Phatr_bicluster_0234 Residual: 0.45
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_0234 0.45 Phaeodactylum tricornutum
Displaying 1 - 28 of 28
PHATRDRAFT_107 leucine-rich repeat transmembrane protein (LRR_RI superfamily)

PHATRDRAFT_107 - leucine-rich repeat transmembrane protein (LRR_RI superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_107
PHATRDRAFT_11811 enoyl-hydratase isomerase (crotonase-like)

PHATRDRAFT_11811 - enoyl-hydratase isomerase (crotonase-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11811
PHATRDRAFT_14327 nli interacting factorfamily protein (NIF)

PHATRDRAFT_14327 - nli interacting factorfamily protein (NIF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14327
PHATRDRAFT_19805 hypersensitive-induced response protein (SPFH_like_u4)

PHATRDRAFT_19805 - hypersensitive-induced response protein (SPFH_like_u4)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19805
PHATRDRAFT_2761 purple acid phosphatase-like protein (MPP_superfamily superfamily)

PHATRDRAFT_2761 - purple acid phosphatase-like protein (MPP_superfamily superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_2761
PHATRDRAFT_33198 mesenchymal stem cell protein dscd75 (4HBT)

PHATRDRAFT_33198 - mesenchymal stem cell protein dscd75 (4HBT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33198
PHATRDRAFT_33901 atp binding protein serine threonine kinase (PLN00113)

PHATRDRAFT_33901 - atp binding protein serine threonine kinase (PLN00113)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33901
PHATRDRAFT_34800 phosphoglycerate dehydrogenase-like protein (PLN02928)

PHATRDRAFT_34800 - phosphoglycerate dehydrogenase-like protein (PLN02928)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34800
PHATRDRAFT_36043 (DUF913 superfamily)

PHATRDRAFT_36043 - (DUF913 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36043
PHATRDRAFT_42500 (Band_7)

PHATRDRAFT_42500 - (Band_7)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42500
PHATRDRAFT_43361

PHATRDRAFT_43361 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43361
PHATRDRAFT_43674 (Beta_propel)

PHATRDRAFT_43674 - (Beta_propel)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43674
PHATRDRAFT_44326 (DUF563)

PHATRDRAFT_44326 - (DUF563)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44326
PHATRDRAFT_44442 nuclear localization sequence binding protein nsr1p (RRM)

PHATRDRAFT_44442 - nuclear localization sequence binding protein nsr1p (RRM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44442
PHATRDRAFT_45416 (WD40 superfamily)

PHATRDRAFT_45416 - (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45416
PHATRDRAFT_46321 prenylated rab acceptor family protein (PRA1 superfamily)

PHATRDRAFT_46321 - prenylated rab acceptor family protein (PRA1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46321
PHATRDRAFT_48247

PHATRDRAFT_48247 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48247
PHATRDRAFT_49007

PHATRDRAFT_49007 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49007
PHATRDRAFT_49277 damaged dna binding protein (BTB)

PHATRDRAFT_49277 - damaged dna binding protein (BTB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49277
PHATRDRAFT_49399 fis1_debha mitochondria fission 1 protein

PHATRDRAFT_49399 - fis1_debha mitochondria fission 1 protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49399
PHATRDRAFT_49894 cyclin a-like protein

PHATRDRAFT_49894 - cyclin a-like protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49894
PHATRDRAFT_49945

PHATRDRAFT_49945 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49945
PHATRDRAFT_50156

PHATRDRAFT_50156 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50156
PHATRDRAFT_50492

PHATRDRAFT_50492 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50492
PHATRDRAFT_50594

PHATRDRAFT_50594 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50594
PHATRDRAFT_54319 secreted trypsin-like serine protease (Tryp_SPc)

PHATRDRAFT_54319 - secreted trypsin-like serine protease (Tryp_SPc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54319
PHATRDRAFT_54658 glue protein

PHATRDRAFT_54658 - glue protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54658
PHATRDRAFT_54743 mgc83346 protein (WD40)

PHATRDRAFT_54743 - mgc83346 protein (WD40)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54743
GO ID Go Term p-value q-value Cluster
GO:0051028 mRNA transport 0.00172882 1 Phatr_bicluster_0234
GO:0006564 L-serine biosynthesis 0.013759 1 Phatr_bicluster_0234
GO:0000074 regulation of cell cycle 0.0573612 1 Phatr_bicluster_0234
GO:0006512 ubiquitin cycle 0.0639203 1 Phatr_bicluster_0234
GO:0008152 metabolism 0.0865285 1 Phatr_bicluster_0234
GO:0006118 electron transport 0.33492 1 Phatr_bicluster_0234
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