Phatr_bicluster_0228 Residual: 0.14
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_0228 0.14 Phaeodactylum tricornutum
Displaying 1 - 16 of 16
PHATRDRAFT_17324 ribosomal proteinx-linked (PLN00036)

PHATRDRAFT_17324 - ribosomal proteinx-linked (PLN00036)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17324
PHATRDRAFT_17414 40s ribosomal protein s8 (PTZ00148)

PHATRDRAFT_17414 - 40s ribosomal protein s8 (PTZ00148)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17414
PHATRDRAFT_17519 40s ribosomal protein s16 (PLN00210)

PHATRDRAFT_17519 - 40s ribosomal protein s16 (PLN00210)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17519
PHATRDRAFT_17846 ribosomal protein l27e (KOW_RPL27)

PHATRDRAFT_17846 - ribosomal protein l27e (KOW_RPL27)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17846
PHATRDRAFT_17954 translation initiation factor 5a (PLN03107)

PHATRDRAFT_17954 - translation initiation factor 5a (PLN03107)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17954
PHATRDRAFT_18859 60s ribosomal protein l36 (Ribosomal_L36e)

PHATRDRAFT_18859 - 60s ribosomal protein l36 (Ribosomal_L36e)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18859
PHATRDRAFT_19615 ribosomal protein l35 (Ribosomal_L29_HIP)

PHATRDRAFT_19615 - ribosomal protein l35 (Ribosomal_L29_HIP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19615
PHATRDRAFT_21073 ribosomal protein (Ribosomal_S25)

PHATRDRAFT_21073 - ribosomal protein (Ribosomal_S25)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21073
PHATRDRAFT_23748 small subunit ribosomal protein 28 (S1_S28E)

PHATRDRAFT_23748 - small subunit ribosomal protein 28 (S1_S28E)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23748
PHATRDRAFT_25375 rpl13a-prov protein (Ribosomal_L13)

PHATRDRAFT_25375 - rpl13a-prov protein (Ribosomal_L13)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25375
PHATRDRAFT_27125 ribosomal protein l31e (Ribosomal_L31e)

PHATRDRAFT_27125 - ribosomal protein l31e (Ribosomal_L31e)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27125
PHATRDRAFT_28234 ribosomal protein l8 (PTZ00180)

PHATRDRAFT_28234 - ribosomal protein l8 (PTZ00180)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28234
PHATRDRAFT_50886 40s ribosomal protein s14 (PTZ00129)

PHATRDRAFT_50886 - 40s ribosomal protein s14 (PTZ00129)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50886
PHATRDRAFT_51018 ribosomal proteincomponent of cytosolic 80s ribosome and 60s large subunit (PLN00185)

PHATRDRAFT_51018 - ribosomal proteincomponent of cytosolic 80s ribosome and 60s large subunit (PLN00185)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51018
PHATRDRAFT_8185 protein component of the largeribosomalidentical to rpl42ap and has similarity to rat l44 required for propagation of the killer toxin-encoding m1 double-stranded rna satellite of the l-a double-stranded rna virus (PTZ00157)

PHATRDRAFT_8185 - protein component of the largeribosomalidentical to rpl42ap and has similarity to rat l44 required for propagation of the killer toxin-encoding m1 double-stranded rna satellite of the l-a double-stranded rna virus (PTZ00157)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8185
PHATRDRAFT_8686 ribosomal protein s12 (Ribosomal_L7Ae)

PHATRDRAFT_8686 - ribosomal protein s12 (Ribosomal_L7Ae)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8686
GO ID Go Term p-value q-value Cluster
GO:0006412 protein biosynthesis 3.76e-17 0.0000000000000874 Phatr_bicluster_0228
GO:0006816 calcium ion transport 0.0132807 1 Phatr_bicluster_0228
GO:0006413 translational initiation 0.101687 1 Phatr_bicluster_0228
GO:0006812 cation transport 0.113688 1 Phatr_bicluster_0228
GO:0008152 metabolism 0.743297 1 Phatr_bicluster_0228
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