Phatr_bicluster_0179 Residual: 0.41
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_0179 0.41 Phaeodactylum tricornutum
Displaying 1 - 27 of 27
PHATRDRAFT_10005 phosphopantothenoylcysteine synthetase (DFP superfamily)

PHATRDRAFT_10005 - phosphopantothenoylcysteine synthetase (DFP superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10005
PHATRDRAFT_28568 snf2 domain-containing protein helicase domain-containing protein ring finger domain-containing protein (SNF2_N)

PHATRDRAFT_28568 - snf2 domain-containing protein helicase domain-containing protein ring finger domain-containing protein (SNF2_N)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28568
PHATRDRAFT_33186 tsr2 protein (WGG superfamily)

PHATRDRAFT_33186 - tsr2 protein (WGG superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33186
PHATRDRAFT_33267

PHATRDRAFT_33267 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33267
PHATRDRAFT_33584 tyw23_orysj trna wybutosine-synthesizing protein 2 3 4 (TYW3 superfamily)

PHATRDRAFT_33584 - tyw23_orysj trna wybutosine-synthesizing protein 2 3 4 (TYW3 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33584
PHATRDRAFT_40691 nitrate transporter

PHATRDRAFT_40691 - nitrate transporter

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40691
PHATRDRAFT_41259 aaa familycdc48 subfamily (AAA)

PHATRDRAFT_41259 - aaa familycdc48 subfamily (AAA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41259
PHATRDRAFT_41639 retinitis pigmentosa gtpase regulator

PHATRDRAFT_41639 - retinitis pigmentosa gtpase regulator

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41639
PHATRDRAFT_42963 ac006341_12 ests gb (DUF2358 superfamily)

PHATRDRAFT_42963 - ac006341_12 ests gb (DUF2358 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42963
PHATRDRAFT_44876 generic methyltransferase (ovoA_Nterm)

PHATRDRAFT_44876 - generic methyltransferase (ovoA_Nterm)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44876
PHATRDRAFT_44978

PHATRDRAFT_44978 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44978
PHATRDRAFT_45108 (COG1258)

PHATRDRAFT_45108 - (COG1258)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45108
PHATRDRAFT_45192 adenylate kinase (adk)

PHATRDRAFT_45192 - adenylate kinase (adk)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45192
PHATRDRAFT_45208

PHATRDRAFT_45208 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45208
PHATRDRAFT_45251 pseudouridine synthase (PseudoU_synth_ScPUS7)

PHATRDRAFT_45251 - pseudouridine synthase (PseudoU_synth_ScPUS7)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45251
PHATRDRAFT_46436 cellulose-family ii

PHATRDRAFT_46436 - cellulose-family ii

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46436
PHATRDRAFT_46703 (Senescence)

PHATRDRAFT_46703 - (Senescence)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46703
PHATRDRAFT_46783

PHATRDRAFT_46783 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46783
PHATRDRAFT_47358 plastid-lipid associated protein pap (PAP_fibrillin superfamily)

PHATRDRAFT_47358 - plastid-lipid associated protein pap (PAP_fibrillin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47358
PHATRDRAFT_47900

PHATRDRAFT_47900 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47900
PHATRDRAFT_48974

PHATRDRAFT_48974 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48974
PHATRDRAFT_50128

PHATRDRAFT_50128 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50128
PHATRDRAFT_51092 glutamine synthetase (PLN02284)

PHATRDRAFT_51092 - glutamine synthetase (PLN02284)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51092
PHATRDRAFT_54681 glycosidefamily 16 (GH16_laminarinase_like)

PHATRDRAFT_54681 - glycosidefamily 16 (GH16_laminarinase_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54681
PHATRDRAFT_54983 nitrate reductase (PLN02252)

PHATRDRAFT_54983 - nitrate reductase (PLN02252)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54983
PHATRDRAFT_6457 cytidylate kinase (UMP_CMP_kin_fam)

PHATRDRAFT_6457 - cytidylate kinase (UMP_CMP_kin_fam)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6457
PHATRDRAFT_7893 ribosomal protein s15 (Ribosomal_S15p_S13e)

PHATRDRAFT_7893 - ribosomal protein s15 (Ribosomal_S15p_S13e)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7893
GO ID Go Term p-value q-value Cluster
GO:0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolism 0.00018625 0.427444 Phatr_bicluster_0179
GO:0006542 glutamine biosynthesis 0.0019758 1 Phatr_bicluster_0179
GO:0006807 nitrogen compound metabolism 0.0273521 1 Phatr_bicluster_0179
GO:0008033 tRNA processing 0.0388725 1 Phatr_bicluster_0179
GO:0016567 protein ubiquitination 0.13382 1 Phatr_bicluster_0179
GO:0006412 protein biosynthesis 0.277391 1 Phatr_bicluster_0179
GO:0006468 protein amino acid phosphorylation 0.2936 1 Phatr_bicluster_0179
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