Phatr_bicluster_0082 Residual: 0.37
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_0082 0.37 Phaeodactylum tricornutum
Displaying 1 - 32 of 32
PHATRDRAFT_11438 undecaprenyl diphosphate synthase (Cis_IPPS)

PHATRDRAFT_11438 - undecaprenyl diphosphate synthase (Cis_IPPS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11438
PHATRDRAFT_12366 rna recognition motif familyexpressed (RRM_SF superfamily)

PHATRDRAFT_12366 - rna recognition motif familyexpressed (RRM_SF superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12366
PHATRDRAFT_32692

PHATRDRAFT_32692 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32692
PHATRDRAFT_33640

PHATRDRAFT_33640 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33640
PHATRDRAFT_33952

PHATRDRAFT_33952 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33952
PHATRDRAFT_36514

PHATRDRAFT_36514 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36514
PHATRDRAFT_37341 acetolactate synthase (acolac_lg)

PHATRDRAFT_37341 - acetolactate synthase (acolac_lg)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37341
PHATRDRAFT_39062 (UBA)

PHATRDRAFT_39062 - (UBA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39062
PHATRDRAFT_41316 extracellular serine-threonine rich protein

PHATRDRAFT_41316 - extracellular serine-threonine rich protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41316
PHATRDRAFT_42169 protein phosphatase (MPP_PP2A_PP4_PP6)

PHATRDRAFT_42169 - protein phosphatase (MPP_PP2A_PP4_PP6)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42169
PHATRDRAFT_42645

PHATRDRAFT_42645 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42645
PHATRDRAFT_42871 extracellular threonine rich

PHATRDRAFT_42871 - extracellular threonine rich

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42871
PHATRDRAFT_43013

PHATRDRAFT_43013 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43013
PHATRDRAFT_43120 2-phosphoglycolate phosphatase (Gph)

PHATRDRAFT_43120 - 2-phosphoglycolate phosphatase (Gph)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43120
PHATRDRAFT_44549 d-amino acid oxidase (DadA)

PHATRDRAFT_44549 - d-amino acid oxidase (DadA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44549
PHATRDRAFT_44835 mgc83623 protein (zf-C3HC4_3)

PHATRDRAFT_44835 - mgc83623 protein (zf-C3HC4_3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44835
PHATRDRAFT_44838 mgc83623 protein (zf-C3HC4_3)

PHATRDRAFT_44838 - mgc83623 protein (zf-C3HC4_3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44838
PHATRDRAFT_45178

PHATRDRAFT_45178 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45178
PHATRDRAFT_45615

PHATRDRAFT_45615 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45615
PHATRDRAFT_45770 mgc83491 protein (Thioredoxin_like superfamily)

PHATRDRAFT_45770 - mgc83491 protein (Thioredoxin_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45770
PHATRDRAFT_45824 amino acid transporter (Aa_trans superfamily)

PHATRDRAFT_45824 - amino acid transporter (Aa_trans superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45824
PHATRDRAFT_46300

PHATRDRAFT_46300 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46300
PHATRDRAFT_46406

PHATRDRAFT_46406 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46406
PHATRDRAFT_46648 platelet-binding glycoprotein

PHATRDRAFT_46648 - platelet-binding glycoprotein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46648
PHATRDRAFT_47015

PHATRDRAFT_47015 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47015
PHATRDRAFT_47710 subtilisin-like serine protease

PHATRDRAFT_47710 - subtilisin-like serine protease

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47710
PHATRDRAFT_48608

PHATRDRAFT_48608 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48608
PHATRDRAFT_48693 leucine-rich repeat family protein extensin family protein

PHATRDRAFT_48693 - leucine-rich repeat family protein extensin family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48693
PHATRDRAFT_49903 cystathionine gamma-synthase (MetC)

PHATRDRAFT_49903 - cystathionine gamma-synthase (MetC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49903
PHATRDRAFT_4994 calcium-dependent calmodulin-independent protein kinase cdpk-like (S_TKc)

PHATRDRAFT_4994 - calcium-dependent calmodulin-independent protein kinase cdpk-like (S_TKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_4994
PHATRDRAFT_51933 nonphototropic hypocotyl 1 (PAS)

PHATRDRAFT_51933 - nonphototropic hypocotyl 1 (PAS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51933
PHATRDRAFT_8691 (6PGL)

PHATRDRAFT_8691 - (6PGL)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8691
GO ID Go Term p-value q-value Cluster
GO:0006520 amino acid metabolism 0.0464863 1 Phatr_bicluster_0082
GO:0006865 amino acid transport 0.0540473 1 Phatr_bicluster_0082
GO:0008152 metabolism 0.0161272 1 Phatr_bicluster_0082
GO:0006468 protein amino acid phosphorylation 0.2936 1 Phatr_bicluster_0082
GO:0016567 protein ubiquitination 0.00814771 1 Phatr_bicluster_0082
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