Phatr_bicluster_0173 Residual: 0.27
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_0173 0.27 Phaeodactylum tricornutum
Displaying 1 - 25 of 25
PHATRDRAFT_12262 peroxisomal membrane protein (Mpv17_PMP22)

PHATRDRAFT_12262 - peroxisomal membrane protein (Mpv17_PMP22)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12262
PHATRDRAFT_13358 petc (photosynthetic electron transfer c) (PRK13474)

PHATRDRAFT_13358 - petc (photosynthetic electron transfer c) (PRK13474)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13358
PHATRDRAFT_13706 long chain (FMN_red superfamily)

PHATRDRAFT_13706 - long chain (FMN_red superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13706
PHATRDRAFT_16421 (DUF791 superfamily)

PHATRDRAFT_16421 - (DUF791 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16421
PHATRDRAFT_32071 (DUF1517 superfamily)

PHATRDRAFT_32071 - (DUF1517 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32071
PHATRDRAFT_34425 bass family transporter: sodium ion bile acid (SBF superfamily)

PHATRDRAFT_34425 - bass family transporter: sodium ion bile acid (SBF superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34425
PHATRDRAFT_37719 acetamidase formamidase (FmdA_AmdA superfamily)

PHATRDRAFT_37719 - acetamidase formamidase (FmdA_AmdA superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37719
PHATRDRAFT_41845 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (lytB_ispH)

PHATRDRAFT_41845 - 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (lytB_ispH)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41845
PHATRDRAFT_42494 large low complexity coiled coil protien with large repeat region

PHATRDRAFT_42494 - large low complexity coiled coil protien with large repeat region

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42494
PHATRDRAFT_42786

PHATRDRAFT_42786 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42786
PHATRDRAFT_42788 (AdoMet_MTases superfamily)

PHATRDRAFT_42788 - (AdoMet_MTases superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42788
PHATRDRAFT_43232 low-co2 inducible protein lcic

PHATRDRAFT_43232 - low-co2 inducible protein lcic

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43232
PHATRDRAFT_43593 lipase-like protein (Lipase_3)

PHATRDRAFT_43593 - lipase-like protein (Lipase_3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43593
PHATRDRAFT_44535 (Ion_trans)

PHATRDRAFT_44535 - (Ion_trans)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44535
PHATRDRAFT_45019

PHATRDRAFT_45019 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45019
PHATRDRAFT_45062

PHATRDRAFT_45062 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45062
PHATRDRAFT_45150

PHATRDRAFT_45150 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45150
PHATRDRAFT_46433

PHATRDRAFT_46433 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46433
PHATRDRAFT_47417 dna topoisomerase family protein (TopA)

PHATRDRAFT_47417 - dna topoisomerase family protein (TopA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47417
PHATRDRAFT_48694 homoserine dehydrogenase (PRK06349)

PHATRDRAFT_48694 - homoserine dehydrogenase (PRK06349)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48694
PHATRDRAFT_54621 loc407614 protein (GT1_ALG11_like)

PHATRDRAFT_54621 - loc407614 protein (GT1_ALG11_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54621
PHATRDRAFT_5928 zeaxanthin epoxidase (NAD_binding_8 superfamily)

PHATRDRAFT_5928 - zeaxanthin epoxidase (NAD_binding_8 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5928
PHATRDRAFT_9046 rieske (2fe-2s) region protein (Rieske_2)

PHATRDRAFT_9046 - rieske (2fe-2s) region protein (Rieske_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9046
PHATRDRAFT_9223 leu phe-trna protein (Leu_Phe_trans superfamily)

PHATRDRAFT_9223 - leu phe-trna protein (Leu_Phe_trans superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9223
PHATRDRAFT_9799 light-harvesting complex i polypeptide (Chloroa_b-bind)

PHATRDRAFT_9799 - light-harvesting complex i polypeptide (Chloroa_b-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9799
GO ID Go Term p-value q-value Cluster
GO:0019288 mevalonate-independent isopentenyl diphosphate biosynthesis 0.00444554 1 Phatr_bicluster_0173
GO:0006118 electron transport 0.0162729 1 Phatr_bicluster_0173
GO:0006304 DNA modification 0.0220418 1 Phatr_bicluster_0173
GO:0006268 DNA unwinding 0.0220418 1 Phatr_bicluster_0173
GO:0008652 amino acid biosynthesis 0.0307293 1 Phatr_bicluster_0173
GO:0006265 DNA topological change 0.0393439 1 Phatr_bicluster_0173
GO:0006814 sodium ion transport 0.0478862 1 Phatr_bicluster_0173
GO:0030163 protein catabolism 0.0478862 1 Phatr_bicluster_0173
GO:0006811 ion transport 0.0478862 1 Phatr_bicluster_0173
GO:0006629 lipid metabolism 0.0772227 1 Phatr_bicluster_0173
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