Phatr_bicluster_0155 Residual: 0.23
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_0155 0.23 Phaeodactylum tricornutum
Displaying 1 - 15 of 15
PHATRDRAFT_15688 nuclear transport factor 2 (NTF2)

PHATRDRAFT_15688 - nuclear transport factor 2 (NTF2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15688
PHATRDRAFT_30502 atp binding protein (Phd_like_TxnDC9)

PHATRDRAFT_30502 - atp binding protein (Phd_like_TxnDC9)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30502
PHATRDRAFT_31748 (DUF4033)

PHATRDRAFT_31748 - (DUF4033)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31748
PHATRDRAFT_35954 (RNase_H2-B superfamily)

PHATRDRAFT_35954 - (RNase_H2-B superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35954
PHATRDRAFT_42702

PHATRDRAFT_42702 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42702
PHATRDRAFT_42932 wd repeat domain 6 protein (WD40 superfamily)

PHATRDRAFT_42932 - wd repeat domain 6 protein (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42932
PHATRDRAFT_43308

PHATRDRAFT_43308 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43308
PHATRDRAFT_43350 family protein (COG2391)

PHATRDRAFT_43350 - family protein (COG2391)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43350
PHATRDRAFT_4413 root border cell-specific protein (Pyrid_oxidase_2 superfamily)

PHATRDRAFT_4413 - root border cell-specific protein (Pyrid_oxidase_2 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_4413
PHATRDRAFT_44622 fatty acid desaturase family protein (Membrane-FADS-like superfamily)

PHATRDRAFT_44622 - fatty acid desaturase family protein (Membrane-FADS-like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44622
PHATRDRAFT_44877 cg10428-pa isoform 1 (Methyltransf_32 superfamily)

PHATRDRAFT_44877 - cg10428-pa isoform 1 (Methyltransf_32 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44877
PHATRDRAFT_45391 heat shock factor (HSF_DNA-bind)

PHATRDRAFT_45391 - heat shock factor (HSF_DNA-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45391
PHATRDRAFT_45998 proteasomealpha type 1 (proteasome_alpha_type_1)

PHATRDRAFT_45998 - proteasomealpha type 1 (proteasome_alpha_type_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45998
PHATRDRAFT_51040 ataxia telangiectasia mutated (PI3Kc_like superfamily)

PHATRDRAFT_51040 - ataxia telangiectasia mutated (PI3Kc_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51040
PHATRDRAFT_51541 af375428_1at4g29590 t16l4_100

PHATRDRAFT_51541 - af375428_1at4g29590 t16l4_100

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51541
GO ID Go Term p-value q-value Cluster
GO:0006606 protein-nucleus import 0.0029615 1 Phatr_bicluster_0155
GO:0006511 ubiquitin-dependent protein catabolism 0.0437357 1 Phatr_bicluster_0155
GO:0006355 regulation of transcription, DNA-dependent 0.199489 1 Phatr_bicluster_0155
GO:0006118 electron transport 0.20782 1 Phatr_bicluster_0155
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