Phatr_bicluster_0041 Residual: 0.40
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_0041 0.40 Phaeodactylum tricornutum
Displaying 1 - 35 of 35
PHATRDRAFT_10208 phosphoribulokinase precursor (PRK)

PHATRDRAFT_10208 - phosphoribulokinase precursor (PRK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10208
PHATRDRAFT_10261 beta-ig-h3 fasciclin (Fasciclin)

PHATRDRAFT_10261 - beta-ig-h3 fasciclin (Fasciclin)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10261
PHATRDRAFT_14682 peptidyl-prolyl cis-transcyclophilin type (cyclophilin)

PHATRDRAFT_14682 - peptidyl-prolyl cis-transcyclophilin type (cyclophilin)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14682
PHATRDRAFT_16481 light harvesting complex protein (Chloroa_b-bind)

PHATRDRAFT_16481 - light harvesting complex protein (Chloroa_b-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16481
PHATRDRAFT_32261 possible gram-negative pili assembly chaperone (PAP_fibrillin superfamily)

PHATRDRAFT_32261 - possible gram-negative pili assembly chaperone (PAP_fibrillin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32261
PHATRDRAFT_33045

PHATRDRAFT_33045 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33045
PHATRDRAFT_34147

PHATRDRAFT_34147 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34147
PHATRDRAFT_34177 rubredoxin familyexpressed

PHATRDRAFT_34177 - rubredoxin familyexpressed

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34177
PHATRDRAFT_34505

PHATRDRAFT_34505 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34505
PHATRDRAFT_34584 (TRX_Fd_family)

PHATRDRAFT_34584 - (TRX_Fd_family)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34584
PHATRDRAFT_38893 mgc86224 protein (ESCRT-II superfamily)

PHATRDRAFT_38893 - mgc86224 protein (ESCRT-II superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38893
PHATRDRAFT_39807

PHATRDRAFT_39807 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39807
PHATRDRAFT_39940 tellurite resistance protein (AdoMet_MTases)

PHATRDRAFT_39940 - tellurite resistance protein (AdoMet_MTases)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39940
PHATRDRAFT_40368

PHATRDRAFT_40368 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40368
PHATRDRAFT_41079 (Cupin_7)

PHATRDRAFT_41079 - (Cupin_7)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41079
PHATRDRAFT_41243 gamma-butyrobetaine hydroxylase (CAS_like superfamily)

PHATRDRAFT_41243 - gamma-butyrobetaine hydroxylase (CAS_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41243
PHATRDRAFT_41512

PHATRDRAFT_41512 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41512
PHATRDRAFT_42883

PHATRDRAFT_42883 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42883
PHATRDRAFT_42977

PHATRDRAFT_42977 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42977
PHATRDRAFT_43208 vegetatible incompatibility protein (WD40 superfamily)

PHATRDRAFT_43208 - vegetatible incompatibility protein (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43208
PHATRDRAFT_43685 ax110p-like protein (GFO_IDH_MocA superfamily)

PHATRDRAFT_43685 - ax110p-like protein (GFO_IDH_MocA superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43685
PHATRDRAFT_43828 ion transport protein (Ion_trans)

PHATRDRAFT_43828 - ion transport protein (Ion_trans)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43828
PHATRDRAFT_44392

PHATRDRAFT_44392 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44392
PHATRDRAFT_44955 4-hydroxy-3-methylbut-2-en-1-yl diphosphatechloroplast precursor (1-hydroxy-2-methyl-2--butenyl 4-diphosphate synthase) (PLN02925)

PHATRDRAFT_44955 - 4-hydroxy-3-methylbut-2-en-1-yl diphosphatechloroplast precursor (1-hydroxy-2-methyl-2--butenyl 4-diphosphate synthase) (PLN02925)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44955
PHATRDRAFT_46657 ucria_soltucytochrome b6-f complex iron-sulfurchloroplast precursor (rieske iron-sulfur protein) (plastohydroquinone:plastocyanin oxidoreductase iron-sulfur protein) (PRK13474)

PHATRDRAFT_46657 - ucria_soltucytochrome b6-f complex iron-sulfurchloroplast precursor (rieske iron-sulfur protein) (plastohydroquinone:plastocyanin oxidoreductase iron-sulfur protein) (PRK13474)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46657
PHATRDRAFT_47052

PHATRDRAFT_47052 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47052
PHATRDRAFT_47426 r 9 protein (DUF760)

PHATRDRAFT_47426 - r 9 protein (DUF760)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47426
PHATRDRAFT_49151 conserved protein (NADB_Rossmann superfamily)

PHATRDRAFT_49151 - conserved protein (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49151
PHATRDRAFT_49747

PHATRDRAFT_49747 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49747
PHATRDRAFT_49777 aldo keto reductase (Aldo_ket_red)

PHATRDRAFT_49777 - aldo keto reductase (Aldo_ket_red)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49777
PHATRDRAFT_49795 (Abhydrolase_5)

PHATRDRAFT_49795 - (Abhydrolase_5)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49795
PHATRDRAFT_50530

PHATRDRAFT_50530 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50530
PHATRDRAFT_54015 at4g37930 f20d10_50 (SHMT)

PHATRDRAFT_54015 - at4g37930 f20d10_50 (SHMT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54015
PHATRDRAFT_54731 thylakoid ascorbate peroxidase (ascorbate_peroxidase)

PHATRDRAFT_54731 - thylakoid ascorbate peroxidase (ascorbate_peroxidase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54731

PHATRDRAFT_7544 - mgc115642 protein (PhyH superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7544
GO ID Go Term p-value q-value Cluster
GO:0016114 terpenoid biosynthesis 0.00542673 1 Phatr_bicluster_0041
GO:0006811 ion transport 0.0295173 1 Phatr_bicluster_0041
GO:0007155 cell adhesion 0.0347981 1 Phatr_bicluster_0041
GO:0006812 cation transport 0.0710389 1 Phatr_bicluster_0041
GO:0009765 photosynthesis light harvesting 0.101113 1 Phatr_bicluster_0041
GO:0009058 biosynthesis 0.115816 1 Phatr_bicluster_0041
GO:0006118 electron transport 0.125163 1 Phatr_bicluster_0041
GO:0005975 carbohydrate metabolism 0.158622 1 Phatr_bicluster_0041
GO:0006457 protein folding 0.275986 1 Phatr_bicluster_0041
GO:0006810 transport 0.412691 1 Phatr_bicluster_0041
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