Phatr_bicluster_0134 Residual: 0.25
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_0134 0.25 Phaeodactylum tricornutum
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Displaying 1 - 25 of 25
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PHATRDRAFT_12252 n-ethylmaleimide sensitive fusion (RPT1)

PHATRDRAFT_12252 - n-ethylmaleimide sensitive fusion (RPT1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12252
PHATRDRAFT_12740 amidase family protein (Amidase superfamily)

PHATRDRAFT_12740 - amidase family protein (Amidase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12740
PHATRDRAFT_14549 protein tyrosine (DSPc superfamily)

PHATRDRAFT_14549 - protein tyrosine (DSPc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14549
PHATRDRAFT_16052 glycoside hydrolase family 28 protein polygalacturonasefamily protein (Pectate_lyase_3 superfamily)

PHATRDRAFT_16052 - glycoside hydrolase family 28 protein polygalacturonasefamily protein (Pectate_lyase_3 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16052
PHATRDRAFT_23706 proteolipid c subunit (ATP-synt_C superfamily)

PHATRDRAFT_23706 - proteolipid c subunit (ATP-synt_C superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23706
PHATRDRAFT_30466 nad-dependent epimerase dehydratase (NADB_Rossmann superfamily)

PHATRDRAFT_30466 - nad-dependent epimerase dehydratase (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30466
PHATRDRAFT_35095

PHATRDRAFT_35095 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35095
PHATRDRAFT_36435 flavin reductase (NADB_Rossmann superfamily)

PHATRDRAFT_36435 - flavin reductase (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36435
PHATRDRAFT_37711 (Lipase superfamily)

PHATRDRAFT_37711 - (Lipase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37711
PHATRDRAFT_41170 quinol-to-oxygen oxidoreductase (Ferritin_like superfamily)

PHATRDRAFT_41170 - quinol-to-oxygen oxidoreductase (Ferritin_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41170
PHATRDRAFT_41947 fad dependent oxidoreductase (PRK11728 superfamily)

PHATRDRAFT_41947 - fad dependent oxidoreductase (PRK11728 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41947
PHATRDRAFT_44461

PHATRDRAFT_44461 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44461
PHATRDRAFT_45084 (TPR)

PHATRDRAFT_45084 - (TPR)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45084
PHATRDRAFT_46937

PHATRDRAFT_46937 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46937
PHATRDRAFT_46949

PHATRDRAFT_46949 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46949
PHATRDRAFT_46953

PHATRDRAFT_46953 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46953
PHATRDRAFT_47483

PHATRDRAFT_47483 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47483
PHATRDRAFT_48144

PHATRDRAFT_48144 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48144
PHATRDRAFT_48564

PHATRDRAFT_48564 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48564
PHATRDRAFT_49391 amino acid transporter (Aa_trans superfamily)

PHATRDRAFT_49391 - amino acid transporter (Aa_trans superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49391
PHATRDRAFT_49879 ac034107_6ests gb

PHATRDRAFT_49879 - ac034107_6ests gb

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49879
PHATRDRAFT_50256

PHATRDRAFT_50256 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50256
PHATRDRAFT_50588

PHATRDRAFT_50588 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50588
PHATRDRAFT_54153 ama1 protein (PLAC8)

PHATRDRAFT_54153 - ama1 protein (PLAC8)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54153
PHATRDRAFT_7337 (Got1)

PHATRDRAFT_7337 - (Got1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7337
GO ID Go Term p-value q-value Cluster
GO:0006629 lipid metabolism 0.0307293 1 Phatr_bicluster_0134
GO:0006470 protein amino acid dephosphorylation 0.0324125 1 Phatr_bicluster_0134
GO:0006865 amino acid transport 0.0474487 1 Phatr_bicluster_0134
GO:0015986 ATP synthesis coupled proton transport 0.0622842 1 Phatr_bicluster_0134
GO:0006810 transport 0.287164 1 Phatr_bicluster_0134
GO:0006118 electron transport 0.33492 1 Phatr_bicluster_0134
GO:0008152 metabolism 0.410263 1 Phatr_bicluster_0134
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