Phatr_bicluster_0084 Residual: 0.29
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_0084 0.29 Phaeodactylum tricornutum
Displaying 1 - 29 of 29
PHATRDRAFT_15980 tetrapyrrole-binding protein (GUN4 superfamily)

PHATRDRAFT_15980 - tetrapyrrole-binding protein (GUN4 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15980
PHATRDRAFT_16140 uroporphyrinogen decarboxylase (PLN02433)

PHATRDRAFT_16140 - uroporphyrinogen decarboxylase (PLN02433)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16140
PHATRDRAFT_16322 fucoxanthin chlorophyll a c binding protein (Chloroa_b-bind superfamily)

PHATRDRAFT_16322 - fucoxanthin chlorophyll a c binding protein (Chloroa_b-bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16322
PHATRDRAFT_20757 uroporphyrinogen decarboxylase (URO-D)

PHATRDRAFT_20757 - uroporphyrinogen decarboxylase (URO-D)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20757
PHATRDRAFT_22819 peroxisomal membrane (Mpv17_PMP22)

PHATRDRAFT_22819 - peroxisomal membrane (Mpv17_PMP22)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22819
PHATRDRAFT_24119 chloroplast light harvesting protein isoform 5 (Chloroa_b-bind)

PHATRDRAFT_24119 - chloroplast light harvesting protein isoform 5 (Chloroa_b-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_24119
PHATRDRAFT_30690 isoflavone reductase (PLN02657)

PHATRDRAFT_30690 - isoflavone reductase (PLN02657)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30690
PHATRDRAFT_31109 plastid protoporphyrinogen oxidase (PLN02576)

PHATRDRAFT_31109 - plastid protoporphyrinogen oxidase (PLN02576)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31109
PHATRDRAFT_33017 mg chelatase subunit (Cob-chelat-sub)

PHATRDRAFT_33017 - mg chelatase subunit (Cob-chelat-sub)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33017
PHATRDRAFT_36103 (TLD superfamily)

PHATRDRAFT_36103 - (TLD superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36103
PHATRDRAFT_36362 peptidylprolyl isomerase (FKBP_C)

PHATRDRAFT_36362 - peptidylprolyl isomerase (FKBP_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36362
PHATRDRAFT_38227

PHATRDRAFT_38227 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38227
PHATRDRAFT_40199 (DUF1995 superfamily)

PHATRDRAFT_40199 - (DUF1995 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40199
PHATRDRAFT_41515 enolase 2 (PLN00191)

PHATRDRAFT_41515 - enolase 2 (PLN00191)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41515
PHATRDRAFT_43786

PHATRDRAFT_43786 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43786
PHATRDRAFT_44056 precursor cytochrome c6 (Cytochrom_C superfamily)

PHATRDRAFT_44056 - precursor cytochrome c6 (Cytochrom_C superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44056
PHATRDRAFT_44202

PHATRDRAFT_44202 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44202
PHATRDRAFT_45339 (SNc)

PHATRDRAFT_45339 - (SNc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45339
PHATRDRAFT_45724

PHATRDRAFT_45724 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45724
PHATRDRAFT_48328 carbohydratefamily 1 (Esterase)

PHATRDRAFT_48328 - carbohydratefamily 1 (Esterase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48328
PHATRDRAFT_48875 la_aedalla protein homolog (la ribonucleoprotein) (la autoantigen homolog) (LAM)

PHATRDRAFT_48875 - la_aedalla protein homolog (la ribonucleoprotein) (la autoantigen homolog) (LAM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48875
PHATRDRAFT_48921

PHATRDRAFT_48921 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48921
PHATRDRAFT_49154

PHATRDRAFT_49154 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49154
PHATRDRAFT_49639 taurine catabolism dioxygenase (TauD)

PHATRDRAFT_49639 - taurine catabolism dioxygenase (TauD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49639
PHATRDRAFT_49850

PHATRDRAFT_49850 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49850
PHATRDRAFT_50705 light harvesting protein (PLN00120)

PHATRDRAFT_50705 - light harvesting protein (PLN00120)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50705
PHATRDRAFT_55046 ests gb

PHATRDRAFT_55046 - ests gb

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55046
PHATRDRAFT_7626 fkbp-type peptidyl-prolyl cis-trans isomerase (FKBP_C)

PHATRDRAFT_7626 - fkbp-type peptidyl-prolyl cis-trans isomerase (FKBP_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7626
PHATRDRAFT_8324 cog1359: uncharacterized conserved protein (ABM superfamily)

PHATRDRAFT_8324 - cog1359: uncharacterized conserved protein (ABM superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8324
GO ID Go Term p-value q-value Cluster
GO:0006779 porphyrin biosynthesis 0.00000389 0.00902469 Phatr_bicluster_0084
GO:0009765 photosynthesis light harvesting 0.000279566 0.640765 Phatr_bicluster_0084
GO:0015995 chlorophyll biosynthesis 0.0103397 1 Phatr_bicluster_0084
GO:0015979 photosynthesis 0.0137641 1 Phatr_bicluster_0084
GO:0017000 antibiotic biosynthesis 0.0171775 1 Phatr_bicluster_0084
GO:0006457 protein folding 0.0600726 1 Phatr_bicluster_0084
GO:0006096 glycolysis 0.114621 1 Phatr_bicluster_0084
GO:0006118 electron transport 0.185759 1 Phatr_bicluster_0084
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