Phatr_bicluster_0020 Residual: 0.35
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_0020 0.35 Phaeodactylum tricornutum
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Displaying 1 - 38 of 38
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PHATRDRAFT_16674 dna methyltransferase 2 (Cyt_C5_DNA_methylase superfamily)

PHATRDRAFT_16674 - dna methyltransferase 2 (Cyt_C5_DNA_methylase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16674
PHATRDRAFT_16859 nad-dependent deacetylase sirtuin 2 homolog (SIR2 superfamily)

PHATRDRAFT_16859 - nad-dependent deacetylase sirtuin 2 homolog (SIR2 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16859
PHATRDRAFT_20188 elongation factor tu gtp binding domain containing 1 isoform 1 (Ras_like_GTPase superfamily)

PHATRDRAFT_20188 - elongation factor tu gtp binding domain containing 1 isoform 1 (Ras_like_GTPase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20188
PHATRDRAFT_29136 actin a (ACTIN)

PHATRDRAFT_29136 - actin a (ACTIN)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29136
PHATRDRAFT_33278 cytosolic 3-hydroxy-3-methylglutaryl-synthase (HMG_CoA_synt_N superfamily)

PHATRDRAFT_33278 - cytosolic 3-hydroxy-3-methylglutaryl-synthase (HMG_CoA_synt_N superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33278
PHATRDRAFT_34343

PHATRDRAFT_34343 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34343
PHATRDRAFT_38076

PHATRDRAFT_38076 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38076
PHATRDRAFT_38493

PHATRDRAFT_38493 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38493
PHATRDRAFT_38809

PHATRDRAFT_38809 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38809
PHATRDRAFT_38892

PHATRDRAFT_38892 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38892
PHATRDRAFT_39077

PHATRDRAFT_39077 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39077
PHATRDRAFT_39744

PHATRDRAFT_39744 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39744
PHATRDRAFT_40630

PHATRDRAFT_40630 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40630
PHATRDRAFT_41129

PHATRDRAFT_41129 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41129
PHATRDRAFT_41291

PHATRDRAFT_41291 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41291
PHATRDRAFT_42913

PHATRDRAFT_42913 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42913
PHATRDRAFT_44031 riken cdnaisoform cra_c

PHATRDRAFT_44031 - riken cdnaisoform cra_c

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44031
PHATRDRAFT_44582 hsf2 protein (HSF_DNA-bind superfamily)

PHATRDRAFT_44582 - hsf2 protein (HSF_DNA-bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44582
PHATRDRAFT_44879

PHATRDRAFT_44879 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44879
PHATRDRAFT_47369 (RecQ)

PHATRDRAFT_47369 - (RecQ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47369
PHATRDRAFT_48002

PHATRDRAFT_48002 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48002
PHATRDRAFT_48317

PHATRDRAFT_48317 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48317
PHATRDRAFT_48375 guanylate cyclase (CHD)

PHATRDRAFT_48375 - guanylate cyclase (CHD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48375
PHATRDRAFT_48773 calmodulin 4 (calcium-binding protein dd112)

PHATRDRAFT_48773 - calmodulin 4 (calcium-binding protein dd112)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48773
PHATRDRAFT_48792

PHATRDRAFT_48792 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48792
PHATRDRAFT_49069

PHATRDRAFT_49069 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49069
PHATRDRAFT_49187

PHATRDRAFT_49187 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49187
PHATRDRAFT_49225 msx-2 interacting nuclear target protein

PHATRDRAFT_49225 - msx-2 interacting nuclear target protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49225
PHATRDRAFT_49253 nadh dehydrogenase (CoA_CoA_reduc)

PHATRDRAFT_49253 - nadh dehydrogenase (CoA_CoA_reduc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49253
PHATRDRAFT_49373 d3-type cyclin

PHATRDRAFT_49373 - d3-type cyclin

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49373
PHATRDRAFT_49520

PHATRDRAFT_49520 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49520
PHATRDRAFT_49723

PHATRDRAFT_49723 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49723
PHATRDRAFT_49735

PHATRDRAFT_49735 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49735
PHATRDRAFT_49921

PHATRDRAFT_49921 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49921
PHATRDRAFT_49948 cg9520-isoform b

PHATRDRAFT_49948 - cg9520-isoform b

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49948
PHATRDRAFT_50137 cog0579: dehydrogenase (DAO)

PHATRDRAFT_50137 - cog0579: dehydrogenase (DAO)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50137
PHATRDRAFT_50338

PHATRDRAFT_50338 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50338
PHATRDRAFT_52468 p type cation copper-transporter (ZntA)

PHATRDRAFT_52468 - p type cation copper-transporter (ZntA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52468
GO ID Go Term p-value q-value Cluster
GO:0006342 chromatin silencing 0.0191218 1 Phatr_bicluster_0020
GO:0009190 cyclic nucleotide biosynthesis 0.0533044 1 Phatr_bicluster_0020
GO:0006259 DNA metabolism 0.0379055 1 Phatr_bicluster_0020
GO:0006306 DNA methylation 0.0624342 1 Phatr_bicluster_0020
GO:0006118 electron transport 0.165064 1 Phatr_bicluster_0020
GO:0007242 intracellular signaling cascade 0.126943 1 Phatr_bicluster_0020
GO:0006412 protein biosynthesis 0.410379 1 Phatr_bicluster_0020
GO:0006464 protein modification 0.184674 1 Phatr_bicluster_0020
GO:0000074 regulation of cell cycle 0.103975 1 Phatr_bicluster_0020
GO:0006355 regulation of transcription, DNA-dependent 0.153654 1 Phatr_bicluster_0020
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