Phatr_bicluster_0140 Residual: 0.20
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_0140 0.20 Phaeodactylum tricornutum
Displaying 1 - 23 of 23
PHATRDRAFT_11048 integral membrane protein (SRPBCC superfamily)

PHATRDRAFT_11048 - integral membrane protein (SRPBCC superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11048
PHATRDRAFT_12533 isopentenyl pyrophosphate:dimethylallyl pyrophosphate isomerase (IPP_Isomerase)

PHATRDRAFT_12533 - isopentenyl pyrophosphate:dimethylallyl pyrophosphate isomerase (IPP_Isomerase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12533
PHATRDRAFT_12807 chlorophyll synthetase (PT_UbiA_chlorophyll)

PHATRDRAFT_12807 - chlorophyll synthetase (PT_UbiA_chlorophyll)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12807
PHATRDRAFT_13265 (PLN03069)

PHATRDRAFT_13265 - (PLN03069)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13265
PHATRDRAFT_15068 chloroplast coproporphyrinogen iii oxidase (PLN02873)

PHATRDRAFT_15068 - chloroplast coproporphyrinogen iii oxidase (PLN02873)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15068
PHATRDRAFT_18872 mg-protoporphyrin ix methyl transferase (UbiG)

PHATRDRAFT_18872 - mg-protoporphyrin ix methyl transferase (UbiG)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18872
PHATRDRAFT_19000 geranylgeranyl pyrophosphate synthase (Trans_IPPS_HT)

PHATRDRAFT_19000 - geranylgeranyl pyrophosphate synthase (Trans_IPPS_HT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19000
PHATRDRAFT_31683 chloroplast geranylgeranyl reductase hydrogenase (PLN00093)

PHATRDRAFT_31683 - chloroplast geranylgeranyl reductase hydrogenase (PLN00093)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31683
PHATRDRAFT_36347 glutamate-1-semialdehyde aminotransferase (PRK00062)

PHATRDRAFT_36347 - glutamate-1-semialdehyde aminotransferase (PRK00062)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36347
PHATRDRAFT_41746 ala dehydratase (ALAD_PBGS_aspartate_rich)

PHATRDRAFT_41746 - ala dehydratase (ALAD_PBGS_aspartate_rich)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41746
PHATRDRAFT_42483 (NADB_Rossmann superfamily)

PHATRDRAFT_42483 - (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42483
PHATRDRAFT_43209

PHATRDRAFT_43209 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43209
PHATRDRAFT_43443

PHATRDRAFT_43443 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43443
PHATRDRAFT_43737 phytanoyl-dioxygenase (PhyH superfamily)

PHATRDRAFT_43737 - phytanoyl-dioxygenase (PhyH superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43737
PHATRDRAFT_44770 syringomycin synthesis regulator (TauD)

PHATRDRAFT_44770 - syringomycin synthesis regulator (TauD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44770
PHATRDRAFT_44908 short-chain dehydrogenase reductase nyc1 (SDR_c)

PHATRDRAFT_44908 - short-chain dehydrogenase reductase nyc1 (SDR_c)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44908
PHATRDRAFT_46411 ppf-1 protein (60KD_IMP)

PHATRDRAFT_46411 - ppf-1 protein (60KD_IMP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46411
PHATRDRAFT_48966 (cyclophilin superfamily)

PHATRDRAFT_48966 - (cyclophilin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48966
PHATRDRAFT_49288 2og-feoxygenase family (2OG-FeII_Oxy_4)

PHATRDRAFT_49288 - 2og-feoxygenase family (2OG-FeII_Oxy_4)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49288
PHATRDRAFT_51811 porphobilinogen deaminase (hemC)

PHATRDRAFT_51811 - porphobilinogen deaminase (hemC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51811
PHATRDRAFT_54952 pyridoxamine 5-phosphate oxidase-fmn-binding (Pyrid_oxidase_2 superfamily)

PHATRDRAFT_54952 - pyridoxamine 5-phosphate oxidase-fmn-binding (Pyrid_oxidase_2 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54952
PHATRDRAFT_54956 nucleic acid binding (Alba)

PHATRDRAFT_54956 - nucleic acid binding (Alba)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54956
PHATRDRAFT_9210 cog1233: phytoene dehydrogenase and related proteins (COG1233)

PHATRDRAFT_9210 - cog1233: phytoene dehydrogenase and related proteins (COG1233)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9210
GO ID Go Term p-value q-value Cluster
GO:0015995 chlorophyll biosynthesis 0.0000766 0.176641 Phatr_bicluster_0140
GO:0015979 photosynthesis 0.000152788 0.35126 Phatr_bicluster_0140
GO:0006779 porphyrin biosynthesis 0.00112458 1 Phatr_bicluster_0140
GO:0030494 bacteriochlorophyll biosynthesis 0.00518647 1 Phatr_bicluster_0140
GO:0016117 carotenoid biosynthesis 0.0154826 1 Phatr_bicluster_0140
GO:0051205 protein insertion into membrane 0.0205926 1 Phatr_bicluster_0140
GO:0006783 heme biosynthesis 0.0205926 1 Phatr_bicluster_0140
GO:0006725 aromatic compound metabolism 0.0989952 1 Phatr_bicluster_0140
GO:0019538 protein metabolism 0.171397 1 Phatr_bicluster_0140
GO:0008152 metabolism 0.192268 1 Phatr_bicluster_0140
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