Phatr_bicluster_0195 Residual: 0.22
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_0195 0.22 Phaeodactylum tricornutum
Displaying 1 - 23 of 23
PHATRDRAFT_12004 10 kda heat shockmitochondrial (cpn10)

PHATRDRAFT_12004 - 10 kda heat shockmitochondrial (cpn10)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12004
PHATRDRAFT_1690 bifunctional dihydrofolate reductase-thymidylate synthase 2 dhfr-ts (PTZ00164)

PHATRDRAFT_1690 - bifunctional dihydrofolate reductase-thymidylate synthase 2 dhfr-ts (PTZ00164)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_1690
PHATRDRAFT_17633 chaperone protein (dnaK)

PHATRDRAFT_17633 - chaperone protein (dnaK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17633
PHATRDRAFT_18319 s-adenosyl-l-homocysteine hydrolase (PRK05476)

PHATRDRAFT_18319 - s-adenosyl-l-homocysteine hydrolase (PRK05476)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18319
PHATRDRAFT_24820 ch61_maizechaperonin cpn60-mitochondrial precursor (hsp60-1) (groEL)

PHATRDRAFT_24820 - ch61_maizechaperonin cpn60-mitochondrial precursor (hsp60-1) (groEL)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_24820
PHATRDRAFT_25308 af063804_1triosephosphate isomerase glyceraldehyde-3-phosphate dehydrogenase precursor (GapA)

PHATRDRAFT_25308 - af063804_1triosephosphate isomerase glyceraldehyde-3-phosphate dehydrogenase precursor (GapA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25308
PHATRDRAFT_31408 dnaj-like sec63 (Sec63)

PHATRDRAFT_27039 - dnaj-like sec63 (Sec63)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27039
PHATRDRAFT_31474 hydrolase acyltransferase (alpha beta hydrolase superfamily) (Abhydrolase_6)

PHATRDRAFT_31408 - hydrolase acyltransferase (alpha beta hydrolase superfamily) (Abhydrolase_6)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31408
PHATRDRAFT_31999 protein of clr family (RAP)

PHATRDRAFT_31474 - protein of clr family (RAP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31474
PHATRDRAFT_32471 thioesterase superfamily memberpartial (PaaI_thioesterase)

PHATRDRAFT_31999 - thioesterase superfamily memberpartial (PaaI_thioesterase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31999
PHATRDRAFT_32747

PHATRDRAFT_32471 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32471
PHATRDRAFT_34120 mitochondrial glyceraldehyde-3-phosphate dehydrogenase (GapA)

PHATRDRAFT_32747 - mitochondrial glyceraldehyde-3-phosphate dehydrogenase (GapA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32747
PHATRDRAFT_43041 2-dehydro-3-deoxyphosphogluconate aldolase (KDPG_aldolase)

PHATRDRAFT_34120 - 2-dehydro-3-deoxyphosphogluconate aldolase (KDPG_aldolase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34120
PHATRDRAFT_44343

PHATRDRAFT_43041 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43041
PHATRDRAFT_45845

PHATRDRAFT_44343 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44343
PHATRDRAFT_46626 zeaxanthin epoxidase precursor (PRK06847)

PHATRDRAFT_45845 - zeaxanthin epoxidase precursor (PRK06847)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45845
PHATRDRAFT_49384 isochorismatase hydrolase (cysteine_hydrolases)

PHATRDRAFT_46626 - isochorismatase hydrolase (cysteine_hydrolases)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46626
PHATRDRAFT_54246 cg1358-isoform a (MFS)

PHATRDRAFT_49384 - cg1358-isoform a (MFS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49384
PHATRDRAFT_7614 binding protein 1 (HSP70)

PHATRDRAFT_54246 - binding protein 1 (HSP70)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54246
PHATRDRAFT_8987 bromodomain and phd finger3 (Bromodomain)

PHATRDRAFT_7614 - bromodomain and phd finger3 (Bromodomain)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7614
PHATRDRAFT_8990 mitochondrial phosphate transport protein (Mito_carr)

PHATRDRAFT_8987 - mitochondrial phosphate transport protein (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8987
PHATRDRAFT_9090 mitochondrial 2-oxoglutarate malate carrier protein(solute carrier family 25 member 11) (Mito_carr)

PHATRDRAFT_8990 - mitochondrial 2-oxoglutarate malate carrier protein(solute carrier family 25 member 11) (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8990

PHATRDRAFT_9090 - 26s proteasome regulatory particle triple-a atpase subunit5a (RPT1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9090
GO ID Go Term p-value q-value Cluster
GO:0006006 glucose metabolism 0.000529756 1 Phatr_bicluster_0195
GO:0006725 aromatic compound metabolism 0.00460206 1 Phatr_bicluster_0195
GO:0006545 glycine biosynthesis 0.00518647 1 Phatr_bicluster_0195
GO:0006231 dTMP biosynthesis 0.0103473 1 Phatr_bicluster_0195
GO:0006096 glycolysis 0.0137532 1 Phatr_bicluster_0195
GO:0006730 one-carbon compound metabolism 0.0205926 1 Phatr_bicluster_0195
GO:0009165 nucleotide biosynthesis 0.0205926 1 Phatr_bicluster_0195
GO:0044267 cellular protein metabolism 0.0507259 1 Phatr_bicluster_0195
GO:0030163 protein catabolism 0.0556614 1 Phatr_bicluster_0195
GO:0008152 metabolism 0.0610585 1 Phatr_bicluster_0195
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