Phatr_bicluster_0180 Residual: 0.25
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_0180 0.25 Phaeodactylum tricornutum
Displaying 1 - 26 of 26
PHATRDRAFT_12172 riboflavin kinase (Flavokinase)

PHATRDRAFT_12172 - riboflavin kinase (Flavokinase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12172
PHATRDRAFT_12330 2c-methyl-d-erythritol-cyclodiphosphate synthase (MECDP_synthase)

PHATRDRAFT_12330 - 2c-methyl-d-erythritol-cyclodiphosphate synthase (MECDP_synthase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12330
PHATRDRAFT_16962 ribosomal subunit interface protein (RaiA)

PHATRDRAFT_16962 - ribosomal subunit interface protein (RaiA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16962
PHATRDRAFT_18335 insulin-degrading enzyme (Ptr)

PHATRDRAFT_18335 - insulin-degrading enzyme (Ptr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18335
PHATRDRAFT_20124 small gtp-binding protein (Obg_CgtA)

PHATRDRAFT_20124 - small gtp-binding protein (Obg_CgtA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20124
PHATRDRAFT_23552 nicotinamide nucleotide transhydrogenase (pntA)

PHATRDRAFT_23552 - nicotinamide nucleotide transhydrogenase (pntA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23552
PHATRDRAFT_29702 ure urease (PLN02303)

PHATRDRAFT_29702 - ure urease (PLN02303)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29702
PHATRDRAFT_35977 cog4399: uncharacterized protein conserved in bacteria (COG4399 superfamily)

PHATRDRAFT_35977 - cog4399: uncharacterized protein conserved in bacteria (COG4399 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35977
PHATRDRAFT_36048 vde_spiolviolaxanthin de-chloroplast precursor (VDE superfamily)

PHATRDRAFT_36048 - vde_spiolviolaxanthin de-chloroplast precursor (VDE superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36048
PHATRDRAFT_38067 anaerobic glycerol-3-phosphate dehydrogenase protein (COG0579)

PHATRDRAFT_38067 - anaerobic glycerol-3-phosphate dehydrogenase protein (COG0579)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38067
PHATRDRAFT_40048 ribosome recycling factor (RRF)

PHATRDRAFT_40048 - ribosome recycling factor (RRF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40048
PHATRDRAFT_40461 phospholipid glycerol acyltransferase (LPLAT_AGPAT-like)

PHATRDRAFT_40461 - phospholipid glycerol acyltransferase (LPLAT_AGPAT-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40461
PHATRDRAFT_41282 ribosome releasing factor (RRF)

PHATRDRAFT_41282 - ribosome releasing factor (RRF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41282
PHATRDRAFT_4286 bass family transporter: sodium ion bile acid (COG0385)

PHATRDRAFT_4286 - bass family transporter: sodium ion bile acid (COG0385)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_4286
PHATRDRAFT_43164 short-chain dehydrogenase reductasesuperfamily protein (NADB_Rossmann superfamily)

PHATRDRAFT_43164 - short-chain dehydrogenase reductasesuperfamily protein (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43164
PHATRDRAFT_43750

PHATRDRAFT_43750 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43750
PHATRDRAFT_43853

PHATRDRAFT_43853 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43853
PHATRDRAFT_43945

PHATRDRAFT_43945 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43945
PHATRDRAFT_45332

PHATRDRAFT_45332 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45332
PHATRDRAFT_45515 (WcaG)

PHATRDRAFT_45515 - (WcaG)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45515
PHATRDRAFT_46097 chloride channel 7 (Voltage_gated_ClC superfamily)

PHATRDRAFT_46097 - chloride channel 7 (Voltage_gated_ClC superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46097
PHATRDRAFT_47341

PHATRDRAFT_47341 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47341
PHATRDRAFT_47513 (2OG-FeII_Oxy_3 superfamily)

PHATRDRAFT_47513 - (2OG-FeII_Oxy_3 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47513
PHATRDRAFT_49708 acyltransferase ws dgat mgat family protein (acyl_WS_DGAT)

PHATRDRAFT_49708 - acyltransferase ws dgat mgat family protein (acyl_WS_DGAT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49708
PHATRDRAFT_5145 urease accessory protein (Fer4_NifH superfamily)

PHATRDRAFT_5145 - urease accessory protein (Fer4_NifH superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5145
PHATRDRAFT_51608 (Aldo_ket_red)

PHATRDRAFT_51608 - (Aldo_ket_red)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51608
GO ID Go Term p-value q-value Cluster
GO:0016114 terpenoid biosynthesis 0.00690418 1 Phatr_bicluster_0180
GO:0006461 protein complex assembly 0.0137641 1 Phatr_bicluster_0180
GO:0009231 riboflavin biosynthesis 0.02058 1 Phatr_bicluster_0180
GO:0006821 chloride transport 0.0239715 1 Phatr_bicluster_0180
GO:0006814 sodium ion transport 0.0374288 1 Phatr_bicluster_0180
GO:0015992 proton transport 0.0474084 1 Phatr_bicluster_0180
GO:0006807 nitrogen compound metabolism 0.0474084 1 Phatr_bicluster_0180
GO:0006412 protein biosynthesis 0.104611 1 Phatr_bicluster_0180
GO:0019538 protein metabolism 0.117709 1 Phatr_bicluster_0180
GO:0008152 metabolism 0.270353 1 Phatr_bicluster_0180
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