Phatr_bicluster_0067 Residual: 0.34
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_0067 0.34 Phaeodactylum tricornutum
Displaying 1 - 20 of 20
PHATRDRAFT_10865 protein kinase a catalytic subunit isoform 1 (PKc_like superfamily)

PHATRDRAFT_10865 - protein kinase a catalytic subunit isoform 1 (PKc_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10865
PHATRDRAFT_13001 nadph:protochlorophyllide oxidoreductase a (NADB_Rossmann superfamily)

PHATRDRAFT_13001 - nadph:protochlorophyllide oxidoreductase a (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13001
PHATRDRAFT_13125 possible l-asparaginase ii (rSAM_SeCys)

PHATRDRAFT_13125 - possible l-asparaginase ii (rSAM_SeCys)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13125
PHATRDRAFT_14453 mitogen-activated protein kinase (STKc_MAPK)

PHATRDRAFT_14453 - mitogen-activated protein kinase (STKc_MAPK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14453
PHATRDRAFT_15016 transcription factor c-myb (SANT)

PHATRDRAFT_15016 - transcription factor c-myb (SANT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15016
PHATRDRAFT_18549 (Raptor_N)

PHATRDRAFT_18549 - (Raptor_N)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18549
PHATRDRAFT_2819 serine protease-like protein (XendoU)

PHATRDRAFT_2819 - serine protease-like protein (XendoU)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_2819
PHATRDRAFT_29861 ribosomal protein l11 methyltransferase (PrmA)

PHATRDRAFT_29861 - ribosomal protein l11 methyltransferase (PrmA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29861
PHATRDRAFT_30394 receptor mediated endocytosis family member (rme-1) (EHD)

PHATRDRAFT_30394 - receptor mediated endocytosis family member (rme-1) (EHD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30394
PHATRDRAFT_3311 cysteine synthase (CBS_like)

PHATRDRAFT_3311 - cysteine synthase (CBS_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3311
PHATRDRAFT_35250 tetracycline antiporter protein (MFS_1)

PHATRDRAFT_35250 - tetracycline antiporter protein (MFS_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35250
PHATRDRAFT_38085 thiamin biosynthesis protein (PLN02444)

PHATRDRAFT_38085 - thiamin biosynthesis protein (PLN02444)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38085
PHATRDRAFT_43302

PHATRDRAFT_43302 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43302
PHATRDRAFT_44690 riboflavin biosynthesis protein:riboflavin-specific deaminase-like (RibD)

PHATRDRAFT_44690 - riboflavin biosynthesis protein:riboflavin-specific deaminase-like (RibD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44690
PHATRDRAFT_49310 (NCA2 superfamily)

PHATRDRAFT_49310 - (NCA2 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49310
PHATRDRAFT_49924 flavonol synthase dioxygenase (PcbC)

PHATRDRAFT_49924 - flavonol synthase dioxygenase (PcbC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49924
PHATRDRAFT_51516 rh antigen (Ammonium_transp superfamily)

PHATRDRAFT_51516 - rh antigen (Ammonium_transp superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51516
PHATRDRAFT_54751 dynamin 1-like (DLP_1)

PHATRDRAFT_54751 - dynamin 1-like (DLP_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54751
PHATRDRAFT_54873 (Peptidase_C14)

PHATRDRAFT_54873 - (Peptidase_C14)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54873
PHATRDRAFT_859 outer mitochondrial carnitineminor ethanol-inducible enzyme involved in transport of activated acyl groups from the cytoplasm into the mitochondrial matrix phosphorylated (Carn_acyltransf superfamily)

PHATRDRAFT_859 - outer mitochondrial carnitineminor ethanol-inducible enzyme involved in transport of activated acyl groups from the cytoplasm into the mitochondrial matrix phosphorylated (Carn_acyltransf superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_859
GO ID Go Term p-value q-value Cluster
GO:0009239 enterobactin biosynthesis 0.00271672 1 Phatr_bicluster_0067
GO:0006479 protein amino acid methylation 0.00542673 1 Phatr_bicluster_0067
GO:0006535 cysteine biosynthesis from serine 0.00813004 1 Phatr_bicluster_0067
GO:0050757 thymidylate synthase biosynthesis 0.00813004 1 Phatr_bicluster_0067
GO:0009228 thiamin biosynthesis 0.00813004 1 Phatr_bicluster_0067
GO:0015904 tetracycline transport 0.0108267 1 Phatr_bicluster_0067
GO:0009231 riboflavin biosynthesis 0.0162 1 Phatr_bicluster_0067
GO:0006468 protein amino acid phosphorylation 0.0767082 1 Phatr_bicluster_0067
GO:0008152 metabolism 0.187614 1 Phatr_bicluster_0067
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