Phatr_bicluster_0157 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_0157 0.27 Phaeodactylum tricornutum
Displaying 1 - 23 of 23
PHATRDRAFT_11368 pdk1 (3-phosphoinositide-dependent protein kinase 1) kinase (PKc_like superfamily)

PHATRDRAFT_11368 - pdk1 (3-phosphoinositide-dependent protein kinase 1) kinase (PKc_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11368
PHATRDRAFT_1862 ammonium transporter-like protein amt1 (Ammonium_transp superfamily)

PHATRDRAFT_1862 - ammonium transporter-like protein amt1 (Ammonium_transp superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_1862
PHATRDRAFT_34230

PHATRDRAFT_34230 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34230
PHATRDRAFT_34586

PHATRDRAFT_34586 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34586
PHATRDRAFT_35603

PHATRDRAFT_35603 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35603
PHATRDRAFT_37052 hsf-type dna-binding domain containing protein (HSF_DNA-bind superfamily)

PHATRDRAFT_37052 - hsf-type dna-binding domain containing protein (HSF_DNA-bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37052
PHATRDRAFT_37053 kismet cg3696-isoform a

PHATRDRAFT_37053 - kismet cg3696-isoform a

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37053
PHATRDRAFT_43297

PHATRDRAFT_43297 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43297
PHATRDRAFT_43631 gene family 7 (TPM)

PHATRDRAFT_43631 - gene family 7 (TPM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43631
PHATRDRAFT_45111 yfjf_bacsu upf0060 membrane protein yfjf (PRK02237)

PHATRDRAFT_45111 - yfjf_bacsu upf0060 membrane protein yfjf (PRK02237)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45111
PHATRDRAFT_45163 (Glyco_tranf_2_4)

PHATRDRAFT_45163 - (Glyco_tranf_2_4)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45163
PHATRDRAFT_46007 (SNF2_N)

PHATRDRAFT_46007 - (SNF2_N)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46007
PHATRDRAFT_46851

PHATRDRAFT_46851 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46851
PHATRDRAFT_46884 transducin family protein wd-40 repeat family protein

PHATRDRAFT_46884 - transducin family protein wd-40 repeat family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46884
PHATRDRAFT_47038

PHATRDRAFT_47038 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47038
PHATRDRAFT_47146

PHATRDRAFT_47146 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47146
PHATRDRAFT_47877

PHATRDRAFT_47877 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47877
PHATRDRAFT_4918 phosphatidylinositol 3- and 4-kinase family protein ubiquitin family protein (PI3Kc_like superfamily)

PHATRDRAFT_4918 - phosphatidylinositol 3- and 4-kinase family protein ubiquitin family protein (PI3Kc_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_4918
PHATRDRAFT_51825 member ras oncogene family (Ras_like_GTPase superfamily)

PHATRDRAFT_51825 - member ras oncogene family (Ras_like_GTPase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51825
PHATRDRAFT_54119 (AMN1 superfamily)

PHATRDRAFT_54119 - (AMN1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54119
PHATRDRAFT_5526 atg1_debha serine threonine-protein kinase atg1 (autophagy-related protein 1) (S_TKc)

PHATRDRAFT_5526 - atg1_debha serine threonine-protein kinase atg1 (autophagy-related protein 1) (S_TKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5526
PHATRDRAFT_6927 proline betainemfs family protein

PHATRDRAFT_6927 - proline betainemfs family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6927
PHATRDRAFT_8239 chaperone protein dnaj (DnaJ)

PHATRDRAFT_8239 - chaperone protein dnaj (DnaJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8239
GO ID Go Term p-value q-value Cluster
GO:0006468 protein amino acid phosphorylation 0.0424353 1 Phatr_bicluster_0157
GO:0006810 transport 0.0513747 1 Phatr_bicluster_0157
GO:0015986 ATP synthesis coupled proton transport 0.0708679 1 Phatr_bicluster_0157
GO:0016567 protein ubiquitination 0.13382 1 Phatr_bicluster_0157
GO:0006457 protein folding 0.209255 1 Phatr_bicluster_0157
GO:0006355 regulation of transcription, DNA-dependent 0.359328 1 Phatr_bicluster_0157
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