HP_HAP_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42561
PHATRDRAFT_43118 hormone sensitive (Abhydrolase_3)

PHATRDRAFT_43118 - hormone sensitive (Abhydrolase_3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43118
PHATRDRAFT_44000

PHATRDRAFT_44000 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44000
PHATRDRAFT_44525 (SET)

PHATRDRAFT_44525 - (SET)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44525
PHATRDRAFT_44809 chromosome 3 open reading frame 37 (DUF159)

PHATRDRAFT_44809 - chromosome 3 open reading frame 37 (DUF159)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44809
PHATRDRAFT_44923

PHATRDRAFT_44923 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44923
PHATRDRAFT_45141 3-hydroxyisobutyrate dehydrogenase (HIBADH)

PHATRDRAFT_45141 - 3-hydroxyisobutyrate dehydrogenase (HIBADH)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45141
PHATRDRAFT_45728 at3g52570 f22o6_50 (MhpC)

PHATRDRAFT_45728 - at3g52570 f22o6_50 (MhpC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45728
PHATRDRAFT_45755 taurine catabolism dioxygenasefamily (CAS_like superfamily)

PHATRDRAFT_45755 - taurine catabolism dioxygenasefamily (CAS_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45755
PHATRDRAFT_45982 cg13101-isoform a

PHATRDRAFT_45982 - cg13101-isoform a

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45982
PHATRDRAFT_45986 flagellar calcium-binding (EFh)

PHATRDRAFT_45986 - flagellar calcium-binding (EFh)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45986
PHATRDRAFT_46890

PHATRDRAFT_46890 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46890
PHATRDRAFT_47077 family protein (NADB_Rossmann superfamily)

PHATRDRAFT_47077 - family protein (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47077
PHATRDRAFT_47141 zinc-binding oxidoreductase (MDR_like_2)

PHATRDRAFT_47141 - zinc-binding oxidoreductase (MDR_like_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47141
PHATRDRAFT_49064 (NhaC)

PHATRDRAFT_49064 - (NhaC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49064
PHATRDRAFT_49251 cral trio domain containing protein (SEC14)

PHATRDRAFT_49251 - cral trio domain containing protein (SEC14)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49251
PHATRDRAFT_50281 fumarylacetoacetase (PLN02856)

PHATRDRAFT_50281 - fumarylacetoacetase (PLN02856)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50281
PHATRDRAFT_51609 tyrosine aminotransferase (tyr_nico_aTase)

PHATRDRAFT_51609 - tyrosine aminotransferase (tyr_nico_aTase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51609
PHATRDRAFT_54560 nitrate transporter (2A0108)

PHATRDRAFT_54560 - nitrate transporter (2A0108)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54560
PHATRDRAFT_6848 maleylacetoacetate isomerase (Thioredoxin_like superfamily)

PHATRDRAFT_6848 - maleylacetoacetate isomerase (Thioredoxin_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6848
PHATRDRAFT_843 methylcrotonoyl-carboxylase alphamitochondrialexpressed (PRK08591)

PHATRDRAFT_843 - methylcrotonoyl-carboxylase alphamitochondrialexpressed (PRK08591)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_843
PHATRDRAFT_9476 2-oxoisovalerate dehydrogenase alphamitochondrialexpressed (TPP_E1_PDC_ADC_BCADC)

PHATRDRAFT_9476 - 2-oxoisovalerate dehydrogenase alphamitochondrialexpressed (TPP_E1_PDC_ADC_BCADC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9476
PHATRDRAFT_9728 carbon-sulfur lyase (GFA superfamily)

PHATRDRAFT_9728 - carbon-sulfur lyase (GFA superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9728
GO ID Go Term p-value q-value Cluster
GO:0008152 metabolism 0.00154435 1 Phatr_bicluster_0221
GO:0006082 organic acid metabolism 0.00321067 1 Phatr_bicluster_0221
GO:0009072 aromatic amino acid family metabolism 0.00960348 1 Phatr_bicluster_0221
GO:0006573 valine metabolism 0.00960348 1 Phatr_bicluster_0221
GO:0006098 pentose-phosphate shunt 0.0191218 1 Phatr_bicluster_0221
GO:0006885 regulation of pH 0.0254203 1 Phatr_bicluster_0221
GO:0006814 sodium ion transport 0.0347981 1 Phatr_bicluster_0221
GO:0016310 phosphorylation 0.0440926 1 Phatr_bicluster_0221
GO:0006810 transport 0.466944 1 Phatr_bicluster_0221
Log in to post comments