Phatr_bicluster_0218 Residual: 0.32
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_0218 0.32 Phaeodactylum tricornutum
Displaying 1 - 21 of 21
PHATRDRAFT_13894 dihydrolipoamide s-acetyltransferase precursor (PDHac_trf_mito)

PHATRDRAFT_13894 - dihydrolipoamide s-acetyltransferase precursor (PDHac_trf_mito)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13894
PHATRDRAFT_29016 2-oxoglutarate dehydrogenase e1 oxoglutarate alpha-ketoglutaric (sucA)

PHATRDRAFT_29016 - 2-oxoglutarate dehydrogenase e1 oxoglutarate alpha-ketoglutaric (sucA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29016
PHATRDRAFT_33218 (ArsB_NhaD_permease superfamily)

PHATRDRAFT_33218 - (ArsB_NhaD_permease superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33218
PHATRDRAFT_36398 agmatine deiminase (PLN02690)

PHATRDRAFT_36398 - agmatine deiminase (PLN02690)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36398
PHATRDRAFT_38362 2-isopropylmalate synthase (PRK12344)

PHATRDRAFT_38362 - 2-isopropylmalate synthase (PRK12344)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38362
PHATRDRAFT_39438 loc779553 protein

PHATRDRAFT_39438 - loc779553 protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39438
PHATRDRAFT_43090 methyltransferase type 11

PHATRDRAFT_43090 - methyltransferase type 11

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43090
PHATRDRAFT_47491

PHATRDRAFT_47491 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47491
PHATRDRAFT_47510 aldo keto reductase-like protein (Aldo_ket_red)

PHATRDRAFT_47510 - aldo keto reductase-like protein (Aldo_ket_red)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47510
PHATRDRAFT_47517 gyltl1b protein (Glyco_transf_49 superfamily)

PHATRDRAFT_47517 - gyltl1b protein (Glyco_transf_49 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47517
PHATRDRAFT_47703

PHATRDRAFT_47703 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47703
PHATRDRAFT_47932

PHATRDRAFT_47932 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47932
PHATRDRAFT_48603 amineflavin-containing superfamily (Amino_oxidase)

PHATRDRAFT_48603 - amineflavin-containing superfamily (Amino_oxidase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48603
PHATRDRAFT_48809

PHATRDRAFT_48809 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48809
PHATRDRAFT_48955 (Cation_efflux superfamily)

PHATRDRAFT_48955 - (Cation_efflux superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48955
PHATRDRAFT_48979

PHATRDRAFT_48979 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48979
PHATRDRAFT_49115 (AlgLyase superfamily)

PHATRDRAFT_49115 - (AlgLyase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49115
PHATRDRAFT_49604

PHATRDRAFT_49604 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49604
PHATRDRAFT_49734 protein familywith a coiled coil-4 domain (Methyltransf_22)

PHATRDRAFT_49734 - protein familywith a coiled coil-4 domain (Methyltransf_22)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49734
PHATRDRAFT_50434

PHATRDRAFT_50434 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50434
PHATRDRAFT_605 mitochondrial helicase twinkle (RecA-like_NTPases superfamily)

PHATRDRAFT_605 - mitochondrial helicase twinkle (RecA-like_NTPases superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_605
GO ID Go Term p-value q-value Cluster
GO:0019752 carboxylic acid metabolism 0.00444115 1 Phatr_bicluster_0218
GO:0051341 regulation of oxidoreductase activity 0.0350414 1 Phatr_bicluster_0218
GO:0006812 cation transport 0.058495 1 Phatr_bicluster_0218
GO:0015031 protein transport 0.066897 1 Phatr_bicluster_0218
GO:0008152 metabolism 0.134877 1 Phatr_bicluster_0218
GO:0006412 protein biosynthesis 0.306181 1 Phatr_bicluster_0218
GO:0006508 proteolysis and peptidolysis 0.401138 1 Phatr_bicluster_0218
GO:0006118 electron transport 0.408154 1 Phatr_bicluster_0218
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