Phatr_bicluster_0251 Residual: 0.21
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_0251 0.21 Phaeodactylum tricornutum
Displaying 1 - 26 of 26
PHATRDRAFT_10122 rna binding motif protein 22 (RRM_SF superfamily)

PHATRDRAFT_10122 - rna binding motif protein 22 (RRM_SF superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10122
PHATRDRAFT_12401 cog0121: glutamine amidotransferase (YafJ)

PHATRDRAFT_12401 - cog0121: glutamine amidotransferase (YafJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12401
PHATRDRAFT_12431 phospholipase d (PLN02270)

PHATRDRAFT_12431 - phospholipase d (PLN02270)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12431
PHATRDRAFT_14198 (ANK)

PHATRDRAFT_14198 - (ANK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14198
PHATRDRAFT_31831 ef hand family protein

PHATRDRAFT_31831 - ef hand family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31831
PHATRDRAFT_33731 (PAP_fibrillin superfamily)

PHATRDRAFT_33731 - (PAP_fibrillin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33731
PHATRDRAFT_34712 prp3 pre-mrna processing factor 3 homolog (PRP3 superfamily)

PHATRDRAFT_34712 - prp3 pre-mrna processing factor 3 homolog (PRP3 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34712
PHATRDRAFT_34799

PHATRDRAFT_34799 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34799
PHATRDRAFT_35510

PHATRDRAFT_35510 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35510
PHATRDRAFT_35721

PHATRDRAFT_35721 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35721
PHATRDRAFT_35809

PHATRDRAFT_35809 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35809
PHATRDRAFT_35813 atp binding alanine-trna ligase (PLN02961)

PHATRDRAFT_35813 - atp binding alanine-trna ligase (PLN02961)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35813
PHATRDRAFT_35839

PHATRDRAFT_35839 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35839
PHATRDRAFT_42548 glucose inhibited division protein (GidB)

PHATRDRAFT_42548 - glucose inhibited division protein (GidB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42548
PHATRDRAFT_43303

PHATRDRAFT_43303 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43303
PHATRDRAFT_43539 clan s-familyrhomboid-like serine peptidase (COG0705)

PHATRDRAFT_43539 - clan s-familyrhomboid-like serine peptidase (COG0705)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43539
PHATRDRAFT_44656 (VPS9 superfamily)

PHATRDRAFT_44656 - (VPS9 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44656
PHATRDRAFT_44785 serine threonine rich antigen (PHA03247)

PHATRDRAFT_44785 - serine threonine rich antigen (PHA03247)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44785
PHATRDRAFT_44938 selenoprotein u (AhpC-TSA_2)

PHATRDRAFT_44938 - selenoprotein u (AhpC-TSA_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44938
PHATRDRAFT_45586

PHATRDRAFT_45586 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45586
PHATRDRAFT_46537 (U-box superfamily)

PHATRDRAFT_46537 - (U-box superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46537
PHATRDRAFT_46852

PHATRDRAFT_46852 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46852
PHATRDRAFT_46865 (AlkA)

PHATRDRAFT_46865 - (AlkA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46865
PHATRDRAFT_47919 cytoplasmic pre-60s factor required for the correct recycling of shuttling factorsarx1 and tif6 at the end of the ribosomal large subunit biogenesis involved in bud growth in the mitotic signaling network (zf-C2H2_2)

PHATRDRAFT_47919 - cytoplasmic pre-60s factor required for the correct recycling of shuttling factorsarx1 and tif6 at the end of the ribosomal large subunit biogenesis involved in bud growth in the mitotic signaling network (zf-C2H2_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47919
PHATRDRAFT_8827 sirt1_caebrnad-dependent deacetylase sir2 homolog (protein sir-) (SIR2 superfamily)

PHATRDRAFT_8827 - sirt1_caebrnad-dependent deacetylase sir2 homolog (protein sir-) (SIR2 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8827
PHATRDRAFT_9180 atp-bindingsub-family c (cftr mrp)member 4 (CFTR_protein)

PHATRDRAFT_9180 - atp-bindingsub-family c (cftr mrp)member 4 (CFTR_protein)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9180
GO ID Go Term p-value q-value Cluster
GO:0006284 base-excision repair 0.00813004 1 Phatr_bicluster_0251
GO:0006419 alanyl-tRNA aminoacylation 0.00813004 1 Phatr_bicluster_0251
GO:0006342 chromatin silencing 0.0162 1 Phatr_bicluster_0251
GO:0007049 cell cycle 0.0162 1 Phatr_bicluster_0251
GO:0007242 intracellular signaling cascade 0.108492 1 Phatr_bicluster_0251
GO:0006355 regulation of transcription, DNA-dependent 0.116151 1 Phatr_bicluster_0251
GO:0016567 protein ubiquitination 0.17931 1 Phatr_bicluster_0251
GO:0008152 metabolism 0.187614 1 Phatr_bicluster_0251
GO:0006810 transport 0.412691 1 Phatr_bicluster_0251
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