Phatr_bicluster_0124 Residual: 0.32
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_0124 0.32 Phaeodactylum tricornutum
Displaying 1 - 27 of 27
PHATRDRAFT_10774 50s ribosomal protein l15 (rplO)

PHATRDRAFT_10774 - 50s ribosomal protein l15 (rplO)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10774
PHATRDRAFT_11965 pseudouridinesynthase homolog 1 (PseudoU_synth superfamily)

PHATRDRAFT_11965 - pseudouridinesynthase homolog 1 (PseudoU_synth superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11965
PHATRDRAFT_12161 u2 snrnp-specific a protein (LRR_9)

PHATRDRAFT_12161 - u2 snrnp-specific a protein (LRR_9)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12161
PHATRDRAFT_12902 nitrite reductase (nirA)

PHATRDRAFT_12902 - nitrite reductase (nirA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12902
PHATRDRAFT_13076 nitrite transporter nar1 (Form_Nir_trans)

PHATRDRAFT_13076 - nitrite transporter nar1 (Form_Nir_trans)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13076
PHATRDRAFT_19568 ruvbl1 protein (TIP49)

PHATRDRAFT_19568 - ruvbl1 protein (TIP49)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19568
PHATRDRAFT_24772 alpha-isopropylmalate isomerase (IPMI)

PHATRDRAFT_24772 - alpha-isopropylmalate isomerase (IPMI)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_24772
PHATRDRAFT_26029 nitrate transporter (2A0108)

PHATRDRAFT_26029 - nitrate transporter (2A0108)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_26029
PHATRDRAFT_29217 dna-binding protein gbp16 (PA2G4-like)

PHATRDRAFT_29217 - dna-binding protein gbp16 (PA2G4-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29217
PHATRDRAFT_35002 phosphoglycerate mutase

PHATRDRAFT_35002 - phosphoglycerate mutase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35002
PHATRDRAFT_35363 uba thif-type nad fad binding protein (COG1179)

PHATRDRAFT_35363 - uba thif-type nad fad binding protein (COG1179)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35363
PHATRDRAFT_36383

PHATRDRAFT_36383 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36383
PHATRDRAFT_36446

PHATRDRAFT_36446 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36446
PHATRDRAFT_36899 mitochondrial protein 18 kda (MTP18 superfamily)

PHATRDRAFT_36899 - mitochondrial protein 18 kda (MTP18 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36899
PHATRDRAFT_37009 tfp pilus assembly

PHATRDRAFT_37009 - tfp pilus assembly

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37009
PHATRDRAFT_43326 novel protein (cytidine_deaminase-like superfamily)

PHATRDRAFT_43326 - novel protein (cytidine_deaminase-like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43326
PHATRDRAFT_43387 queuine trna-ribosyltransferase (TGT superfamily)

PHATRDRAFT_43387 - queuine trna-ribosyltransferase (TGT superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43387
PHATRDRAFT_43579 lethal in the absence of ssd1-v (Las1 superfamily)

PHATRDRAFT_43579 - lethal in the absence of ssd1-v (Las1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43579
PHATRDRAFT_44274

PHATRDRAFT_44274 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44274
PHATRDRAFT_44572 helicase domain protein (HA)

PHATRDRAFT_44572 - helicase domain protein (HA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44572
PHATRDRAFT_45590

PHATRDRAFT_45590 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45590
PHATRDRAFT_46093 methyltransferase small (COG1092)

PHATRDRAFT_46093 - methyltransferase small (COG1092)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46093
PHATRDRAFT_48817 serine protease a (Peptidases_S8_PCSK9_ProteinaseK_like)

PHATRDRAFT_48493 - serine protease a (Peptidases_S8_PCSK9_ProteinaseK_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48493
PHATRDRAFT_50024

PHATRDRAFT_48817 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48817
PHATRDRAFT_7349

PHATRDRAFT_50024 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50024
PHATRDRAFT_9235 small nucleolar rnp protein (Gar1 superfamily)

PHATRDRAFT_7349 - small nucleolar rnp protein (Gar1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7349

PHATRDRAFT_9235 - rpa2_schpo probable dna-directed rna polymerase i subunit rpa2 (dna-directed rna polymerase i polypeptide 2) (rna polymerase i subunit 2) (RpoB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9235
GO ID Go Term p-value q-value Cluster
GO:0006306 DNA methylation 0.0945003 1 Phatr_bicluster_0124
GO:0006118 electron transport 0.688767 1 Phatr_bicluster_0124
GO:0015698 inorganic anion transport 0.00493949 1 Phatr_bicluster_0124
GO:0009098 leucine biosynthesis 0.014749 1 Phatr_bicluster_0124
GO:0008152 metabolism 0.432155 1 Phatr_bicluster_0124
GO:0043086 negative regulation of enzyme activity 0.0244666 1 Phatr_bicluster_0124
GO:0042128 nitrate assimilation 0.00493949 1 Phatr_bicluster_0124
GO:0006412 protein biosynthesis 0.556674 1 Phatr_bicluster_0124
GO:0006508 proteolysis and peptidolysis 0.680496 1 Phatr_bicluster_0124
GO:0008616 queuosine biosynthesis 0.014749 1 Phatr_bicluster_0124
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