Phatr_bicluster_0223 Residual: 0.26
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_0223 0.26 Phaeodactylum tricornutum
Displaying 1 - 27 of 27
PHATRDRAFT_12668 ribulose-phosphate 3-epimerase (RPE)

PHATRDRAFT_12668 - ribulose-phosphate 3-epimerase (RPE)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12668
PHATRDRAFT_12881 carbohydrate kinase fggy (NBD_sugar-kinase_HSP70_actin superfamily)

PHATRDRAFT_12881 - carbohydrate kinase fggy (NBD_sugar-kinase_HSP70_actin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12881
PHATRDRAFT_20192 d-lactate dehydrogenase (GlcD)

PHATRDRAFT_20192 - d-lactate dehydrogenase (GlcD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20192
PHATRDRAFT_2793 chloroplast fructose--bisphosphatase (FBPase)

PHATRDRAFT_2793 - chloroplast fructose--bisphosphatase (FBPase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_2793
PHATRDRAFT_37212 sac3 ganp domain protein (SAC3_GANP)

PHATRDRAFT_37212 - sac3 ganp domain protein (SAC3_GANP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37212
PHATRDRAFT_37749 protein n-methyltransferase

PHATRDRAFT_37749 - protein n-methyltransferase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37749
PHATRDRAFT_38303

PHATRDRAFT_38303 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38303
PHATRDRAFT_42595 phd finger protein 8 (JmjC superfamily)

PHATRDRAFT_42595 - phd finger protein 8 (JmjC superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42595
PHATRDRAFT_42694 (DUF4205 superfamily)

PHATRDRAFT_42694 - (DUF4205 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42694
PHATRDRAFT_42834 kelch motif family protein (BTB)

PHATRDRAFT_42834 - kelch motif family protein (BTB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42834
PHATRDRAFT_43063 (DUF3082 superfamily)

PHATRDRAFT_43063 - (DUF3082 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43063
PHATRDRAFT_43070

PHATRDRAFT_43070 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43070
PHATRDRAFT_43165 protein tyrosinemitochondrial 1 (CDC14)

PHATRDRAFT_43165 - protein tyrosinemitochondrial 1 (CDC14)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43165
PHATRDRAFT_43213

PHATRDRAFT_43213 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43213
PHATRDRAFT_43496

PHATRDRAFT_43496 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43496
PHATRDRAFT_43727 (DUF599 superfamily)

PHATRDRAFT_43727 - (DUF599 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43727
PHATRDRAFT_43747 zincmynd-type containing 15 isoform 1

PHATRDRAFT_43747 - zincmynd-type containing 15 isoform 1

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43747
PHATRDRAFT_44398 abc transporter g family protein (ABC_ATPase)

PHATRDRAFT_44398 - abc transporter g family protein (ABC_ATPase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44398
PHATRDRAFT_44973

PHATRDRAFT_44973 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44973
PHATRDRAFT_45364 wd-repeat protein (WD40 superfamily)

PHATRDRAFT_45364 - wd-repeat protein (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45364
PHATRDRAFT_45821

PHATRDRAFT_45821 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45821
PHATRDRAFT_46527

PHATRDRAFT_46527 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46527
PHATRDRAFT_46737 vad1 (vascular associated death1)

PHATRDRAFT_46737 - vad1 (vascular associated death1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46737
PHATRDRAFT_47546

PHATRDRAFT_47546 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47546
PHATRDRAFT_49206 (NCA2 superfamily)

PHATRDRAFT_49206 - (NCA2 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49206
PHATRDRAFT_50961 mitochondrial pyruvate dehydrogenase kinase (BCDHK_Adom3)

PHATRDRAFT_50961 - mitochondrial pyruvate dehydrogenase kinase (BCDHK_Adom3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50961
PHATRDRAFT_6635 member ras oncogene family like (Ras_like_GTPase superfamily)

PHATRDRAFT_6635 - member ras oncogene family like (Ras_like_GTPase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6635
GO ID Go Term p-value q-value Cluster
GO:0005975 carbohydrate metabolism 0.000282174 0.64646 Phatr_bicluster_0223
GO:0016310 phosphorylation 0.0307218 1 Phatr_bicluster_0223
GO:0006470 protein amino acid dephosphorylation 0.0414888 1 Phatr_bicluster_0223
GO:0007264 small GTPase mediated signal transduction 0.0457657 1 Phatr_bicluster_0223
GO:0015031 protein transport 0.066897 1 Phatr_bicluster_0223
GO:0006468 protein amino acid phosphorylation 0.323667 1 Phatr_bicluster_0223
GO:0006118 electron transport 0.408154 1 Phatr_bicluster_0223
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