Phatr_bicluster_0093 Residual: 0.28
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_0093 0.28 Phaeodactylum tricornutum
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Displaying 1 - 24 of 24
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PHATRDRAFT_10779 branched-chain amino acid aminotransferase (PRK13357)

PHATRDRAFT_10779 - branched-chain amino acid aminotransferase (PRK13357)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10779
PHATRDRAFT_11189 translation elongation factor g (PRK00007)

PHATRDRAFT_11189 - translation elongation factor g (PRK00007)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11189
PHATRDRAFT_15211 glycine-rich protein 2 (CSP_CDS)

PHATRDRAFT_15211 - glycine-rich protein 2 (CSP_CDS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15211
PHATRDRAFT_20809 at5g66120 k2a18_20 (DHQS)

PHATRDRAFT_20809 - at5g66120 k2a18_20 (DHQS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20809
PHATRDRAFT_22909 ll-diaminopimelate aminotransferase (COG0436)

PHATRDRAFT_22909 - ll-diaminopimelate aminotransferase (COG0436)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22909
PHATRDRAFT_29885 vitamin b6 biosynthesis protein (pdxS)

PHATRDRAFT_29885 - vitamin b6 biosynthesis protein (pdxS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29885
PHATRDRAFT_32916 had superfamily (subfamily ia)tigr01548 (COG0637)

PHATRDRAFT_32916 - had superfamily (subfamily ia)tigr01548 (COG0637)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32916
PHATRDRAFT_37198

PHATRDRAFT_37198 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37198
PHATRDRAFT_41511 translation elongation factor p (PRK00529)

PHATRDRAFT_41511 - translation elongation factor p (PRK00529)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41511
PHATRDRAFT_43334

PHATRDRAFT_43334 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43334
PHATRDRAFT_43464 (DRIM superfamily)

PHATRDRAFT_43464 - (DRIM superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43464
PHATRDRAFT_43609

PHATRDRAFT_43609 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43609
PHATRDRAFT_44340

PHATRDRAFT_44340 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44340
PHATRDRAFT_45243 amine oxidase (COG1233)

PHATRDRAFT_45243 - amine oxidase (COG1233)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45243
PHATRDRAFT_45701 1 aminotransferase (AAT_I superfamily)

PHATRDRAFT_45701 - 1 aminotransferase (AAT_I superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45701
PHATRDRAFT_45964 atpcme (prenylcysteine methylesterase) prenylcysteine methylesterase (Aes)

PHATRDRAFT_45964 - atpcme (prenylcysteine methylesterase) prenylcysteine methylesterase (Aes)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45964
PHATRDRAFT_45965 dmt family transporter: drug metabolite (RhaT)

PHATRDRAFT_45965 - dmt family transporter: drug metabolite (RhaT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45965
PHATRDRAFT_46046

PHATRDRAFT_46046 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46046
PHATRDRAFT_46363 craniofacial development protein 1 (BCNT)

PHATRDRAFT_46363 - craniofacial development protein 1 (BCNT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46363
PHATRDRAFT_46612 mitochondrial carrier protein

PHATRDRAFT_46612 - mitochondrial carrier protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46612
PHATRDRAFT_48044

PHATRDRAFT_48044 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48044
PHATRDRAFT_50738 triosephosphate isomerase (TIM)

PHATRDRAFT_50738 - triosephosphate isomerase (TIM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50738
PHATRDRAFT_6277 lysine decarboxylase (DNA_processg_A superfamily)

PHATRDRAFT_6277 - lysine decarboxylase (DNA_processg_A superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6277
PHATRDRAFT_8363 mitochondrial import inner membrane translocase subunit tim10 (zf-Tim10_DDP)

PHATRDRAFT_8363 - mitochondrial import inner membrane translocase subunit tim10 (zf-Tim10_DDP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8363
GO ID Go Term p-value q-value Cluster
GO:0006414 translational elongation 0.00164601 1 Phatr_bicluster_0093
GO:0051339 regulation of lyase activity 0.00444554 1 Phatr_bicluster_0093
GO:0016117 carotenoid biosynthesis 0.0132807 1 Phatr_bicluster_0093
GO:0009081 branched chain family amino acid metabolism 0.0132807 1 Phatr_bicluster_0093
GO:0045039 mitochondrial inner membrane protein import 0.0132807 1 Phatr_bicluster_0093
GO:0006626 protein-mitochondrial targeting 0.0132807 1 Phatr_bicluster_0093
GO:0009073 aromatic amino acid family biosynthesis 0.0220418 1 Phatr_bicluster_0093
GO:0000105 histidine biosynthesis 0.0393439 1 Phatr_bicluster_0093
GO:0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system 0.0436241 1 Phatr_bicluster_0093
GO:0008152 metabolism 0.137805 1 Phatr_bicluster_0093
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