Phatr_bicluster_0089 Residual: 0.28
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_0089 0.28 Phaeodactylum tricornutum
Displaying 1 - 24 of 24
PHATRDRAFT_13047 (CAP_C)

PHATRDRAFT_13047 - (CAP_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13047
PHATRDRAFT_18067 human ran binding protein 16-like (IBN_N)

PHATRDRAFT_18067 - human ran binding protein 16-like (IBN_N)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18067
PHATRDRAFT_19901 cg8363-isoform a (nt_trans superfamily)

PHATRDRAFT_19901 - cg8363-isoform a (nt_trans superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19901
PHATRDRAFT_34457 mgc80931 protein

PHATRDRAFT_34457 - mgc80931 protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34457
PHATRDRAFT_36060 methyltransferase protein (Methyltransf_21)

PHATRDRAFT_36060 - methyltransferase protein (Methyltransf_21)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36060
PHATRDRAFT_39115

PHATRDRAFT_39115 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39115
PHATRDRAFT_42458 phosphoserine aminotransferase (AAT_I)

PHATRDRAFT_42458 - phosphoserine aminotransferase (AAT_I)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42458
PHATRDRAFT_45120 myo-inositol-1-phosphate synthase (PLN02438)

PHATRDRAFT_45120 - myo-inositol-1-phosphate synthase (PLN02438)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45120
PHATRDRAFT_45476 actin binding protein (VHP superfamily)

PHATRDRAFT_45476 - actin binding protein (VHP superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45476
PHATRDRAFT_45580 coronin 6 clipin e type c isoform 1 (DUF1900)

PHATRDRAFT_45580 - coronin 6 clipin e type c isoform 1 (DUF1900)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45580
PHATRDRAFT_46109 core alpha-fucosyltransferase (Glyco_transf_10 superfamily)

PHATRDRAFT_46109 - core alpha-fucosyltransferase (Glyco_transf_10 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46109
PHATRDRAFT_46446

PHATRDRAFT_46446 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46446
PHATRDRAFT_46834

PHATRDRAFT_46834 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46834
PHATRDRAFT_47010 transducin family protein wd-40 repeat family protein (WD40 superfamily)

PHATRDRAFT_47010 - transducin family protein wd-40 repeat family protein (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47010
PHATRDRAFT_47314 (Spc97_Spc98)

PHATRDRAFT_47314 - (Spc97_Spc98)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47314
PHATRDRAFT_48381 actin cortical patch (WD40 superfamily)

PHATRDRAFT_48381 - actin cortical patch (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48381
PHATRDRAFT_48456

PHATRDRAFT_48456 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48456
PHATRDRAFT_48488

PHATRDRAFT_48488 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48488
PHATRDRAFT_48491 alkaline serine protease (Peptidases_S8_PCSK9_ProteinaseK_like)

PHATRDRAFT_48491 - alkaline serine protease (Peptidases_S8_PCSK9_ProteinaseK_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48491
PHATRDRAFT_48622 aspartyl asparaginyl beta-hydroxylase

PHATRDRAFT_48622 - aspartyl asparaginyl beta-hydroxylase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48622
PHATRDRAFT_48795 silk fibroin

PHATRDRAFT_48795 - silk fibroin

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48795
PHATRDRAFT_50095 exostosin family protein (Exostosin)

PHATRDRAFT_50095 - exostosin family protein (Exostosin)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50095
PHATRDRAFT_50463 16isoform cra_c (Peptidase_S28 superfamily)

PHATRDRAFT_50463 - 16isoform cra_c (Peptidase_S28 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50463
PHATRDRAFT_54169 glucosidase ii beta subunit (PRKCSH superfamily)

PHATRDRAFT_54169 - glucosidase ii beta subunit (PRKCSH superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54169
GO ID Go Term p-value q-value Cluster
GO:0007010 cytoskeleton organization and biogenesis 0.00246975 1 Phatr_bicluster_0089
GO:0006021 myo-inositol biosynthesis 0.00246975 1 Phatr_bicluster_0089
GO:0000226 microtubule cytoskeleton organization and biogenesis 0.004934 1 Phatr_bicluster_0089
GO:0000103 sulfate assimilation 0.004934 1 Phatr_bicluster_0089
GO:0000059 protein-nucleus import, docking 0.0122939 1 Phatr_bicluster_0089
GO:0008654 phospholipid biosynthesis 0.0220309 1 Phatr_bicluster_0089
GO:0006508 proteolysis and peptidolysis 0.1023 1 Phatr_bicluster_0089
GO:0009058 biosynthesis 0.105854 1 Phatr_bicluster_0089
GO:0008152 metabolism 0.529843 1 Phatr_bicluster_0089
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