Phatr_bicluster_0245 Residual: 0.30
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_0245 0.30 Phaeodactylum tricornutum
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Displaying 1 - 28 of 28
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PHATRDRAFT_10531 at3g53030 f8j2_200 (S_TKc)

PHATRDRAFT_10531 - at3g53030 f8j2_200 (S_TKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10531
PHATRDRAFT_11633 ppk4_schpo serine threonine-protein kinase ppk4 precursor (RNase_Ire1_like superfamily)

PHATRDRAFT_11633 - ppk4_schpo serine threonine-protein kinase ppk4 precursor (RNase_Ire1_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11633
PHATRDRAFT_17936 vacuolar protein sorting 29 (MPP_Vps29)

PHATRDRAFT_17936 - vacuolar protein sorting 29 (MPP_Vps29)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17936
PHATRDRAFT_31486

PHATRDRAFT_31486 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31486
PHATRDRAFT_32327

PHATRDRAFT_32327 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32327
PHATRDRAFT_32665 conserved protein with diacylglycerol kinase catalytic domain

PHATRDRAFT_32665 - conserved protein with diacylglycerol kinase catalytic domain

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32665
PHATRDRAFT_37521 ankyrin protein (PKc_like superfamily)

PHATRDRAFT_37521 - ankyrin protein (PKc_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37521
PHATRDRAFT_37960 retinal pigment epithelial membrane (RPE65 superfamily)

PHATRDRAFT_37960 - retinal pigment epithelial membrane (RPE65 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37960
PHATRDRAFT_42779 (GLTP superfamily)

PHATRDRAFT_42779 - (GLTP superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42779
PHATRDRAFT_43790

PHATRDRAFT_43790 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43790
PHATRDRAFT_43793

PHATRDRAFT_43793 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43793
PHATRDRAFT_44136 emb2219 (embryo defective 2219) transferase (mTERF superfamily)

PHATRDRAFT_44136 - emb2219 (embryo defective 2219) transferase (mTERF superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44136
PHATRDRAFT_44516 riken cdna 1810011o16 (Eapp_C superfamily)

PHATRDRAFT_44516 - riken cdna 1810011o16 (Eapp_C superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44516
PHATRDRAFT_44708 atr protein (PI3Kc_like superfamily)

PHATRDRAFT_44708 - atr protein (PI3Kc_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44708
PHATRDRAFT_44766 sec14-like 1 (SEC14)

PHATRDRAFT_44766 - sec14-like 1 (SEC14)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44766
PHATRDRAFT_44845 (DENN)

PHATRDRAFT_44845 - (DENN)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44845
PHATRDRAFT_44931

PHATRDRAFT_44931 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44931
PHATRDRAFT_44935 (zf-CW)

PHATRDRAFT_44935 - (zf-CW)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44935
PHATRDRAFT_45116 (SNF2_N)

PHATRDRAFT_45116 - (SNF2_N)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45116
PHATRDRAFT_45187

PHATRDRAFT_45187 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45187
PHATRDRAFT_46043 zinc finger protein (RING)

PHATRDRAFT_46043 - zinc finger protein (RING)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46043
PHATRDRAFT_46484 lactoferrin binding protein

PHATRDRAFT_46484 - lactoferrin binding protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46484
PHATRDRAFT_47542

PHATRDRAFT_47542 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47542
PHATRDRAFT_49010 repressor of rna polymerase iii transcription (Maf1 superfamily)

PHATRDRAFT_49010 - repressor of rna polymerase iii transcription (Maf1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49010
PHATRDRAFT_49165 deoxyribodipyrimidine photolyase (FAD_binding_7 superfamily)

PHATRDRAFT_49165 - deoxyribodipyrimidine photolyase (FAD_binding_7 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49165
PHATRDRAFT_49563 mgc173657 protein (GH20_hexosaminidase superfamily)

PHATRDRAFT_49563 - mgc173657 protein (GH20_hexosaminidase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49563
PHATRDRAFT_50564 elicitin-like protein 6 precursor

PHATRDRAFT_50564 - elicitin-like protein 6 precursor

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50564
PHATRDRAFT_9546 novel proteincatechol-o-methyltransferase comt (AdoMet_MTases superfamily)

PHATRDRAFT_9546 - novel proteincatechol-o-methyltransferase comt (AdoMet_MTases superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9546
GO ID Go Term p-value q-value Cluster
GO:0006468 protein amino acid phosphorylation 0.00360249 1 Phatr_bicluster_0245
GO:0016567 protein ubiquitination 0.00814771 1 Phatr_bicluster_0245
GO:0006397 mRNA processing 0.0445878 1 Phatr_bicluster_0245
GO:0006281 DNA repair 0.0652904 1 Phatr_bicluster_0245
GO:0005975 carbohydrate metabolism 0.118 1 Phatr_bicluster_0245
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