Phatr_bicluster_0120 Residual: 0.36
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_0120 0.36 Phaeodactylum tricornutum
Displaying 1 - 23 of 23
PHATRDRAFT_10593 atp-dependent clp protease proteolytic subunit (S14_ClpP_2)

PHATRDRAFT_10593 - atp-dependent clp protease proteolytic subunit (S14_ClpP_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10593
PHATRDRAFT_13921 microsomal signal peptidase 12 kda subunit family protein (SPC12)

PHATRDRAFT_13921 - microsomal signal peptidase 12 kda subunit family protein (SPC12)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13921
PHATRDRAFT_14472 flj43980 protein (ANK)

PHATRDRAFT_14472 - flj43980 protein (ANK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14472
PHATRDRAFT_14762 isocitrate dehydrogenase (Iso_dh superfamily)

PHATRDRAFT_14762 - isocitrate dehydrogenase (Iso_dh superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14762
PHATRDRAFT_14927 frda_schpo frataxinmitochondrial precursor (Frataxin superfamily)

PHATRDRAFT_14927 - frda_schpo frataxinmitochondrial precursor (Frataxin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14927
PHATRDRAFT_15214 at1g65820 f1e22_4

PHATRDRAFT_15214 - at1g65820 f1e22_4

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15214
PHATRDRAFT_18665 shm4 (serine hydroxymethyltransferase 4) glycine hydroxymethyltransferase (SHMT)

PHATRDRAFT_18665 - shm4 (serine hydroxymethyltransferase 4) glycine hydroxymethyltransferase (SHMT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18665
PHATRDRAFT_19093 mgc80063 protein (Coatomer_E)

PHATRDRAFT_19093 - mgc80063 protein (Coatomer_E)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19093
PHATRDRAFT_21535 af228419_1rab6 protein (Rab6)

PHATRDRAFT_21535 - af228419_1rab6 protein (Rab6)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21535
PHATRDRAFT_22896 (ArsA_ATPase)

PHATRDRAFT_22896 - (ArsA_ATPase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22896
PHATRDRAFT_29758 puromycin sensitive aminopeptidase cg1009-isoform a (M1_APN_2)

PHATRDRAFT_29758 - puromycin sensitive aminopeptidase cg1009-isoform a (M1_APN_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29758
PHATRDRAFT_30471 methylenetetrahydrofolate reductase (MTHFR)

PHATRDRAFT_30471 - methylenetetrahydrofolate reductase (MTHFR)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30471
PHATRDRAFT_37658 glutathione s-transferase-like protein (GST_N_Sigma_like)

PHATRDRAFT_37658 - glutathione s-transferase-like protein (GST_N_Sigma_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37658
PHATRDRAFT_40933 atp-dependent clpproteolytic subunit (S14_ClpP_2)

PHATRDRAFT_40933 - atp-dependent clpproteolytic subunit (S14_ClpP_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40933
PHATRDRAFT_43061 dna j-like protein 1 (DnaJ)

PHATRDRAFT_43061 - dna j-like protein 1 (DnaJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43061
PHATRDRAFT_44139

PHATRDRAFT_44139 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44139
PHATRDRAFT_45833

PHATRDRAFT_45833 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45833
PHATRDRAFT_50476 glutathione peroxidase-like protein (Thioredoxin_like superfamily)

PHATRDRAFT_50476 - glutathione peroxidase-like protein (Thioredoxin_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50476
PHATRDRAFT_51242 adenosine kinase isoform 1t-like protein (PTZ00247)

PHATRDRAFT_51242 - adenosine kinase isoform 1t-like protein (PTZ00247)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51242
PHATRDRAFT_54589 sec61beta family protein

PHATRDRAFT_54589 - sec61beta family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54589
PHATRDRAFT_6756 (HAM1)

PHATRDRAFT_6756 - (HAM1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6756
PHATRDRAFT_7237 transport protein (Sm_multidrug_ex)

PHATRDRAFT_7237 - transport protein (Sm_multidrug_ex)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7237
PHATRDRAFT_7528 nucleoredoxin 1 (Thioredoxin_like superfamily)

PHATRDRAFT_7528 - nucleoredoxin 1 (Thioredoxin_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7528
GO ID Go Term p-value q-value Cluster
GO:0006166 purine ribonucleoside salvage 0.00370462 1 Phatr_bicluster_0120
GO:0006563 L-serine metabolism 0.00739642 1 Phatr_bicluster_0120
GO:0006555 methionine metabolism 0.00739642 1 Phatr_bicluster_0120
GO:0006886 intracellular protein transport 0.00921303 1 Phatr_bicluster_0120
GO:0006544 glycine metabolism 0.0110755 1 Phatr_bicluster_0120
GO:0006465 signal peptide processing 0.0147418 1 Phatr_bicluster_0120
GO:0006820 anion transport 0.0436188 1 Phatr_bicluster_0120
GO:0006508 proteolysis and peptidolysis 0.0464053 1 Phatr_bicluster_0120
GO:0007264 small GTPase mediated signal transduction 0.0751604 1 Phatr_bicluster_0120
GO:0015031 protein transport 0.109067 1 Phatr_bicluster_0120
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