Phatr_bicluster_0187 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_0187 0.25 Phaeodactylum tricornutum
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Displaying 1 - 25 of 25
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PHATRDRAFT_10293 transmembrane protein 34 (Solute_trans_a superfamily)

PHATRDRAFT_10293 - transmembrane protein 34 (Solute_trans_a superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10293
PHATRDRAFT_10781 phosphatidylinositol-4-phosphate 5-kinase (MORN superfamily)

PHATRDRAFT_10781 - phosphatidylinositol-4-phosphate 5-kinase (MORN superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10781
PHATRDRAFT_11145 splicing factor u2af largepartial (RRM2_U2AF65)

PHATRDRAFT_11145 - splicing factor u2af largepartial (RRM2_U2AF65)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11145
PHATRDRAFT_12044 abc1 family protein (AarF)

PHATRDRAFT_12044 - abc1 family protein (AarF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12044
PHATRDRAFT_15031 phosphoinositide-3-class 3 (PI3Kc_like superfamily)

PHATRDRAFT_15031 - phosphoinositide-3-class 3 (PI3Kc_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15031
PHATRDRAFT_15863 mitochondrial single-subunit rna polymerase (RNA_pol)

PHATRDRAFT_15863 - mitochondrial single-subunit rna polymerase (RNA_pol)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15863
PHATRDRAFT_25551

PHATRDRAFT_25551 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25551
PHATRDRAFT_26853 atp-dependent rna helicase (DEADc)

PHATRDRAFT_26853 - atp-dependent rna helicase (DEADc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_26853
PHATRDRAFT_3251 phosphatidylserine receptor (JmjC superfamily)

PHATRDRAFT_3251 - phosphatidylserine receptor (JmjC superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3251
PHATRDRAFT_32688

PHATRDRAFT_32688 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32688
PHATRDRAFT_33770 ferredoxin-dependent bilin reductase (Fe_bilin_red superfamily)

PHATRDRAFT_33770 - ferredoxin-dependent bilin reductase (Fe_bilin_red superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33770
PHATRDRAFT_35473 loc495079 protein (MFS_2)

PHATRDRAFT_35473 - loc495079 protein (MFS_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35473
PHATRDRAFT_41268 two-component sensor histidine kinase (BaeS)

PHATRDRAFT_41268 - two-component sensor histidine kinase (BaeS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41268
PHATRDRAFT_42690

PHATRDRAFT_42690 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42690
PHATRDRAFT_43447 ad24 protein (NOC3)

PHATRDRAFT_43447 - ad24 protein (NOC3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43447
PHATRDRAFT_43673 rhomboid family protein ubiquitin-associated ts-n domain-containing protein (Rhomboid superfamily)

PHATRDRAFT_43673 - rhomboid family protein ubiquitin-associated ts-n domain-containing protein (Rhomboid superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43673
PHATRDRAFT_44331 myb-like dna-bindingshaqkyf class family protein (SANT)

PHATRDRAFT_44331 - myb-like dna-bindingshaqkyf class family protein (SANT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44331
PHATRDRAFT_44645 (Ceramidase superfamily)

PHATRDRAFT_44645 - (Ceramidase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44645
PHATRDRAFT_45618 mgc97716 protein (Atx10homo_assoc superfamily)

PHATRDRAFT_45618 - mgc97716 protein (Atx10homo_assoc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45618
PHATRDRAFT_45822

PHATRDRAFT_45822 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45822
PHATRDRAFT_46457

PHATRDRAFT_46457 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46457
PHATRDRAFT_46485

PHATRDRAFT_46485 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46485
PHATRDRAFT_46490 dual-specificity protein phosphatase (DSPc)

PHATRDRAFT_46490 - dual-specificity protein phosphatase (DSPc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46490
PHATRDRAFT_48996

PHATRDRAFT_48996 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48996
PHATRDRAFT_8475 trna pseudouridine synthase a (PseudoU_synth superfamily)

PHATRDRAFT_8475 - trna pseudouridine synthase a (PseudoU_synth superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8475
GO ID Go Term p-value q-value Cluster
GO:0010024 phytochromobilin biosynthesis 0.00370096 1 Phatr_bicluster_0187
GO:0006470 protein amino acid dephosphorylation 0.0232548 1 Phatr_bicluster_0187
GO:0006350 transcription 0.0256773 1 Phatr_bicluster_0187
GO:0006396 RNA processing 0.0672986 1 Phatr_bicluster_0187
GO:0006468 protein amino acid phosphorylation 0.195192 1 Phatr_bicluster_0187
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