Phatr_bicluster_0175 Residual: 0.30
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_0175 0.30 Phaeodactylum tricornutum
Displaying 1 - 22 of 22
PHATRDRAFT_17683 synaptobrevin-like protein (Synaptobrevin)

PHATRDRAFT_17683 - synaptobrevin-like protein (Synaptobrevin)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17683
PHATRDRAFT_1859 protein kinase domain containing protein (S_TKc)

PHATRDRAFT_1859 - protein kinase domain containing protein (S_TKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_1859
PHATRDRAFT_31741 (Ycf34 superfamily)

PHATRDRAFT_31741 - (Ycf34 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31741
PHATRDRAFT_35165

PHATRDRAFT_35165 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35165
PHATRDRAFT_35252 capping protein alpha cg10540-pa (F-actin_cap_A superfamily)

PHATRDRAFT_35252 - capping protein alpha cg10540-pa (F-actin_cap_A superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35252
PHATRDRAFT_43025 exonuclease familyexpressed (REX1_like)

PHATRDRAFT_42642 - exonuclease familyexpressed (REX1_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42642
PHATRDRAFT_43234 esterase-like protein (Abhydrolase_6)

PHATRDRAFT_43025 - esterase-like protein (Abhydrolase_6)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43025
PHATRDRAFT_43360 low-co2-inducible protein

PHATRDRAFT_43234 - low-co2-inducible protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43234
PHATRDRAFT_44359 (DUF2061 superfamily)

PHATRDRAFT_43360 - (DUF2061 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43360
PHATRDRAFT_45048 (PrsW-protease)

PHATRDRAFT_44359 - (PrsW-protease)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44359
PHATRDRAFT_45223

PHATRDRAFT_45048 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45048
PHATRDRAFT_45404 transmembrane protein 30a (CDC50)

PHATRDRAFT_45223 - transmembrane protein 30a (CDC50)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45223
PHATRDRAFT_45939 abc transporter (atp-binding protein) (ABC_ATPase superfamily)

PHATRDRAFT_45404 - abc transporter (atp-binding protein) (ABC_ATPase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45404
PHATRDRAFT_46044

PHATRDRAFT_45939 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45939
PHATRDRAFT_46086

PHATRDRAFT_46044 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46044
PHATRDRAFT_46138 temporarily assigned gene name family member (tag-167) (Uup)

PHATRDRAFT_46086 - temporarily assigned gene name family member (tag-167) (Uup)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46086
PHATRDRAFT_47966

PHATRDRAFT_46138 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46138
PHATRDRAFT_48211 glycoprotein endo-alpha-- (GH99_GH71_like_1)

PHATRDRAFT_47966 - glycoprotein endo-alpha-- (GH99_GH71_like_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47966
PHATRDRAFT_50123

PHATRDRAFT_48211 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48211
PHATRDRAFT_53964 kef-type k+ transportnad-binding component (Ion_trans)

PHATRDRAFT_50123 - kef-type k+ transportnad-binding component (Ion_trans)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50123
PHATRDRAFT_9143 testis secretory pathway calcium transporting atpase (ATPase-IIA2_Ca)

PHATRDRAFT_53964 - testis secretory pathway calcium transporting atpase (ATPase-IIA2_Ca)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_53964

PHATRDRAFT_9143 - rna-binding protein puf1 (Pumilio superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9143
GO ID Go Term p-value q-value Cluster
GO:0030036 actin cytoskeleton organization and biogenesis 0.00394818 1 Phatr_bicluster_0175
GO:0016071 mRNA metabolism 0.00788271 1 Phatr_bicluster_0175
GO:0006811 ion transport 0.0215467 1 Phatr_bicluster_0175
GO:0016192 vesicle-mediated transport 0.0254203 1 Phatr_bicluster_0175
GO:0006813 potassium ion transport 0.0388725 1 Phatr_bicluster_0175
GO:0006812 cation transport 0.052162 1 Phatr_bicluster_0175
GO:0009058 biosynthesis 0.0855993 1 Phatr_bicluster_0175
GO:0006468 protein amino acid phosphorylation 0.2936 1 Phatr_bicluster_0175
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