Phatr_bicluster_0189 Residual: 0.30
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_0189 0.30 Phaeodactylum tricornutum
Displaying 1 - 28 of 28
PHATRDRAFT_10902 n-acetylglutamate synthase (PRK05279)

PHATRDRAFT_10902 - n-acetylglutamate synthase (PRK05279)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10902
PHATRDRAFT_31772 atp-bindingsub-family b (mdr tap)member 10 (MdlB)

PHATRDRAFT_18473 - atp-bindingsub-family b (mdr tap)member 10 (MdlB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18473
PHATRDRAFT_33318 ubiquitin-specific protease 4 (Peptidase_C19)

PHATRDRAFT_31772 - ubiquitin-specific protease 4 (Peptidase_C19)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31772
PHATRDRAFT_34600

PHATRDRAFT_33318 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33318
PHATRDRAFT_34756

PHATRDRAFT_34600 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34600
PHATRDRAFT_35158

PHATRDRAFT_34756 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34756
PHATRDRAFT_36981 heat shock protein (ACD_sHsps-like)

PHATRDRAFT_35158 - heat shock protein (ACD_sHsps-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35158
PHATRDRAFT_41348 heat shock protein hsp20 (ACD_sHsps-like)

PHATRDRAFT_36981 - heat shock protein hsp20 (ACD_sHsps-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36981
PHATRDRAFT_42523 ae016811_126 uncharacterized protein conserved in bacteria (DUF924)

PHATRDRAFT_41348 - ae016811_126 uncharacterized protein conserved in bacteria (DUF924)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41348
PHATRDRAFT_42543 antibiotic biosynthesis monooxygenase (COG2329)

PHATRDRAFT_42523 - antibiotic biosynthesis monooxygenase (COG2329)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42523
PHATRDRAFT_42552

PHATRDRAFT_42543 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42543
PHATRDRAFT_42569

PHATRDRAFT_42552 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42552
PHATRDRAFT_43040 helicase domain protein (HA)

PHATRDRAFT_42569 - helicase domain protein (HA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42569
PHATRDRAFT_43917

PHATRDRAFT_43040 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43040
PHATRDRAFT_44438 inositol polyphosphate phosphatase-like 1 (EEP superfamily)

PHATRDRAFT_43917 - inositol polyphosphate phosphatase-like 1 (EEP superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43917
PHATRDRAFT_45016 (Abi)

PHATRDRAFT_44438 - (Abi)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44438
PHATRDRAFT_45663

PHATRDRAFT_45016 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45016
PHATRDRAFT_45816 class v (AAT_I superfamily)

PHATRDRAFT_45663 - class v (AAT_I superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45663
PHATRDRAFT_45959 heat shock transcription factor hsf1 (HSF_DNA-bind)

PHATRDRAFT_45816 - heat shock transcription factor hsf1 (HSF_DNA-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45816
PHATRDRAFT_45993 phosphodiesterase alkaline phosphatase d (MPP_PhoD)

PHATRDRAFT_45959 - phosphodiesterase alkaline phosphatase d (MPP_PhoD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45959
PHATRDRAFT_46010 isoamyl acetate-hydrolyzing esterase and related enzymes (BCIP)

PHATRDRAFT_45993 - isoamyl acetate-hydrolyzing esterase and related enzymes (BCIP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45993
PHATRDRAFT_46212 (SET)

PHATRDRAFT_46010 - (SET)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46010
PHATRDRAFT_49867 cyst wall protein 1

PHATRDRAFT_46212 - cyst wall protein 1

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46212
PHATRDRAFT_54343 fatty-acyl elongase (ELO)

PHATRDRAFT_49867 - fatty-acyl elongase (ELO)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49867
PHATRDRAFT_7136 mgc81978 protein

PHATRDRAFT_54343 - mgc81978 protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54343
PHATRDRAFT_7660 (DUF1230 superfamily)

PHATRDRAFT_7136 - (DUF1230 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7136
PHATRDRAFT_9947 ferredoxin (bacterial type ferredoxin family) (Fer4_15)

PHATRDRAFT_7660 - ferredoxin (bacterial type ferredoxin family) (Fer4_15)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7660

PHATRDRAFT_9947 - plt4_arath probable polyol transporter 4 (Sugar_tr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9947
GO ID Go Term p-value q-value Cluster
GO:0017000 antibiotic biosynthesis 0.00984487 1 Phatr_bicluster_0189
GO:0006526 arginine biosynthesis 0.013759 1 Phatr_bicluster_0189
GO:0008643 carbohydrate transport 0.0312056 1 Phatr_bicluster_0189
GO:0006810 transport 0.0513747 1 Phatr_bicluster_0189
GO:0006511 ubiquitin-dependent protein catabolism 0.0855993 1 Phatr_bicluster_0189
GO:0006355 regulation of transcription, DNA-dependent 0.359328 1 Phatr_bicluster_0189
GO:0006118 electron transport 0.3726 1 Phatr_bicluster_0189
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