Phatr_bicluster_0200 Residual: 0.32
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_0200 0.32 Phaeodactylum tricornutum
Displaying 1 - 23 of 23
PHATRDRAFT_10835 translation initiation factor if-2 (IF-2)

PHATRDRAFT_10835 - translation initiation factor if-2 (IF-2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10835
PHATRDRAFT_12679 mgc140358 protein (Brix)

PHATRDRAFT_12679 - mgc140358 protein (Brix)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12679
PHATRDRAFT_13235 dead (asp-glu-ala-asp) box polypeptide 10 (DEADc)

PHATRDRAFT_13235 - dead (asp-glu-ala-asp) box polypeptide 10 (DEADc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13235
PHATRDRAFT_16592 peroxisomal membrane protein 22 (Mpv17_PMP22)

PHATRDRAFT_16592 - peroxisomal membrane protein 22 (Mpv17_PMP22)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16592
PHATRDRAFT_16633 rna-binding protein (RRM_1)

PHATRDRAFT_16633 - rna-binding protein (RRM_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16633
PHATRDRAFT_19579 glucose inhibited division protein a (PRK05192)

PHATRDRAFT_19579 - glucose inhibited division protein a (PRK05192)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19579
PHATRDRAFT_35057 indole-3-glycerol-phosphate synthase (TIM_phosphate_binding superfamily)

PHATRDRAFT_35057 - indole-3-glycerol-phosphate synthase (TIM_phosphate_binding superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35057
PHATRDRAFT_37260 mitochondrial rna splicing protein (Mrs2_Mfm1p-like)

PHATRDRAFT_37260 - mitochondrial rna splicing protein (Mrs2_Mfm1p-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37260
PHATRDRAFT_37681 eukaryotic translation initiation factor 3 subunit (SAP)

PHATRDRAFT_37681 - eukaryotic translation initiation factor 3 subunit (SAP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37681
PHATRDRAFT_38628 membrane protein

PHATRDRAFT_38628 - membrane protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38628
PHATRDRAFT_43482 serine threonine protein kinase (MPP_PPP_family)

PHATRDRAFT_43482 - serine threonine protein kinase (MPP_PPP_family)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43482
PHATRDRAFT_43627 (IKI3)

PHATRDRAFT_43627 - (IKI3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43627
PHATRDRAFT_43705

PHATRDRAFT_43705 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43705
PHATRDRAFT_43763

PHATRDRAFT_43763 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43763
PHATRDRAFT_44863 polyribonucleotide nucleotidyltransferase (PRK11824)

PHATRDRAFT_44863 - polyribonucleotide nucleotidyltransferase (PRK11824)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44863
PHATRDRAFT_45529 ribonucleoside-diphosphate reductase large subunit (PLN02437)

PHATRDRAFT_45529 - ribonucleoside-diphosphate reductase large subunit (PLN02437)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45529
PHATRDRAFT_46041 dna binding nuclease (SnoaL_3)

PHATRDRAFT_46041 - dna binding nuclease (SnoaL_3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46041
PHATRDRAFT_46130 mgc80131 protein (zf-MYND)

PHATRDRAFT_46130 - mgc80131 protein (zf-MYND)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46130
PHATRDRAFT_46782 alkylated dna repair protein alkb homolog (2OG-FeII_Oxy_2)

PHATRDRAFT_46782 - alkylated dna repair protein alkb homolog (2OG-FeII_Oxy_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46782
PHATRDRAFT_47170

PHATRDRAFT_47170 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47170
PHATRDRAFT_47890 y3488_glovi upf0090 protein glr3488 (Sm_like superfamily)

PHATRDRAFT_47890 - y3488_glovi upf0090 protein glr3488 (Sm_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47890
PHATRDRAFT_48308

PHATRDRAFT_48308 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48308

PHATRDRAFT_6454 - bifunctional-dihydroxy-2-butanone 4-phosphate synthase gtp cyclohydrolase ii protein (DHBP_synthase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6454
GO ID Go Term p-value q-value Cluster
GO:0009231 riboflavin biosynthesis 0.0103346 1 Phatr_bicluster_0200
GO:0006568 tryptophan metabolism 0.0103346 1 Phatr_bicluster_0200
GO:0030001 metal ion transport 0.0273554 1 Phatr_bicluster_0200
GO:0006413 translational initiation 0.0407909 1 Phatr_bicluster_0200
GO:0006260 DNA replication 0.0441247 1 Phatr_bicluster_0200
GO:0006396 RNA processing 0.0929544 1 Phatr_bicluster_0200
GO:0006412 protein biosynthesis 0.247414 1 Phatr_bicluster_0200
Log in to post comments