Phatr_bicluster_0118 Residual: 0.28
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_0118 0.28 Phaeodactylum tricornutum
Displaying 1 - 23 of 23
PHATRDRAFT_10768 rna-binding s4 domain protein (RsuA)

PHATRDRAFT_10768 - rna-binding s4 domain protein (RsuA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10768
PHATRDRAFT_13309 rexo4_ustma rna exonuclease 4 (REX4_like)

PHATRDRAFT_13309 - rexo4_ustma rna exonuclease 4 (REX4_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13309
PHATRDRAFT_13534 estrogen receptor binding protein (Fcf2)

PHATRDRAFT_13534 - estrogen receptor binding protein (Fcf2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13534
PHATRDRAFT_19438 (HSR1_MMR1)

PHATRDRAFT_19438 - (HSR1_MMR1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19438
PHATRDRAFT_31617 translocase inner membrane-like protein (Tim17)

PHATRDRAFT_31617 - translocase inner membrane-like protein (Tim17)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31617
PHATRDRAFT_31981 indole-3-glycerol phosphate synthase (TIM_phosphate_binding superfamily)

PHATRDRAFT_31981 - indole-3-glycerol phosphate synthase (TIM_phosphate_binding superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31981
PHATRDRAFT_32646 bfr2_schpo protein bfr2 (TRAUB superfamily)

PHATRDRAFT_32646 - bfr2_schpo protein bfr2 (TRAUB superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32646
PHATRDRAFT_3334 nol1 nop2 sun domain family 2 protein (Sun)

PHATRDRAFT_3334 - nol1 nop2 sun domain family 2 protein (Sun)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3334
PHATRDRAFT_37253

PHATRDRAFT_37253 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37253
PHATRDRAFT_42452

PHATRDRAFT_42452 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42452
PHATRDRAFT_43377 sel1-like repeat (COG0790)

PHATRDRAFT_43377 - sel1-like repeat (COG0790)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43377
PHATRDRAFT_43446 fog: ppr repeat (Methyltransf_4 superfamily)

PHATRDRAFT_43446 - fog: ppr repeat (Methyltransf_4 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43446
PHATRDRAFT_43504

PHATRDRAFT_43504 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43504
PHATRDRAFT_44011 disease resistance protein

PHATRDRAFT_44011 - disease resistance protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44011
PHATRDRAFT_44592 ankyrin-like protein (ANK)

PHATRDRAFT_44592 - ankyrin-like protein (ANK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44592
PHATRDRAFT_44687 eif4e binding protein

PHATRDRAFT_44687 - eif4e binding protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44687
PHATRDRAFT_44807

PHATRDRAFT_44807 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44807
PHATRDRAFT_45001 sperm nuclear basic protein pl-i isoform plib

PHATRDRAFT_45001 - sperm nuclear basic protein pl-i isoform plib

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45001
PHATRDRAFT_46145 loc443584 protein (RRM1_RBM34)

PHATRDRAFT_46145 - loc443584 protein (RRM1_RBM34)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46145
PHATRDRAFT_5424 elongation protein 3 homolog (ELP3)

PHATRDRAFT_50848 - elongation protein 3 homolog (ELP3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50848
PHATRDRAFT_7426 loc539270 protein (RRM_ABT1_like)

PHATRDRAFT_5424 - loc539270 protein (RRM_ABT1_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5424
PHATRDRAFT_9893 rna binding (RRM)

PHATRDRAFT_7426 - rna binding (RRM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7426

PHATRDRAFT_9893 - dead deah box (DEXDc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9893
GO ID Go Term p-value q-value Cluster
GO:0015031 protein transport 0.030286 1 Phatr_bicluster_0118
GO:0006355 regulation of transcription, DNA-dependent 0.199489 1 Phatr_bicluster_0118
GO:0006396 RNA processing 0.0542048 1 Phatr_bicluster_0118
GO:0006568 tryptophan metabolism 0.00591641 1 Phatr_bicluster_0118
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