Phatr_bicluster_0039 Residual: 0.39
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_0039 0.39 Phaeodactylum tricornutum
Displaying 1 - 38 of 38
PHATRDRAFT_10497 mitochondrial trans-2-enoyl-reductase (ETR)

PHATRDRAFT_10497 - mitochondrial trans-2-enoyl-reductase (ETR)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10497
PHATRDRAFT_13922 cg32576-isoform b (Got1 superfamily)

PHATRDRAFT_13922 - cg32576-isoform b (Got1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13922
PHATRDRAFT_15126 g-protein associated signal transduction protein (DUF202 superfamily)

PHATRDRAFT_15126 - g-protein associated signal transduction protein (DUF202 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15126
PHATRDRAFT_15180 geranyl diphosphat synthase (Trans_IPPS_HT)

PHATRDRAFT_15180 - geranyl diphosphat synthase (Trans_IPPS_HT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15180
PHATRDRAFT_21543 silent information regulator protein sir2 (SIR2 superfamily)

PHATRDRAFT_21543 - silent information regulator protein sir2 (SIR2 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21543
PHATRDRAFT_21912 alpha beta hydrolase fold (Hydrolase_4 superfamily)

PHATRDRAFT_21912 - alpha beta hydrolase fold (Hydrolase_4 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21912
PHATRDRAFT_30823 (Aldo_ket_red)

PHATRDRAFT_30823 - (Aldo_ket_red)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30823
PHATRDRAFT_32401 low-co2 inducible protein lcic

PHATRDRAFT_32401 - low-co2 inducible protein lcic

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32401
PHATRDRAFT_33342 intracellular chloride channel (ECM4)

PHATRDRAFT_33342 - intracellular chloride channel (ECM4)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33342
PHATRDRAFT_33380 heat shock factor 3 (HSF_DNA-bind)

PHATRDRAFT_33380 - heat shock factor 3 (HSF_DNA-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33380
PHATRDRAFT_33622 heat shock transcription factor (HSF_DNA-bind)

PHATRDRAFT_33622 - heat shock transcription factor (HSF_DNA-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33622
PHATRDRAFT_35785

PHATRDRAFT_35785 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35785
PHATRDRAFT_37632 conserved membrane protein (VIT1)

PHATRDRAFT_37632 - conserved membrane protein (VIT1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37632
PHATRDRAFT_37659

PHATRDRAFT_37659 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37659
PHATRDRAFT_37837

PHATRDRAFT_37837 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37837
PHATRDRAFT_37967 ring finger protein (RING)

PHATRDRAFT_37967 - ring finger protein (RING)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37967
PHATRDRAFT_38107

PHATRDRAFT_38107 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38107
PHATRDRAFT_39711 glutathione s-c-terminal domain containing protein (Gst)

PHATRDRAFT_39711 - glutathione s-c-terminal domain containing protein (Gst)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39711
PHATRDRAFT_39766

PHATRDRAFT_39766 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39766
PHATRDRAFT_40022 core 1 udp-galactose:n-acetylgalactosamine-alpha-r beta- galactosy

PHATRDRAFT_40022 - core 1 udp-galactose:n-acetylgalactosamine-alpha-r beta- galactosy

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40022
PHATRDRAFT_40162 novel protein (Cyt-b5)

PHATRDRAFT_40162 - novel protein (Cyt-b5)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40162
PHATRDRAFT_40273 (PUB superfamily)

PHATRDRAFT_40273 - (PUB superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40273
PHATRDRAFT_41450 heterogeneous nuclear ribonucleoprotein (RRM_SF superfamily)

PHATRDRAFT_41450 - heterogeneous nuclear ribonucleoprotein (RRM_SF superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41450
PHATRDRAFT_43666 transmembrane protein 53 (DUF829 superfamily)

PHATRDRAFT_43666 - transmembrane protein 53 (DUF829 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43666
PHATRDRAFT_43941

PHATRDRAFT_43941 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43941
PHATRDRAFT_45011 ring finger protein (RING)

PHATRDRAFT_45011 - ring finger protein (RING)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45011
PHATRDRAFT_47352 10 tms drug metabolitedmedmt superfamily

PHATRDRAFT_47352 - 10 tms drug metabolitedmedmt superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47352
PHATRDRAFT_47364

PHATRDRAFT_47364 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47364
PHATRDRAFT_47400

PHATRDRAFT_47400 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47400
PHATRDRAFT_47434 ids-4 protein (SPX)

PHATRDRAFT_47434 - ids-4 protein (SPX)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47434
PHATRDRAFT_48085

PHATRDRAFT_48085 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48085
PHATRDRAFT_48406

PHATRDRAFT_48406 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48406
PHATRDRAFT_48535 serine threonine protein kinase and signal transduction histidine kinasewith gaf sensor (COG3899)

PHATRDRAFT_48535 - serine threonine protein kinase and signal transduction histidine kinasewith gaf sensor (COG3899)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48535
PHATRDRAFT_49122

PHATRDRAFT_49122 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49122
PHATRDRAFT_49283

PHATRDRAFT_49283 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49283
PHATRDRAFT_49455

PHATRDRAFT_49455 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49455
PHATRDRAFT_50457 mechanosensitive ion channel domain-containing (MscS)

PHATRDRAFT_50457 - mechanosensitive ion channel domain-containing (MscS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50457
PHATRDRAFT_54409 respiratory burst oxidase-like protein (NOX_Duox_like_FAD_NADP)

PHATRDRAFT_54409 - respiratory burst oxidase-like protein (NOX_Duox_like_FAD_NADP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54409
GO ID Go Term p-value q-value Cluster
GO:0030655 beta-lactam antibiotic catabolism 0.00813004 1 Phatr_bicluster_0039
GO:0046677 response to antibiotic 0.0108267 1 Phatr_bicluster_0039
GO:0016567 protein ubiquitination 0.015462 1 Phatr_bicluster_0039
GO:0006342 chromatin silencing 0.0162 1 Phatr_bicluster_0039
GO:0006355 regulation of transcription, DNA-dependent 0.0186418 1 Phatr_bicluster_0039
GO:0008299 isoprenoid biosynthesis 0.0242101 1 Phatr_bicluster_0039
GO:0016192 vesicle-mediated transport 0.0347981 1 Phatr_bicluster_0039
GO:0006725 aromatic compound metabolism 0.0530761 1 Phatr_bicluster_0039
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