Phatr_bicluster_0086 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_0086 0.15 Phaeodactylum tricornutum
Displaying 1 - 15 of 15
PHATRDRAFT_11823 histone h2b (PLN00158)

PHATRDRAFT_11823 - histone h2b (PLN00158)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11823
PHATRDRAFT_11841 histone 3 (PTZ00018)

PHATRDRAFT_11841 - histone 3 (PTZ00018)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11841
PHATRDRAFT_30352 (Smc)

PHATRDRAFT_30352 - (Smc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30352
PHATRDRAFT_32786 kelch repeat-containing protein (PLN02193)

PHATRDRAFT_32786 - kelch repeat-containing protein (PLN02193)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32786
PHATRDRAFT_35642

PHATRDRAFT_35642 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35642
PHATRDRAFT_42993 200 kda antigen p200 (PTZ00121)

PHATRDRAFT_42993 - 200 kda antigen p200 (PTZ00121)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42993
PHATRDRAFT_43196 metalloprotease mep1 homolog (ZnMc superfamily)

PHATRDRAFT_43196 - metalloprotease mep1 homolog (ZnMc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43196
PHATRDRAFT_45915 rna binding protein

PHATRDRAFT_45915 - rna binding protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45915
PHATRDRAFT_47179 excision repair cross-complementing rodent repair deficiency complementation group 6 - like (SNF2_N)

PHATRDRAFT_47179 - excision repair cross-complementing rodent repair deficiency complementation group 6 - like (SNF2_N)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47179
PHATRDRAFT_47761 glycoprotein 340

PHATRDRAFT_47761 - glycoprotein 340

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47761
PHATRDRAFT_48434

PHATRDRAFT_48434 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48434
PHATRDRAFT_48451 (CHAT superfamily)

PHATRDRAFT_48451 - (CHAT superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48451
PHATRDRAFT_50429 secreted lipopolysaccharide sugar transferase like family 8 glycosyltransferase (Glyco_tranf_GTA_type superfamily)

PHATRDRAFT_50429 - secreted lipopolysaccharide sugar transferase like family 8 glycosyltransferase (Glyco_tranf_GTA_type superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50429
PHATRDRAFT_54381 multiple banded antigen (H15)

PHATRDRAFT_54381 - multiple banded antigen (H15)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54381
PHATRDRAFT_54591 (PLN03076)

PHATRDRAFT_54591 - (PLN03076)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54591
GO ID Go Term p-value q-value Cluster
GO:0006334 nucleosome assembly 0.000303969 0.69609 Phatr_bicluster_0086
GO:0007001 chromosome organization and biogenesis (sensu Eukaryota) 0.000344214 0.787907 Phatr_bicluster_0086
GO:0016051 carbohydrate biosynthesis 0.00689992 1 Phatr_bicluster_0086
GO:0051276 chromosome organization and biogenesis 0.00689992 1 Phatr_bicluster_0086
GO:0006508 proteolysis and peptidolysis 0.328797 1 Phatr_bicluster_0086
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