Phatr_bicluster_0170 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_0170 0.28 Phaeodactylum tricornutum
Displaying 1 - 26 of 26
PHATRDRAFT_12104 thiol-disulfide interchange like protein (Thioredoxin_like superfamily)

PHATRDRAFT_12104 - thiol-disulfide interchange like protein (Thioredoxin_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12104
PHATRDRAFT_16283 ubiquitin carboxyl-terminal hydrolase family protein (UCH)

PHATRDRAFT_12752 - ubiquitin carboxyl-terminal hydrolase family protein (UCH)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12752
PHATRDRAFT_26714 (NAD_binding_8 superfamily)

PHATRDRAFT_16283 - (NAD_binding_8 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16283
PHATRDRAFT_26862 condensing enzyme (CHS_like)

PHATRDRAFT_26714 - condensing enzyme (CHS_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_26714
PHATRDRAFT_31584 nad-dependent epimerase dehydratase (NADB_Rossmann superfamily)

PHATRDRAFT_26862 - nad-dependent epimerase dehydratase (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_26862
PHATRDRAFT_31652 mule cg5505-isoform a (Peptidase_C19)

PHATRDRAFT_31584 - mule cg5505-isoform a (Peptidase_C19)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31584
PHATRDRAFT_32274 (TLD)

PHATRDRAFT_31652 - (TLD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31652
PHATRDRAFT_32877

PHATRDRAFT_32274 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32274
PHATRDRAFT_3362 sel1 domain protein repeat-containing protein (COG0790)

PHATRDRAFT_32877 - sel1 domain protein repeat-containing protein (COG0790)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32877
PHATRDRAFT_33768 mus musculuss-adenosylmethionine decarboxylase 1 (PLN02524)

PHATRDRAFT_3362 - mus musculuss-adenosylmethionine decarboxylase 1 (PLN02524)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3362
PHATRDRAFT_33776 peroxisomal membrane 22 kda family protein

PHATRDRAFT_33768 - peroxisomal membrane 22 kda family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33768
PHATRDRAFT_34815

PHATRDRAFT_33776 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33776
PHATRDRAFT_41686

PHATRDRAFT_34815 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34815
PHATRDRAFT_43467 aminotransferase class-iii (BioA)

PHATRDRAFT_41686 - aminotransferase class-iii (BioA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41686
PHATRDRAFT_44871 cytochromefamilysubfamilypolypeptide 11 (CypX)

PHATRDRAFT_43467 - cytochromefamilysubfamilypolypeptide 11 (CypX)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43467
PHATRDRAFT_45215 glycerol uptake facilitator protein (MIP superfamily)

PHATRDRAFT_44871 - glycerol uptake facilitator protein (MIP superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44871
PHATRDRAFT_45377 (DUF1995 superfamily)

PHATRDRAFT_45215 - (DUF1995 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45215
PHATRDRAFT_45418 ectonucleoside triphosphate diphosphohydrolase 1 (GDA1_CD39 superfamily)

PHATRDRAFT_45377 - ectonucleoside triphosphate diphosphohydrolase 1 (GDA1_CD39 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45377
PHATRDRAFT_45617 exg_canolglucan-beta-glucosidase precursor (exo--beta-glucanase) (BglC)

PHATRDRAFT_45418 - exg_canolglucan-beta-glucosidase precursor (exo--beta-glucanase) (BglC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45418
PHATRDRAFT_47026

PHATRDRAFT_45617 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45617
PHATRDRAFT_49869 transmembrane protein 163 (Cation_efflux superfamily)

PHATRDRAFT_47026 - transmembrane protein 163 (Cation_efflux superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47026
PHATRDRAFT_50022 muc2_humanmucin-2 precursor (intestinal mucin-2)

PHATRDRAFT_49869 - muc2_humanmucin-2 precursor (intestinal mucin-2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49869
PHATRDRAFT_7108

PHATRDRAFT_50022 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50022
PHATRDRAFT_8963 protease u48 caax prenyl protease rce1

PHATRDRAFT_7108 - protease u48 caax prenyl protease rce1

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7108
PHATRDRAFT_9316 peroxisomal membrane (Mpv17_PMP22)

PHATRDRAFT_8963 - peroxisomal membrane (Mpv17_PMP22)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8963

PHATRDRAFT_9316 - chloroplast acyl-acp desaturase (Acyl_ACP_Desat)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9316
GO ID Go Term p-value q-value Cluster
GO:0008295 spermidine biosynthesis 0.00370462 1 Phatr_bicluster_0170
GO:0006597 spermine biosynthesis 0.00370462 1 Phatr_bicluster_0170
GO:0006631 fatty acid metabolism 0.0110755 1 Phatr_bicluster_0170
GO:0006511 ubiquitin-dependent protein catabolism 0.0115692 1 Phatr_bicluster_0170
GO:0009225 nucleotide-sugar metabolism 0.0256647 1 Phatr_bicluster_0170
GO:0006118 electron transport 0.0490442 1 Phatr_bicluster_0170
GO:0006725 aromatic compound metabolism 0.0717043 1 Phatr_bicluster_0170
GO:0009058 biosynthesis 0.15459 1 Phatr_bicluster_0170
GO:0005975 carbohydrate metabolism 0.209932 1 Phatr_bicluster_0170
GO:0006468 protein amino acid phosphorylation 0.479142 1 Phatr_bicluster_0170
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