Phatr_bicluster_0107 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_0107 0.29 Phaeodactylum tricornutum
Displaying 1 - 28 of 28
PHATRDRAFT_10830 ferredoxin-dependent bilin reductase (Fe_bilin_red superfamily)

PHATRDRAFT_10830 - ferredoxin-dependent bilin reductase (Fe_bilin_red superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10830
PHATRDRAFT_12420 amp-dependent synthetase and ligase (FAA1)

PHATRDRAFT_12420 - amp-dependent synthetase and ligase (FAA1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12420
PHATRDRAFT_16545 methionyl-trna synthetase (tRNA_bind_EMAP-II_like)

PHATRDRAFT_16545 - methionyl-trna synthetase (tRNA_bind_EMAP-II_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16545
PHATRDRAFT_18893 quinone oxidoreductase (QOR2)

PHATRDRAFT_18893 - quinone oxidoreductase (QOR2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18893
PHATRDRAFT_23639 usp_cucmeudp-sugar pyrophospharylase (udp-galactose glucose pyrophosphorylase) (PLN02830)

PHATRDRAFT_23639 - usp_cucmeudp-sugar pyrophospharylase (udp-galactose glucose pyrophosphorylase) (PLN02830)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23639
PHATRDRAFT_29157 phosphoglycerate kinase (Phosphoglycerate_kinase)

PHATRDRAFT_29157 - phosphoglycerate kinase (Phosphoglycerate_kinase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29157
PHATRDRAFT_30113 lipoamide dehydrogenase (PRK06416)

PHATRDRAFT_30113 - lipoamide dehydrogenase (PRK06416)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30113
PHATRDRAFT_31409 thioesterase family protein (HopJ superfamily)

PHATRDRAFT_31409 - thioesterase family protein (HopJ superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31409
PHATRDRAFT_33530 mpbq msbq transferase cyanobacterial type (AdoMet_MTases)

PHATRDRAFT_33530 - mpbq msbq transferase cyanobacterial type (AdoMet_MTases)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33530
PHATRDRAFT_33543 hydrogenase component

PHATRDRAFT_33543 - hydrogenase component

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33543
PHATRDRAFT_37652 malonyl-:acp transacylase (PLN02752)

PHATRDRAFT_37652 - malonyl-:acp transacylase (PLN02752)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37652
PHATRDRAFT_38175

PHATRDRAFT_38175 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38175
PHATRDRAFT_38769

PHATRDRAFT_38769 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38769
PHATRDRAFT_40877

PHATRDRAFT_40877 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40877
PHATRDRAFT_41856 plastid transketolase (PLN02790)

PHATRDRAFT_41856 - plastid transketolase (PLN02790)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41856
PHATRDRAFT_41878 phytoene synthase (Trans_IPPS_HH)

PHATRDRAFT_41878 - phytoene synthase (Trans_IPPS_HH)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41878
PHATRDRAFT_43169 mrna binding protein precursor (PLN00016)

PHATRDRAFT_43169 - mrna binding protein precursor (PLN00016)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43169
PHATRDRAFT_43831 at1g26760 t24p13_13 (GH43_62_32_68 superfamily)

PHATRDRAFT_43831 - at1g26760 t24p13_13 (GH43_62_32_68 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43831
PHATRDRAFT_44335 at1g06690 f4h5_17 (Aldo_ket_red superfamily)

PHATRDRAFT_44335 - at1g06690 f4h5_17 (Aldo_ket_red superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44335
PHATRDRAFT_44486 peptidase m50 (S2P-M50_like_2)

PHATRDRAFT_44486 - peptidase m50 (S2P-M50_like_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44486
PHATRDRAFT_44651 dimethylmenaquinone methyltransferase (Methyltransf_6 superfamily)

PHATRDRAFT_44651 - dimethylmenaquinone methyltransferase (Methyltransf_6 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44651
PHATRDRAFT_45424

PHATRDRAFT_45424 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45424
PHATRDRAFT_45846 violaxanthin de-epoxidasechloroplast (VDE superfamily)

PHATRDRAFT_45846 - violaxanthin de-epoxidasechloroplast (VDE superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45846
PHATRDRAFT_46395 (DUF1118 superfamily)

PHATRDRAFT_46395 - (DUF1118 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46395
PHATRDRAFT_51703 violaxanthin de-epoxidase (VDE superfamily)

PHATRDRAFT_51703 - violaxanthin de-epoxidase (VDE superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51703
PHATRDRAFT_53935 ribulose-phosphate 3-epimerase (RPE)

PHATRDRAFT_53935 - ribulose-phosphate 3-epimerase (RPE)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_53935
PHATRDRAFT_54082 malic enzyme (PLN03129)

PHATRDRAFT_54082 - malic enzyme (PLN03129)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54082
PHATRDRAFT_9312 sigma-70 factor (Sig70-cyanoRpoD)

PHATRDRAFT_9312 - sigma-70 factor (Sig70-cyanoRpoD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9312
GO ID Go Term p-value q-value Cluster
GO:0010024 phytochromobilin biosynthesis 0.00886694 1 Phatr_bicluster_0107
GO:0006352 transcription initiation 0.0350372 1 Phatr_bicluster_0107
GO:0006633 fatty acid biosynthesis 0.0379055 1 Phatr_bicluster_0107
GO:0006306 DNA methylation 0.0577662 1 Phatr_bicluster_0107
GO:0006096 glycolysis 0.0990654 1 Phatr_bicluster_0107
GO:0009058 biosynthesis 0.125669 1 Phatr_bicluster_0107
GO:0006508 proteolysis and peptidolysis 0.13969 1 Phatr_bicluster_0107
GO:0008152 metabolism 0.21493 1 Phatr_bicluster_0107
GO:0006355 regulation of transcription, DNA-dependent 0.487367 1 Phatr_bicluster_0107
GO:0006118 electron transport 0.503223 1 Phatr_bicluster_0107
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