Phatr_bicluster_0198 Residual: 0.32
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_0198 0.32 Phaeodactylum tricornutum
Displaying 1 - 29 of 29
PHATRDRAFT_13175 phenylalanine hydroxylase (arom_aa_hydroxylase superfamily)

PHATRDRAFT_13175 - phenylalanine hydroxylase (arom_aa_hydroxylase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13175
PHATRDRAFT_34805 methyl chloride transferase

PHATRDRAFT_34805 - methyl chloride transferase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34805
PHATRDRAFT_35573

PHATRDRAFT_35573 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35573
PHATRDRAFT_35582

PHATRDRAFT_35582 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35582
PHATRDRAFT_35756

PHATRDRAFT_35756 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35756
PHATRDRAFT_42469

PHATRDRAFT_42469 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42469
PHATRDRAFT_42564

PHATRDRAFT_42564 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42564
PHATRDRAFT_43175

PHATRDRAFT_43175 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43175
PHATRDRAFT_43305

PHATRDRAFT_43305 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43305
PHATRDRAFT_43531 tld family protein (TLD)

PHATRDRAFT_43531 - tld family protein (TLD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43531
PHATRDRAFT_44256 myb-like dna-bindingshaqkyf class family protein (SANT)

PHATRDRAFT_44256 - myb-like dna-bindingshaqkyf class family protein (SANT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44256
PHATRDRAFT_44531 protein-l-isoaspartate o-methyltransferase

PHATRDRAFT_44531 - protein-l-isoaspartate o-methyltransferase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44531
PHATRDRAFT_45040

PHATRDRAFT_45040 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45040
PHATRDRAFT_45256

PHATRDRAFT_45256 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45256
PHATRDRAFT_45349

PHATRDRAFT_45349 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45349
PHATRDRAFT_45356 mki67 (fha domain) interacting nucleolar phospho (RRM_SF superfamily)

PHATRDRAFT_45356 - mki67 (fha domain) interacting nucleolar phospho (RRM_SF superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45356
PHATRDRAFT_45610

PHATRDRAFT_45610 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45610
PHATRDRAFT_45988 related to metalloprotease mep1 (ZnMc superfamily)

PHATRDRAFT_45988 - related to metalloprotease mep1 (ZnMc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45988
PHATRDRAFT_46343 tellurite resistance protein (DUF1971)

PHATRDRAFT_46343 - tellurite resistance protein (DUF1971)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46343
PHATRDRAFT_46359 thioredoxin family protein (TRX_family)

PHATRDRAFT_46359 - thioredoxin family protein (TRX_family)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46359
PHATRDRAFT_46445

PHATRDRAFT_46445 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46445
PHATRDRAFT_46456 secreted protein (Abhydrolase_5)

PHATRDRAFT_46456 - secreted protein (Abhydrolase_5)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46456
PHATRDRAFT_46580

PHATRDRAFT_46580 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46580
PHATRDRAFT_46743

PHATRDRAFT_46743 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46743
PHATRDRAFT_47552

PHATRDRAFT_47552 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47552
PHATRDRAFT_49434 conserved protein with yshhsome fused to polo (DUF1115 superfamily)

PHATRDRAFT_49434 - conserved protein with yshhsome fused to polo (DUF1115 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49434
PHATRDRAFT_9266 domain protein (GATase1_Hsp31_like)

PHATRDRAFT_9266 - domain protein (GATase1_Hsp31_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9266
PHATRDRAFT_9277 sp i mismatch endonuclease (S1-P1_nuclease)

PHATRDRAFT_9277 - sp i mismatch endonuclease (S1-P1_nuclease)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9277
PHATRDRAFT_9897 thioredoxin m (TRX_family)

PHATRDRAFT_9897 - thioredoxin m (TRX_family)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9897
GO ID Go Term p-value q-value Cluster
GO:0006308 DNA catabolism 0.0019758 1 Phatr_bicluster_0198
GO:0009072 aromatic amino acid family metabolism 0.00591714 1 Phatr_bicluster_0198
GO:0006118 electron transport 0.0711586 1 Phatr_bicluster_0198
GO:0006464 protein modification 0.118 1 Phatr_bicluster_0198
GO:0006412 protein biosynthesis 0.277391 1 Phatr_bicluster_0198
GO:0006508 proteolysis and peptidolysis 0.365994 1 Phatr_bicluster_0198
GO:0008152 metabolism 0.453158 1 Phatr_bicluster_0198
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