Phatr_bicluster_0214 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_0214 0.23 Phaeodactylum tricornutum
Displaying 1 - 25 of 25
PHATRDRAFT_12394 low-co2-inducible protein (NSA2)

PHATRDRAFT_12394 - low-co2-inducible protein (NSA2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12394
PHATRDRAFT_12452 p-type h+- (ATPase-IIIA_H)

PHATRDRAFT_12452 - p-type h+- (ATPase-IIIA_H)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12452
PHATRDRAFT_13326 dna-directed rna polymerases iia (Zn-ribbon_RPC11)

PHATRDRAFT_13326 - dna-directed rna polymerases iia (Zn-ribbon_RPC11)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13326
PHATRDRAFT_18735 transcription regulatory protein (CDC39)

PHATRDRAFT_18735 - transcription regulatory protein (CDC39)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18735
PHATRDRAFT_31841 (DUF4602)

PHATRDRAFT_31841 - (DUF4602)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31841
PHATRDRAFT_32634

PHATRDRAFT_32634 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32634
PHATRDRAFT_36013

PHATRDRAFT_35507 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35507
PHATRDRAFT_36647 arginyl-trna synthetase (PLN02286)

PHATRDRAFT_36013 - arginyl-trna synthetase (PLN02286)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36013
PHATRDRAFT_36840 low density lipoprotein receptor

PHATRDRAFT_36647 - low density lipoprotein receptor

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36647
PHATRDRAFT_37731 heme activated protein

PHATRDRAFT_36840 - heme activated protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36840
PHATRDRAFT_39838 (zf-UBR)

PHATRDRAFT_37731 - (zf-UBR)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37731
PHATRDRAFT_40842

PHATRDRAFT_39838 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39838
PHATRDRAFT_43183

PHATRDRAFT_40842 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40842
PHATRDRAFT_43288 atipt9 (arabidopsis thaliana isopentenyltransferase 9) atp binding trna isopentenyltransferase (PLN02840)

PHATRDRAFT_43183 - atipt9 (arabidopsis thaliana isopentenyltransferase 9) atp binding trna isopentenyltransferase (PLN02840)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43183
PHATRDRAFT_44859 arogenate dehydrogenase isoform 2 (PLN02256)

PHATRDRAFT_43288 - arogenate dehydrogenase isoform 2 (PLN02256)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43288
PHATRDRAFT_45564 virulent strain associated

PHATRDRAFT_44859 - virulent strain associated

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44859
PHATRDRAFT_46234 loc91893 protein (DUF2431 superfamily)

PHATRDRAFT_45564 - loc91893 protein (DUF2431 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45564
PHATRDRAFT_47215 fb252_arath f-box protein at5g06550 (Cupin_8 superfamily)

PHATRDRAFT_46234 - fb252_arath f-box protein at5g06550 (Cupin_8 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46234
PHATRDRAFT_49996

PHATRDRAFT_47215 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47215
PHATRDRAFT_49998

PHATRDRAFT_49996 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49996
PHATRDRAFT_50000 chromosome segregation 1-like

PHATRDRAFT_49998 - chromosome segregation 1-like

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49998
PHATRDRAFT_50796 chromosome segregation 1-like

PHATRDRAFT_50000 - chromosome segregation 1-like

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50000
PHATRDRAFT_52248 cg5605-isoform a (eRF1)

PHATRDRAFT_50796 - cg5605-isoform a (eRF1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50796
PHATRDRAFT_9161 classmember 1 (GH38-57_N_LamB_YdjC_SF superfamily)

PHATRDRAFT_52248 - classmember 1 (GH38-57_N_LamB_YdjC_SF superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52248

PHATRDRAFT_9161 - cg6404-isoform b (60KD_IMP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9161
GO ID Go Term p-value q-value Cluster
GO:0006420 arginyl-tRNA aminoacylation 0.00591934 1 Phatr_bicluster_0214
GO:0006354 RNA elongation 0.00886694 1 Phatr_bicluster_0214
GO:0051205 protein insertion into membrane 0.0118065 1 Phatr_bicluster_0214
GO:0006415 translational termination 0.0205774 1 Phatr_bicluster_0214
GO:0015992 proton transport 0.0407661 1 Phatr_bicluster_0214
GO:0006306 DNA methylation 0.0577662 1 Phatr_bicluster_0214
GO:0008033 tRNA processing 0.0577662 1 Phatr_bicluster_0214
GO:0006812 cation transport 0.0772504 1 Phatr_bicluster_0214
GO:0006512 ubiquitin cycle 0.107123 1 Phatr_bicluster_0214
GO:0006418 tRNA aminoacylation for protein translation 0.143861 1 Phatr_bicluster_0214
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