Phatr_bicluster_0028 Residual: 0.40
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_0028 0.40 Phaeodactylum tricornutum
Displaying 1 - 36 of 36
PHATRDRAFT_10723 abc1 family protein (AarF)

PHATRDRAFT_10723 - abc1 family protein (AarF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10723
PHATRDRAFT_11358 acetyltransferasedomain-containing protein (RimI)

PHATRDRAFT_11358 - acetyltransferasedomain-containing protein (RimI)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11358
PHATRDRAFT_13834 ssu72-like family protein (Ssu72 superfamily)

PHATRDRAFT_13834 - ssu72-like family protein (Ssu72 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13834
PHATRDRAFT_14163 at5g01350 t10o8_60

PHATRDRAFT_14163 - at5g01350 t10o8_60

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14163
PHATRDRAFT_15536 nitrilasemember 2 (nit)

PHATRDRAFT_15536 - nitrilasemember 2 (nit)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15536
PHATRDRAFT_15747 domain containing protein (DnaJ)

PHATRDRAFT_15747 - domain containing protein (DnaJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15747
PHATRDRAFT_15806 amine oxidase (COG3349)

PHATRDRAFT_15806 - amine oxidase (COG3349)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15806
PHATRDRAFT_25619 alpha beta fold family protein (PLN02824)

PHATRDRAFT_25619 - alpha beta fold family protein (PLN02824)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25619
PHATRDRAFT_27534 alportmentalmidface hypoplasia and elliptocytosis chromosomalgene 1 (AMMECR1)

PHATRDRAFT_27534 - alportmentalmidface hypoplasia and elliptocytosis chromosomalgene 1 (AMMECR1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27534
PHATRDRAFT_3145 eukaryotic pantothenate kinase family protein (Fumble)

PHATRDRAFT_3145 - eukaryotic pantothenate kinase family protein (Fumble)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3145
PHATRDRAFT_37873

PHATRDRAFT_37873 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37873
PHATRDRAFT_38261 adenylate kinase (DUF1995 superfamily)

PHATRDRAFT_38261 - adenylate kinase (DUF1995 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38261
PHATRDRAFT_38781

PHATRDRAFT_38781 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38781
PHATRDRAFT_39066 hydroxymethylbutenyl pyrophosphate reductase (S1_like superfamily)

PHATRDRAFT_39066 - hydroxymethylbutenyl pyrophosphate reductase (S1_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39066
PHATRDRAFT_39283

PHATRDRAFT_39283 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39283
PHATRDRAFT_44187

PHATRDRAFT_44187 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44187
PHATRDRAFT_46271

PHATRDRAFT_46271 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46271
PHATRDRAFT_46278 kelch motif family protein

PHATRDRAFT_46278 - kelch motif family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46278
PHATRDRAFT_46448 heat shock protein hsp20 (ACD_sHsps-like)

PHATRDRAFT_46448 - heat shock protein hsp20 (ACD_sHsps-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46448
PHATRDRAFT_47300

PHATRDRAFT_47300 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47300
PHATRDRAFT_47398 protein kinase domain containing protein (zf-MYND)

PHATRDRAFT_47398 - protein kinase domain containing protein (zf-MYND)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47398
PHATRDRAFT_47672

PHATRDRAFT_47672 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47672
PHATRDRAFT_48034 rnf13 protein (RING)

PHATRDRAFT_48034 - rnf13 protein (RING)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48034
PHATRDRAFT_48069

PHATRDRAFT_48069 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48069
PHATRDRAFT_48652

PHATRDRAFT_48652 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48652
PHATRDRAFT_48859

PHATRDRAFT_48859 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48859
PHATRDRAFT_48932 monooxygenase involved in coenzyme qbiosynthesis (NAD_binding_8 superfamily)

PHATRDRAFT_48932 - monooxygenase involved in coenzyme qbiosynthesis (NAD_binding_8 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48932
PHATRDRAFT_49057 (Cation_efflux superfamily)

PHATRDRAFT_49057 - (Cation_efflux superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49057
PHATRDRAFT_49088

PHATRDRAFT_49088 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49088
PHATRDRAFT_49209

PHATRDRAFT_49209 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49209
PHATRDRAFT_49267

PHATRDRAFT_49267 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49267
PHATRDRAFT_49505 beta-eliminating lyase family protein (TnaA)

PHATRDRAFT_49505 - beta-eliminating lyase family protein (TnaA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49505
PHATRDRAFT_49598

PHATRDRAFT_49598 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49598
PHATRDRAFT_49725 (NYN)

PHATRDRAFT_49725 - (NYN)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49725
PHATRDRAFT_49811

PHATRDRAFT_49811 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49811
PHATRDRAFT_7629 gtp pyrophosphokinase (HD_4 superfamily)

PHATRDRAFT_7629 - gtp pyrophosphokinase (HD_4 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7629
GO ID Go Term p-value q-value Cluster
GO:0015937 coenzyme A biosynthesis 0.004934 1 Phatr_bicluster_0028
GO:0009072 aromatic amino acid family metabolism 0.00739277 1 Phatr_bicluster_0028
GO:0006807 nitrogen compound metabolism 0.0340807 1 Phatr_bicluster_0028
GO:0006725 aromatic compound metabolism 0.0483639 1 Phatr_bicluster_0028
GO:0006118 electron transport 0.106225 1 Phatr_bicluster_0028
GO:0016567 protein ubiquitination 0.164415 1 Phatr_bicluster_0028
GO:0006457 protein folding 0.254387 1 Phatr_bicluster_0028
GO:0006468 protein amino acid phosphorylation 0.352461 1 Phatr_bicluster_0028
GO:0008152 metabolism 0.529843 1 Phatr_bicluster_0028
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