Phatr_bicluster_0226 Residual: 0.15
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_0226 0.15 Phaeodactylum tricornutum
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Displaying 1 - 17 of 17
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PHATRDRAFT_10544 (DUF1253)

PHATRDRAFT_10544 - (DUF1253)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10544
PHATRDRAFT_14032 dead deah box (DEADc)

PHATRDRAFT_14032 - dead deah box (DEADc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14032
PHATRDRAFT_14068 chromosome 9 open reading frame 114 (Methyltrn_RNA_3)

PHATRDRAFT_14068 - chromosome 9 open reading frame 114 (Methyltrn_RNA_3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14068
PHATRDRAFT_1840 amidophosphoribosyltransferase (PRK09246)

PHATRDRAFT_1840 - amidophosphoribosyltransferase (PRK09246)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_1840
PHATRDRAFT_22658 rna cyclase homolog (18S_RNA_Rcl1p)

PHATRDRAFT_22658 - rna cyclase homolog (18S_RNA_Rcl1p)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22658
PHATRDRAFT_23865 atp-dependent rna helicase-like protein (HA2)

PHATRDRAFT_23865 - atp-dependent rna helicase-like protein (HA2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23865
PHATRDRAFT_41002 thif family (YgdL_like)

PHATRDRAFT_41002 - thif family (YgdL_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41002
PHATRDRAFT_47420 mgc148433 protein (APH_ChoK_like superfamily)

PHATRDRAFT_47420 - mgc148433 protein (APH_ChoK_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47420
PHATRDRAFT_47446 heat shock proteindomain protein (DnaJ)

PHATRDRAFT_47446 - heat shock proteindomain protein (DnaJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47446
PHATRDRAFT_47526 small nucleolar ribonucleoprotein complex component (Utp12 superfamily)

PHATRDRAFT_47526 - small nucleolar ribonucleoprotein complex component (Utp12 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47526
PHATRDRAFT_47947 glutamate-rich wd repeat containing 1 (COG2319)

PHATRDRAFT_47947 - glutamate-rich wd repeat containing 1 (COG2319)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47947
PHATRDRAFT_48320 phytanoyl-dioxygenase family protein (PhyH superfamily)

PHATRDRAFT_48320 - phytanoyl-dioxygenase family protein (PhyH superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48320
PHATRDRAFT_50135 rio kinase 1 (RIO1_euk)

PHATRDRAFT_50135 - rio kinase 1 (RIO1_euk)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50135
PHATRDRAFT_50246 (Utp14)

PHATRDRAFT_50246 - (Utp14)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50246
PHATRDRAFT_50326 superkiller viralicidic activity 2-like 2 (COG4581)

PHATRDRAFT_50326 - superkiller viralicidic activity 2-like 2 (COG4581)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50326
PHATRDRAFT_5128 proteasome component pre2 precursor (Ntn_hydrolase superfamily)

PHATRDRAFT_5128 - proteasome component pre2 precursor (Ntn_hydrolase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5128
PHATRDRAFT_7346 mgc53444 protein (Ribosomal_L24e_L24)

PHATRDRAFT_7346 - mgc53444 protein (Ribosomal_L24e_L24)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7346
GO ID Go Term p-value q-value Cluster
GO:0006412 protein biosynthesis 0.216202 1 Phatr_bicluster_0226
GO:0008152 metabolism 0.364015 1 Phatr_bicluster_0226
GO:0009113 purine base biosynthesis 0.00296186 1 Phatr_bicluster_0226
GO:0009116 nucleoside metabolism 0.0132709 1 Phatr_bicluster_0226
GO:0006511 ubiquitin-dependent protein catabolism 0.0648966 1 Phatr_bicluster_0226
GO:0006457 protein folding 0.161416 1 Phatr_bicluster_0226
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