Phatr_bicluster_0229 Residual: 0.31
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_0229 0.31 Phaeodactylum tricornutum
Displaying 1 - 25 of 25
PHATRDRAFT_13331 peptidase s41a (prc)

PHATRDRAFT_13331 - peptidase s41a (prc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13331
PHATRDRAFT_14064 protein kinase c inhibitor (PKCI_related)

PHATRDRAFT_14064 - protein kinase c inhibitor (PKCI_related)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14064
PHATRDRAFT_17401 dihydrolipoamide s-acetyltransferase (e2 component of pyruvate dehydrogenase complex)isoform cra_a (PDHac_trf_mito)

PHATRDRAFT_17401 - dihydrolipoamide s-acetyltransferase (e2 component of pyruvate dehydrogenase complex)isoform cra_a (PDHac_trf_mito)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17401
PHATRDRAFT_20183 at5g50850 k16e14_1 (PLN02683)

PHATRDRAFT_20183 - at5g50850 k16e14_1 (PLN02683)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20183
PHATRDRAFT_21122 beta-tubulin (PLN00220)

PHATRDRAFT_21122 - beta-tubulin (PLN00220)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21122
PHATRDRAFT_28730 peptidyl-prolyl cis-trans isomerase (PTZ00356)

PHATRDRAFT_28730 - peptidyl-prolyl cis-trans isomerase (PTZ00356)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28730
PHATRDRAFT_31620

PHATRDRAFT_31620 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31620
PHATRDRAFT_34590

PHATRDRAFT_34590 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34590
PHATRDRAFT_35063 snrnp protein (Sm_B)

PHATRDRAFT_35063 - snrnp protein (Sm_B)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35063
PHATRDRAFT_35580 prune homolog (PPX1)

PHATRDRAFT_35580 - prune homolog (PPX1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35580
PHATRDRAFT_39252 ubiquitin family protein (UBL)

PHATRDRAFT_39252 - ubiquitin family protein (UBL)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39252
PHATRDRAFT_40761

PHATRDRAFT_40761 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40761
PHATRDRAFT_42545 mg2+ transporter (MgtE)

PHATRDRAFT_42545 - mg2+ transporter (MgtE)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42545
PHATRDRAFT_44204 cog2940: proteins containing set domain (SET)

PHATRDRAFT_44204 - cog2940: proteins containing set domain (SET)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44204
PHATRDRAFT_44425 asparagine-linked glycosylation 12 homolog (alpha--mannosyltransferase) (Glyco_transf_22 superfamily)

PHATRDRAFT_44425 - asparagine-linked glycosylation 12 homolog (alpha--mannosyltransferase) (Glyco_transf_22 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44425
PHATRDRAFT_44639 abc(binding protein) family transporter: phosphate (Phosphonate-bd superfamily)

PHATRDRAFT_44639 - abc(binding protein) family transporter: phosphate (Phosphonate-bd superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44639
PHATRDRAFT_45249

PHATRDRAFT_45249 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45249
PHATRDRAFT_46613 xanthine phosphoribosyltransferase (PRTases_typeI)

PHATRDRAFT_46613 - xanthine phosphoribosyltransferase (PRTases_typeI)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46613
PHATRDRAFT_46710 proteophosphoglycan 5

PHATRDRAFT_46710 - proteophosphoglycan 5

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46710
PHATRDRAFT_47852

PHATRDRAFT_47852 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47852
PHATRDRAFT_49630 (EMP24_GP25L)

PHATRDRAFT_49630 - (EMP24_GP25L)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49630
PHATRDRAFT_50148 protein phosphatase 2c (PP2Cc)

PHATRDRAFT_50148 - protein phosphatase 2c (PP2Cc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50148
PHATRDRAFT_54086 atp synthase beta subunit (PRK09280)

PHATRDRAFT_54086 - atp synthase beta subunit (PRK09280)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54086
PHATRDRAFT_54730 beta-adaptin-like protein a (Adaptin_N)

PHATRDRAFT_54730 - beta-adaptin-like protein a (Adaptin_N)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54730
PHATRDRAFT_9348 dcmp deaminase isoform 3 (deoxycytidylate_deaminase)

PHATRDRAFT_9348 - dcmp deaminase isoform 3 (deoxycytidylate_deaminase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9348
GO ID Go Term p-value q-value Cluster
GO:0043101 purine salvage 0.00271672 1 Phatr_bicluster_0229
GO:0046110 xanthine metabolism 0.00271672 1 Phatr_bicluster_0229
GO:0051258 protein polymerization 0.0135166 1 Phatr_bicluster_0229
GO:0009116 nucleoside metabolism 0.0242101 1 Phatr_bicluster_0229
GO:0006397 mRNA processing 0.0608128 1 Phatr_bicluster_0229
GO:0006812 cation transport 0.0710389 1 Phatr_bicluster_0229
GO:0007018 microtubule-based movement 0.078642 1 Phatr_bicluster_0229
GO:0006464 protein modification 0.158622 1 Phatr_bicluster_0229
GO:0006810 transport 0.412691 1 Phatr_bicluster_0229
GO:0006508 proteolysis and peptidolysis 0.465714 1 Phatr_bicluster_0229
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