Phatr_bicluster_0011 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_0011 0.40 Phaeodactylum tricornutum
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Displaying 1 - 24 of 24
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PHATRDRAFT_14627 casein kinase ii beta chain (CK_II_beta superfamily)

PHATRDRAFT_14627 - casein kinase ii beta chain (CK_II_beta superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14627
PHATRDRAFT_15138 (DnaJ-X superfamily)

PHATRDRAFT_15138 - (DnaJ-X superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15138
PHATRDRAFT_32286

PHATRDRAFT_32286 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32286
PHATRDRAFT_32365

PHATRDRAFT_32365 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32365
PHATRDRAFT_34307 at1g03630 f21b7_11 (NADB_Rossmann superfamily)

PHATRDRAFT_34307 - at1g03630 f21b7_11 (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34307
PHATRDRAFT_34708 ankyrin repeat protein (ANK)

PHATRDRAFT_34708 - ankyrin repeat protein (ANK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34708
PHATRDRAFT_35605

PHATRDRAFT_35605 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35605
PHATRDRAFT_36993

PHATRDRAFT_36993 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36993
PHATRDRAFT_40917 chondroitin sulfate proteoglycan 2

PHATRDRAFT_40917 - chondroitin sulfate proteoglycan 2

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40917
PHATRDRAFT_42586

PHATRDRAFT_42586 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42586
PHATRDRAFT_43214 (AFD_class_I superfamily)

PHATRDRAFT_43214 - (AFD_class_I superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43214
PHATRDRAFT_44258 amidohydrolase 2 (metallo-dependent_hydrolases superfamily)

PHATRDRAFT_44258 - amidohydrolase 2 (metallo-dependent_hydrolases superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44258
PHATRDRAFT_44411 loc100036669 protein (AhpC-TSA_2)

PHATRDRAFT_44411 - loc100036669 protein (AhpC-TSA_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44411
PHATRDRAFT_44925

PHATRDRAFT_44925 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44925
PHATRDRAFT_45060 ran binding protein 10 (SPRY_RanBP_like)

PHATRDRAFT_45060 - ran binding protein 10 (SPRY_RanBP_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45060
PHATRDRAFT_45656 anion exchanger 1 (HCO3_cotransp superfamily)

PHATRDRAFT_45656 - anion exchanger 1 (HCO3_cotransp superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45656
PHATRDRAFT_45662 nucleosome binding protein (HMGB-UBF_HMG-box)

PHATRDRAFT_45662 - nucleosome binding protein (HMGB-UBF_HMG-box)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45662
PHATRDRAFT_45797 alkaline serine protease (PHA03269)

PHATRDRAFT_45797 - alkaline serine protease (PHA03269)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45797
PHATRDRAFT_47230

PHATRDRAFT_47230 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47230
PHATRDRAFT_48137

PHATRDRAFT_48137 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48137
PHATRDRAFT_48316 ribosome recycling factor (RRF)

PHATRDRAFT_48316 - ribosome recycling factor (RRF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48316
PHATRDRAFT_49733 duf84-like protein

PHATRDRAFT_49733 - duf84-like protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49733
PHATRDRAFT_50621 heat shock transcription factor 4 isoform 1 (HSF_DNA-bind)

PHATRDRAFT_50621 - heat shock transcription factor 4 isoform 1 (HSF_DNA-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50621
PHATRDRAFT_55150 pbx knotted 1 homeobox 1 (homeodomain)

PHATRDRAFT_55150 - pbx knotted 1 homeobox 1 (homeodomain)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55150
GO ID Go Term p-value q-value Cluster
GO:0006820 anion transport 0.0234852 1 Phatr_bicluster_0011
GO:0006355 regulation of transcription, DNA-dependent 0.065721 1 Phatr_bicluster_0011
GO:0006418 tRNA aminoacylation for protein translation 0.0983212 1 Phatr_bicluster_0011
GO:0006457 protein folding 0.209255 1 Phatr_bicluster_0011
GO:0006412 protein biosynthesis 0.277391 1 Phatr_bicluster_0011
GO:0006508 proteolysis and peptidolysis 0.365994 1 Phatr_bicluster_0011
GO:0008152 metabolism 0.453158 1 Phatr_bicluster_0011
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