Phatr_bicluster_0244 Residual: 0.33
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_0244 0.33 Phaeodactylum tricornutum
Displaying 1 - 29 of 29
PHATRDRAFT_10391 ch032_bovinuncharacterized protein c8orf32 homolog (Nt_Gln_amidase superfamily)

PHATRDRAFT_10391 - ch032_bovinuncharacterized protein c8orf32 homolog (Nt_Gln_amidase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10391
PHATRDRAFT_12820 calcium-dependent protein kinase (S_TKc)

PHATRDRAFT_12820 - calcium-dependent protein kinase (S_TKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12820
PHATRDRAFT_12884 galactolipid galactosyltransferase (Glycos_transf_1 superfamily)

PHATRDRAFT_12884 - galactolipid galactosyltransferase (Glycos_transf_1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12884
PHATRDRAFT_13240 protease do-like (s2 serine-type protease) (Trypsin_2)

PHATRDRAFT_13240 - protease do-like (s2 serine-type protease) (Trypsin_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13240
PHATRDRAFT_25433 cysteine protease (Peptidase_C1A)

PHATRDRAFT_25433 - cysteine protease (Peptidase_C1A)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25433
PHATRDRAFT_31878 response regulator receiver domain protein (NTF2_like superfamily)

PHATRDRAFT_31878 - response regulator receiver domain protein (NTF2_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31878
PHATRDRAFT_31991 random cdna clone veg158

PHATRDRAFT_31991 - random cdna clone veg158

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31991
PHATRDRAFT_35616

PHATRDRAFT_35616 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35616
PHATRDRAFT_42791

PHATRDRAFT_42791 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42791
PHATRDRAFT_43408

PHATRDRAFT_43408 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43408
PHATRDRAFT_43953 (Methyltransf_16 superfamily)

PHATRDRAFT_43953 - (Methyltransf_16 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43953
PHATRDRAFT_43978 (Metallophos)

PHATRDRAFT_43978 - (Metallophos)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43978
PHATRDRAFT_44404 isoform 1

PHATRDRAFT_44404 - isoform 1

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44404
PHATRDRAFT_45239 glu leu phe val dehydrogenase family protein (NAD_bind_amino_acid_DH superfamily)

PHATRDRAFT_45239 - glu leu phe val dehydrogenase family protein (NAD_bind_amino_acid_DH superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45239
PHATRDRAFT_45352

PHATRDRAFT_45352 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45352
PHATRDRAFT_45673 bgal1_orysj beta-galactosidase 1 precursor (lactase 1) (Glyco_hydro_35 superfamily)

PHATRDRAFT_45673 - bgal1_orysj beta-galactosidase 1 precursor (lactase 1) (Glyco_hydro_35 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45673
PHATRDRAFT_47078 sjchgc06034 protein (Nudix_Hydrolase superfamily)

PHATRDRAFT_47078 - sjchgc06034 protein (Nudix_Hydrolase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47078
PHATRDRAFT_47538 solute carrier family 24 (sodium potassium calcium exchanger)member 1 (Anoctamin)

PHATRDRAFT_47538 - solute carrier family 24 (sodium potassium calcium exchanger)member 1 (Anoctamin)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47538
PHATRDRAFT_48601 uncharacterized conserved protein (DUF1365 superfamily)

PHATRDRAFT_48601 - uncharacterized conserved protein (DUF1365 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48601
PHATRDRAFT_48924 arginine-trna-protein transferase 1 homolog (ATE_C)

PHATRDRAFT_48924 - arginine-trna-protein transferase 1 homolog (ATE_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48924
PHATRDRAFT_4936 cathepsin z (Peptidase_C1 superfamily)

PHATRDRAFT_4936 - cathepsin z (Peptidase_C1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_4936
PHATRDRAFT_49648

PHATRDRAFT_49648 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49648
PHATRDRAFT_49672 (TRAM_LAG1_CLN8)

PHATRDRAFT_49672 - (TRAM_LAG1_CLN8)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49672
PHATRDRAFT_49776 nod3 protein (LRR_RI superfamily)

PHATRDRAFT_49776 - nod3 protein (LRR_RI superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49776
PHATRDRAFT_50056 glutathione s-transferase family protein (Gst)

PHATRDRAFT_50056 - glutathione s-transferase family protein (Gst)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50056
PHATRDRAFT_50430

PHATRDRAFT_50430 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50430
PHATRDRAFT_54709 integral membrane protein (Cons_hypoth698 superfamily)

PHATRDRAFT_51806 - integral membrane protein (Cons_hypoth698 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51806
PHATRDRAFT_9777 electron transfer flavoprotein-ubiquinone oxidoreductase containing protein (LPLAT superfamily)

PHATRDRAFT_54709 - electron transfer flavoprotein-ubiquinone oxidoreductase containing protein (LPLAT superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54709

PHATRDRAFT_9777 - tpr repeat

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9777
GO ID Go Term p-value q-value Cluster
GO:0016598 protein arginylation 0.00222277 1 Phatr_bicluster_0244
GO:0042176 regulation of protein catabolism 0.00222277 1 Phatr_bicluster_0244
GO:0006508 proteolysis and peptidolysis 0.010945 1 Phatr_bicluster_0244
GO:0006520 amino acid metabolism 0.0521493 1 Phatr_bicluster_0244
GO:0006281 DNA repair 0.0731548 1 Phatr_bicluster_0244
GO:0005975 carbohydrate metabolism 0.13175 1 Phatr_bicluster_0244
GO:0006468 protein amino acid phosphorylation 0.323667 1 Phatr_bicluster_0244
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