Phatr_bicluster_0255 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_0255 0.14 Phaeodactylum tricornutum
Displaying 1 - 17 of 17
PHATRDRAFT_14145 pescadillo n-terminus family protein (NOP7)

PHATRDRAFT_14145 - pescadillo n-terminus family protein (NOP7)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14145
PHATRDRAFT_14450 ribosomal protein l7 (Ribosomal_L7_archeal_euk)

PHATRDRAFT_14450 - ribosomal protein l7 (Ribosomal_L7_archeal_euk)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14450
PHATRDRAFT_15862 (NMD3)

PHATRDRAFT_15862 - (NMD3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15862
PHATRDRAFT_16814 bop1-prov protein (BOP1NT)

PHATRDRAFT_16814 - bop1-prov protein (BOP1NT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16814
PHATRDRAFT_21538 utp11-u3 small nucleolar ribonucleoprotein (Utp11)

PHATRDRAFT_21538 - utp11-u3 small nucleolar ribonucleoprotein (Utp11)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21538
PHATRDRAFT_22868 notchless protein homolog (WD40)

PHATRDRAFT_22868 - notchless protein homolog (WD40)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22868
PHATRDRAFT_30960 rbm13-prov protein (MAK16)

PHATRDRAFT_30960 - rbm13-prov protein (MAK16)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30960
PHATRDRAFT_37596 ltv1 homolog (LTV)

PHATRDRAFT_37596 - ltv1 homolog (LTV)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37596
PHATRDRAFT_44047 wd repeats and sof domain containing 1 (COG2319)

PHATRDRAFT_44047 - wd repeats and sof domain containing 1 (COG2319)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44047
PHATRDRAFT_44055 23s rrna (uracil-5-)-methyltransferase (meth_trns_rumB)

PHATRDRAFT_44055 - 23s rrna (uracil-5-)-methyltransferase (meth_trns_rumB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44055
PHATRDRAFT_46993

PHATRDRAFT_46993 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46993
PHATRDRAFT_46994 u3 snornp protein (Mpp10)

PHATRDRAFT_46994 - u3 snornp protein (Mpp10)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46994
PHATRDRAFT_47259

PHATRDRAFT_47259 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47259
PHATRDRAFT_48417 (P4Hc)

PHATRDRAFT_48417 - (P4Hc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48417
PHATRDRAFT_49433 (COG5638)

PHATRDRAFT_49433 - (COG5638)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49433
PHATRDRAFT_49450 rrna processing protein rrp7 (RRP7_like superfamily)

PHATRDRAFT_49450 - rrna processing protein rrp7 (RRP7_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49450
PHATRDRAFT_50630 ccaat enhancer binding protein zeta isoform 2 (COG5593)

PHATRDRAFT_50630 - ccaat enhancer binding protein zeta isoform 2 (COG5593)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50630
GO ID Go Term p-value q-value Cluster
GO:0008283 cell proliferation 0.00296186 1 Phatr_bicluster_0255
GO:0016071 mRNA metabolism 0.00591641 1 Phatr_bicluster_0255
GO:0006364 rRNA processing 0.0118036 1 Phatr_bicluster_0255
GO:0007186 G-protein coupled receptor protein signaling pathway 0.0191218 1 Phatr_bicluster_0255
GO:0019538 protein metabolism 0.0522062 1 Phatr_bicluster_0255
GO:0006412 protein biosynthesis 0.216202 1 Phatr_bicluster_0255
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