Phatr_bicluster_0130 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_0130 0.35 Phaeodactylum tricornutum
Displaying 1 - 30 of 30
PHATRDRAFT_11131 guanylate kinase (GMPK)

PHATRDRAFT_11131 - guanylate kinase (GMPK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11131
PHATRDRAFT_13386 spermidine synthase (AdoMet_MTases)

PHATRDRAFT_13386 - spermidine synthase (AdoMet_MTases)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13386
PHATRDRAFT_15960 probable 23s rna-specific pseudouridine synthase d (rluA_subfam)

PHATRDRAFT_15960 - probable 23s rna-specific pseudouridine synthase d (rluA_subfam)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15960
PHATRDRAFT_23629 p-typehadsubfamily ic (MgtA)

PHATRDRAFT_23629 - p-typehadsubfamily ic (MgtA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23629
PHATRDRAFT_2607 flag-tagged protein kinase domain ofmitogen-activated protein kinase kinase kinase (Pkinase)

PHATRDRAFT_2607 - flag-tagged protein kinase domain ofmitogen-activated protein kinase kinase kinase (Pkinase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_2607
PHATRDRAFT_32191

PHATRDRAFT_32191 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32191
PHATRDRAFT_34965 radical sam domain protein (TIGR00238 superfamily)

PHATRDRAFT_34965 - radical sam domain protein (TIGR00238 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34965
PHATRDRAFT_36915 (DUF155 superfamily)

PHATRDRAFT_36915 - (DUF155 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36915
PHATRDRAFT_37305

PHATRDRAFT_37305 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37305
PHATRDRAFT_40360 methyltransferase sam dependent (Methyltransf_4 superfamily)

PHATRDRAFT_40360 - methyltransferase sam dependent (Methyltransf_4 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40360
PHATRDRAFT_41701 nuclear distribution gene c homolog (p23_NUDC_like)

PHATRDRAFT_41701 - nuclear distribution gene c homolog (p23_NUDC_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41701
PHATRDRAFT_42556 sulfate transporter family protein (SUL1)

PHATRDRAFT_42556 - sulfate transporter family protein (SUL1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42556
PHATRDRAFT_44287

PHATRDRAFT_44287 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44287
PHATRDRAFT_44310 transmembrane protein (MS_channel superfamily)

PHATRDRAFT_44310 - transmembrane protein (MS_channel superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44310
PHATRDRAFT_44502 septin and tuftelin-interacting protein (TIP_N)

PHATRDRAFT_44502 - septin and tuftelin-interacting protein (TIP_N)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44502
PHATRDRAFT_44886

PHATRDRAFT_44886 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44886
PHATRDRAFT_44926

PHATRDRAFT_44926 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44926
PHATRDRAFT_45843

PHATRDRAFT_45843 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45843
PHATRDRAFT_46062 isoform cra_a

PHATRDRAFT_46062 - isoform cra_a

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46062
PHATRDRAFT_46251 (MFS)

PHATRDRAFT_46251 - (MFS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46251
PHATRDRAFT_47133

PHATRDRAFT_47133 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47133
PHATRDRAFT_47155 (PPP4R2 superfamily)

PHATRDRAFT_47155 - (PPP4R2 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47155
PHATRDRAFT_47984 ribonuclease ii (RNB superfamily)

PHATRDRAFT_47984 - ribonuclease ii (RNB superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47984
PHATRDRAFT_48055

PHATRDRAFT_48055 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48055
PHATRDRAFT_48149

PHATRDRAFT_48149 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48149
PHATRDRAFT_48846 nuclear prelamin a recognition factor-like (Fe_hyd_lg_C superfamily)

PHATRDRAFT_48846 - nuclear prelamin a recognition factor-like (Fe_hyd_lg_C superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48846
PHATRDRAFT_48984

PHATRDRAFT_48984 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48984
PHATRDRAFT_49451 trna rrna methyltransferase (SpoU)

PHATRDRAFT_49451 - trna rrna methyltransferase (SpoU)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49451
PHATRDRAFT_6645 ubiquitin-conjugating enzyme family protein (UBCc superfamily)

PHATRDRAFT_6645 - ubiquitin-conjugating enzyme family protein (UBCc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6645
PHATRDRAFT_6698 enhancer of zeste homolog 1 (enx-2) (SET)

PHATRDRAFT_6698 - enhancer of zeste homolog 1 (enx-2) (SET)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6698
GO ID Go Term p-value q-value Cluster
GO:0006396 RNA processing 0.00953966 1 Phatr_bicluster_0130
GO:0015992 proton transport 0.0374288 1 Phatr_bicluster_0130
GO:0006812 cation transport 0.0710389 1 Phatr_bicluster_0130
GO:0006512 ubiquitin cycle 0.0986411 1 Phatr_bicluster_0130
GO:0006418 tRNA aminoacylation for protein translation 0.132692 1 Phatr_bicluster_0130
GO:0006464 protein modification 0.158622 1 Phatr_bicluster_0130
GO:0006468 protein amino acid phosphorylation 0.380037 1 Phatr_bicluster_0130
GO:0006810 transport 0.412691 1 Phatr_bicluster_0130
GO:0006355 regulation of transcription, DNA-dependent 0.45797 1 Phatr_bicluster_0130
GO:0008152 metabolism 0.564066 1 Phatr_bicluster_0130
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