Phatr_bicluster_0159 Residual: 0.19
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_0159 0.19 Phaeodactylum tricornutum
" class="views-fluidgrid-wrapper clear-block">
Displaying 1 - 18 of 18
" class="views-fluidgrid-wrapper clear-block">
PHATRDRAFT_14269 60s ribosomal protein l29 (Ribosomal_L29e)

PHATRDRAFT_14269 - 60s ribosomal protein l29 (Ribosomal_L29e)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14269
PHATRDRAFT_15619 ribosomal protein l13 isoform 2 (Ribosomal_L13e superfamily)

PHATRDRAFT_15619 - ribosomal protein l13 isoform 2 (Ribosomal_L13e superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15619
PHATRDRAFT_15632 rla2_altal60s acidic ribosomal protein p2 (minor allergen alt a 5) (alt a 6) (alt a vi) (Ribosomal_P1_P2_L12p superfamily)

PHATRDRAFT_15632 - rla2_altal60s acidic ribosomal protein p2 (minor allergen alt a 5) (alt a 6) (alt a vi) (Ribosomal_P1_P2_L12p superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15632
PHATRDRAFT_15852 copper zinc superoxide dismutasensodb (Cu-Zn_Superoxide_Dismutase)

PHATRDRAFT_15852 - copper zinc superoxide dismutasensodb (Cu-Zn_Superoxide_Dismutase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15852
PHATRDRAFT_18475 translation elongation factor 1 alpha (PTZ00141)

PHATRDRAFT_18475 - translation elongation factor 1 alpha (PTZ00141)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18475
PHATRDRAFT_18585 60s ribosomal protein l28 (Ribosomal_L28e)

PHATRDRAFT_18585 - 60s ribosomal protein l28 (Ribosomal_L28e)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18585
PHATRDRAFT_21659 ribosomal protein rpl32 (Ribosomal_L32_L32e)

PHATRDRAFT_21659 - ribosomal protein rpl32 (Ribosomal_L32_L32e)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21659
PHATRDRAFT_23324 ribosomal protein l11-like protein (PTZ00156)

PHATRDRAFT_23324 - ribosomal protein l11-like protein (PTZ00156)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23324
PHATRDRAFT_23687 ribosomal protein l35a (Ribosomal_L35Ae superfamily)

PHATRDRAFT_23687 - ribosomal protein l35a (Ribosomal_L35Ae superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23687
PHATRDRAFT_25577 hydroxyproline-rich glycoprotein 1 (Ribosomal_L14e)

PHATRDRAFT_25577 - hydroxyproline-rich glycoprotein 1 (Ribosomal_L14e)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25577
PHATRDRAFT_28359 60s ribosomal protein l10a (Ribosomal_L1)

PHATRDRAFT_28359 - 60s ribosomal protein l10a (Ribosomal_L1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28359
PHATRDRAFT_28979 ribosomal protein l12 (PLN03072)

PHATRDRAFT_28979 - ribosomal protein l12 (PLN03072)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28979
PHATRDRAFT_29097 40s ribosomal protein s5 (PTZ00091)

PHATRDRAFT_29097 - 40s ribosomal protein s5 (PTZ00091)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29097
PHATRDRAFT_30160 40s ribosomal protein s26 (PLN00186)

PHATRDRAFT_30160 - 40s ribosomal protein s26 (PLN00186)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30160
PHATRDRAFT_30315 ribosomal proteincomponent of cytosolic 80s ribosome and 60s large subunit (Ribosomal_L18e superfamily)

PHATRDRAFT_30315 - ribosomal proteincomponent of cytosolic 80s ribosome and 60s large subunit (Ribosomal_L18e superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30315
PHATRDRAFT_30660 acidic ribosomal phosphoprotein p0 (Ribosomal_P0_L10e)

PHATRDRAFT_30660 - acidic ribosomal phosphoprotein p0 (Ribosomal_P0_L10e)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30660
PHATRDRAFT_43840 60s ribosomal protein l30 (PTZ00106)

PHATRDRAFT_43840 - 60s ribosomal protein l30 (PTZ00106)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43840
PHATRDRAFT_51066 40s ribosomal protein s19 (Ribosomal_S19e)

PHATRDRAFT_51066 - 40s ribosomal protein s19 (Ribosomal_S19e)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51066
GO ID Go Term p-value q-value Cluster
GO:0006412 protein biosynthesis 1.74e-18 0.00000000000000404 Phatr_bicluster_0159
GO:0006414 translational elongation 0.00183602 1 Phatr_bicluster_0159
GO:0006801 superoxide metabolism 0.0186452 1 Phatr_bicluster_0159
GO:0042254 ribosome biogenesis and assembly 0.0278439 1 Phatr_bicluster_0159
Log in to post comments