Phatr_bicluster_0237 Residual: 0.20
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_0237 0.20 Phaeodactylum tricornutum
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Displaying 1 - 21 of 21
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PHATRDRAFT_12144 chromosome 1 open reading frame 33 (Ribosomal_P0_like)

PHATRDRAFT_12144 - chromosome 1 open reading frame 33 (Ribosomal_P0_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12144
PHATRDRAFT_19647 brix domain containing 1 (Brix superfamily)

PHATRDRAFT_19647 - brix domain containing 1 (Brix superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19647
PHATRDRAFT_20740 rna binding motif protein 19 (RRM3_RBM19_RRM2_MRD1)

PHATRDRAFT_20740 - rna binding motif protein 19 (RRM3_RBM19_RRM2_MRD1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20740
PHATRDRAFT_25133 nog2_klula nucleolar gtp-binding protein 2 (NGP_1)

PHATRDRAFT_25133 - nog2_klula nucleolar gtp-binding protein 2 (NGP_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25133
PHATRDRAFT_25549 dead (asp-glu-ala-asp) box polypeptide 56 (DEXDc superfamily)

PHATRDRAFT_25549 - dead (asp-glu-ala-asp) box polypeptide 56 (DEXDc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25549
PHATRDRAFT_26035 (Ribosomal_L1)

PHATRDRAFT_26035 - (Ribosomal_L1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_26035
PHATRDRAFT_27905 peter pan homolog (Brix)

PHATRDRAFT_27905 - peter pan homolog (Brix)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27905
PHATRDRAFT_31725 (PIN_Nob1)

PHATRDRAFT_31725 - (PIN_Nob1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31725
PHATRDRAFT_32758 dead box rna helicase (PRK04837)

PHATRDRAFT_32758 - dead box rna helicase (PRK04837)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32758
PHATRDRAFT_32836 (RRM_Nop6)

PHATRDRAFT_32836 - (RRM_Nop6)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32836
PHATRDRAFT_36897

PHATRDRAFT_36897 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36897
PHATRDRAFT_42464

PHATRDRAFT_42464 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42464
PHATRDRAFT_42570 ribosomal rna processing 12 homolog (NUC173 superfamily)

PHATRDRAFT_42570 - ribosomal rna processing 12 homolog (NUC173 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42570
PHATRDRAFT_43574 transducin family protein wd-40 repeat family protein (WD40 superfamily)

PHATRDRAFT_43574 - transducin family protein wd-40 repeat family protein (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43574
PHATRDRAFT_44555 zz domain protein (Kri1_C)

PHATRDRAFT_44555 - zz domain protein (Kri1_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44555
PHATRDRAFT_45888 nucleolar complex associated 4 homolog (CBF)

PHATRDRAFT_45888 - nucleolar complex associated 4 homolog (CBF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45888
PHATRDRAFT_46846 glioma tumor suppressor candidate region gene 2 isoform 4 (Nop53)

PHATRDRAFT_46846 - glioma tumor suppressor candidate region gene 2 isoform 4 (Nop53)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46846
PHATRDRAFT_47058 (Pumilio superfamily)

PHATRDRAFT_47058 - (Pumilio superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47058
PHATRDRAFT_49441 helicase domain protein (HA)

PHATRDRAFT_49441 - helicase domain protein (HA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49441
PHATRDRAFT_50332

PHATRDRAFT_50332 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50332
PHATRDRAFT_51007 u3 small nucleolar ribonucleoprotein protein (Brix)

PHATRDRAFT_51007 - u3 small nucleolar ribonucleoprotein protein (Brix)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51007
GO ID Go Term p-value q-value Cluster
GO:0016071 mRNA metabolism 0.0029615 1 Phatr_bicluster_0237
GO:0042254 ribosome biogenesis and assembly 0.00444005 1 Phatr_bicluster_0237
GO:0006412 protein biosynthesis 0.114635 1 Phatr_bicluster_0237
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