Phatr_bicluster_0186 Residual: 0.24
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_0186 0.24 Phaeodactylum tricornutum
Displaying 1 - 24 of 24
PHATRDRAFT_12121 atath13 (abc2 homolog 13) (AarF)

PHATRDRAFT_12121 - atath13 (abc2 homolog 13) (AarF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12121
PHATRDRAFT_12663 lactoylglutathione lyase (Glyoxalase_I)

PHATRDRAFT_12663 - lactoylglutathione lyase (Glyoxalase_I)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12663
PHATRDRAFT_14125 monogalactosyldiacylglycerol synthase (PLN02605)

PHATRDRAFT_14125 - monogalactosyldiacylglycerol synthase (PLN02605)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14125
PHATRDRAFT_14307 possible ferredoxin (2fe-2s)

PHATRDRAFT_14307 - possible ferredoxin (2fe-2s)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14307
PHATRDRAFT_26077 d-isomer specific 2-hydroxyacidnad-binding (2-Hacid_dh_1)

PHATRDRAFT_26077 - d-isomer specific 2-hydroxyacidnad-binding (2-Hacid_dh_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_26077
PHATRDRAFT_31525 aspartyl protease family protein (pepsin_retropepsin_like superfamily)

PHATRDRAFT_31525 - aspartyl protease family protein (pepsin_retropepsin_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31525
PHATRDRAFT_32733 peptidase u34 dipeptidase (Peptidase_C69 superfamily)

PHATRDRAFT_32733 - peptidase u34 dipeptidase (Peptidase_C69 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32733
PHATRDRAFT_32841 sel1 domain protein repeat-containing protein (COG0790)

PHATRDRAFT_32841 - sel1 domain protein repeat-containing protein (COG0790)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32841
PHATRDRAFT_34060 pentatricopeptiderepeat-containing protein

PHATRDRAFT_34060 - pentatricopeptiderepeat-containing protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34060
PHATRDRAFT_36844 tpr repeat

PHATRDRAFT_36844 - tpr repeat

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36844
PHATRDRAFT_38508 (DUF1995 superfamily)

PHATRDRAFT_38508 - (DUF1995 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38508
PHATRDRAFT_43140 arylsulfatase b (AslA)

PHATRDRAFT_42934 - arylsulfatase b (AslA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42934
PHATRDRAFT_43177 voltage-gated shaker-like k+subunit beta kcnab (Aldo_ket_red)

PHATRDRAFT_43140 - voltage-gated shaker-like k+subunit beta kcnab (Aldo_ket_red)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43140
PHATRDRAFT_44306 set and mynd domain containing protein

PHATRDRAFT_43177 - set and mynd domain containing protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43177
PHATRDRAFT_44775 protein phosphatase 2c (PP2Cc)

PHATRDRAFT_44306 - protein phosphatase 2c (PP2Cc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44306
PHATRDRAFT_45431 loc100036796 protein (G_glu_transpept superfamily)

PHATRDRAFT_44775 - loc100036796 protein (G_glu_transpept superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44775
PHATRDRAFT_45830 histone deacetylase superfamily (Arginase_HDAC superfamily)

PHATRDRAFT_45431 - histone deacetylase superfamily (Arginase_HDAC superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45431
PHATRDRAFT_46084 (NADB_Rossmann superfamily)

PHATRDRAFT_45830 - (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45830
PHATRDRAFT_46518

PHATRDRAFT_46084 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46084
PHATRDRAFT_47762

PHATRDRAFT_46518 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46518
PHATRDRAFT_48791 arystal structuremidohydrolase bh0493 from bacillus halodurans c-125 (UxaC superfamily)

PHATRDRAFT_47762 - arystal structuremidohydrolase bh0493 from bacillus halodurans c-125 (UxaC superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47762
PHATRDRAFT_49685

PHATRDRAFT_48791 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48791
PHATRDRAFT_54536 thiol-disulphide oxidoreductase dcc (DUF393)

PHATRDRAFT_49685 - thiol-disulphide oxidoreductase dcc (DUF393)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49685

PHATRDRAFT_54536 - glycosidefamily 30 (Glyco_hydro_30 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54536
GO ID Go Term p-value q-value Cluster
GO:0006564 L-serine biosynthesis 0.0234852 1 Phatr_bicluster_0186
GO:0015992 proton transport 0.0407661 1 Phatr_bicluster_0186
GO:0051341 regulation of oxidoreductase activity 0.0464638 1 Phatr_bicluster_0186
GO:0008152 metabolism 0.051036 1 Phatr_bicluster_0186
GO:0009058 biosynthesis 0.125669 1 Phatr_bicluster_0186
GO:0006508 proteolysis and peptidolysis 0.13969 1 Phatr_bicluster_0186
GO:0005975 carbohydrate metabolism 0.171749 1 Phatr_bicluster_0186
GO:0006468 protein amino acid phosphorylation 0.406444 1 Phatr_bicluster_0186
GO:0006118 electron transport 0.503223 1 Phatr_bicluster_0186
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