Phatr_bicluster_0030 Residual: 0.31
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_0030 0.31 Phaeodactylum tricornutum
Displaying 1 - 33 of 33
PHATRDRAFT_10398 uridine kinase (UMPK)

PHATRDRAFT_10398 - uridine kinase (UMPK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10398
PHATRDRAFT_12186 coproporphyrinogen iii oxidase (PLN02873)

PHATRDRAFT_12186 - coproporphyrinogen iii oxidase (PLN02873)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12186
PHATRDRAFT_14412 signal recognition particle-docking protein (ftsY)

PHATRDRAFT_14412 - signal recognition particle-docking protein (ftsY)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14412
PHATRDRAFT_16157 nudix hydrolase (NADH_pyrophosphatase)

PHATRDRAFT_16157 - nudix hydrolase (NADH_pyrophosphatase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16157
PHATRDRAFT_16707 glyoxalase ii (Lactamase_B superfamily)

PHATRDRAFT_16707 - glyoxalase ii (Lactamase_B superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16707
PHATRDRAFT_18826 abc transporter c family protein (ABCC_MRP_domain2)

PHATRDRAFT_18826 - abc transporter c family protein (ABCC_MRP_domain2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18826
PHATRDRAFT_20905 l-asparaginase i (ansA)

PHATRDRAFT_20905 - l-asparaginase i (ansA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20905
PHATRDRAFT_31254 pmp3_neucr plasma membrane proteolipid 3 (Pmp3)

PHATRDRAFT_31254 - pmp3_neucr plasma membrane proteolipid 3 (Pmp3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31254
PHATRDRAFT_35625 mc family transporter (Mito_carr superfamily)

PHATRDRAFT_35625 - mc family transporter (Mito_carr superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35625
PHATRDRAFT_37519 phosphoglycerate bisphosphoglycerate mutase family protein (HP_PGM_like)

PHATRDRAFT_37519 - phosphoglycerate bisphosphoglycerate mutase family protein (HP_PGM_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37519
PHATRDRAFT_37549

PHATRDRAFT_37549 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37549
PHATRDRAFT_38757

PHATRDRAFT_38757 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38757
PHATRDRAFT_39165

PHATRDRAFT_39165 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39165
PHATRDRAFT_39274 potassium transporter (PRK03659)

PHATRDRAFT_39274 - potassium transporter (PRK03659)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39274
PHATRDRAFT_39989

PHATRDRAFT_39989 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39989
PHATRDRAFT_40088

PHATRDRAFT_40088 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40088
PHATRDRAFT_41167 (HrpA)

PHATRDRAFT_41167 - (HrpA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41167
PHATRDRAFT_41476 ribosomal-protein-alanine acetyltransferase (RimI)

PHATRDRAFT_41476 - ribosomal-protein-alanine acetyltransferase (RimI)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41476
PHATRDRAFT_43619 streptomyces cyclase dehydrase (SRPBCC_8)

PHATRDRAFT_43619 - streptomyces cyclase dehydrase (SRPBCC_8)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43619
PHATRDRAFT_43657 oxa1 family transporter: 60 kd inner membraneprotein (60KD_IMP)

PHATRDRAFT_43657 - oxa1 family transporter: 60 kd inner membraneprotein (60KD_IMP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43657
PHATRDRAFT_44038 double-stranded rna-specific editase (A_deamin superfamily)

PHATRDRAFT_44038 - double-stranded rna-specific editase (A_deamin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44038
PHATRDRAFT_47448 at3g61540 f2a19_140

PHATRDRAFT_47448 - at3g61540 f2a19_140

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47448
PHATRDRAFT_47929 (Ptr)

PHATRDRAFT_47929 - (Ptr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47929
PHATRDRAFT_48250 cog4446: uncharacterized protein conserved in bacteria (DUF1499)

PHATRDRAFT_48250 - cog4446: uncharacterized protein conserved in bacteria (DUF1499)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48250
PHATRDRAFT_48402

PHATRDRAFT_48402 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48402
PHATRDRAFT_49341 glycine cleavage t protein (aminomethyl transferase) (GCV_T superfamily)

PHATRDRAFT_49341 - glycine cleavage t protein (aminomethyl transferase) (GCV_T superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49341
PHATRDRAFT_49420 family mitochondrial membrane protein with 2 transmembrane domains at c-terminus (Mrs2_Mfm1p-like)

PHATRDRAFT_49420 - family mitochondrial membrane protein with 2 transmembrane domains at c-terminus (Mrs2_Mfm1p-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49420
PHATRDRAFT_49679 loc616332 protein (CoAse)

PHATRDRAFT_49679 - loc616332 protein (CoAse)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49679
PHATRDRAFT_49702 sterol esterification protein (LCAT)

PHATRDRAFT_49702 - sterol esterification protein (LCAT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49702
PHATRDRAFT_50158

PHATRDRAFT_50158 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50158
PHATRDRAFT_50209

PHATRDRAFT_50209 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50209
PHATRDRAFT_50238 beta-glucan synthesis-associated protein kre6 (Glyco_hydrolase_16 superfamily)

PHATRDRAFT_50238 - beta-glucan synthesis-associated protein kre6 (Glyco_hydrolase_16 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50238
PHATRDRAFT_8950 protein homolog (AAA)

PHATRDRAFT_8950 - protein homolog (AAA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8950
GO ID Go Term p-value q-value Cluster
GO:0051205 protein insertion into membrane 0.0137641 1 Phatr_bicluster_0030
GO:0006614 SRP-dependent cotranslational protein-membrane targeting 0.0171775 1 Phatr_bicluster_0030
GO:0006779 porphyrin biosynthesis 0.0340807 1 Phatr_bicluster_0030
GO:0030001 metal ion transport 0.0540081 1 Phatr_bicluster_0030
GO:0006629 lipid metabolism 0.0605653 1 Phatr_bicluster_0030
GO:0006520 amino acid metabolism 0.0799844 1 Phatr_bicluster_0030
GO:0007018 microtubule-based movement 0.0990303 1 Phatr_bicluster_0030
GO:0006810 transport 0.139001 1 Phatr_bicluster_0030
GO:0009058 biosynthesis 0.145055 1 Phatr_bicluster_0030
GO:0006396 RNA processing 0.177408 1 Phatr_bicluster_0030
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