Phatr_bicluster_0154 Residual: 0.20
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_0154 0.20 Phaeodactylum tricornutum
Displaying 1 - 20 of 20
PHATRDRAFT_10310 dna-directed rna polymerase i subunit (Zn-ribbon_RPA12)

PHATRDRAFT_10310 - dna-directed rna polymerase i subunit (Zn-ribbon_RPA12)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10310
PHATRDRAFT_11894 spb1_schpoet-dependent rrna methyltransferase spb1 (2-o-ribose rna methyltransferase) (s-adenosyl-l-methionine-dependent methyltransferase) (AdoMet_MTases)

PHATRDRAFT_11894 - spb1_schpoet-dependent rrna methyltransferase spb1 (2-o-ribose rna methyltransferase) (s-adenosyl-l-methionine-dependent methyltransferase) (AdoMet_MTases)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11894
PHATRDRAFT_15354 rrp5 protein homolog (programmed cell death protein 11)

PHATRDRAFT_15354 - rrp5 protein homolog (programmed cell death protein 11)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15354
PHATRDRAFT_15639 mitochondrial carrier protein (Mito_carr)

PHATRDRAFT_15639 - mitochondrial carrier protein (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15639
PHATRDRAFT_15757 small nucleolar ribonucleoprotein u3 component (RpsD)

PHATRDRAFT_15757 - small nucleolar ribonucleoprotein u3 component (RpsD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15757
PHATRDRAFT_16603 mitochondrial translation initiation factor if- (PRK04004)

PHATRDRAFT_16603 - mitochondrial translation initiation factor if- (PRK04004)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16603
PHATRDRAFT_16688 cgi-09 protein (Gcd10p superfamily)

PHATRDRAFT_16688 - cgi-09 protein (Gcd10p superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16688
PHATRDRAFT_18579 at1g56110 t6h22_9 (SIK1)

PHATRDRAFT_18579 - at1g56110 t6h22_9 (SIK1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18579
PHATRDRAFT_21557 (Brix superfamily)

PHATRDRAFT_21557 - (Brix superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21557
PHATRDRAFT_23286 3-5 exoribonuclease ph component of the exosome (RNase_PH superfamily)

PHATRDRAFT_23286 - 3-5 exoribonuclease ph component of the exosome (RNase_PH superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23286
PHATRDRAFT_25666 periodic tryptophan protein 2 (WD40)

PHATRDRAFT_25666 - periodic tryptophan protein 2 (WD40)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25666
PHATRDRAFT_28984 mgc81303 protein (DEADc)

PHATRDRAFT_28984 - mgc81303 protein (DEADc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28984
PHATRDRAFT_30965 radical samcfr familyexpressed (COG0820)

PHATRDRAFT_30965 - radical samcfr familyexpressed (COG0820)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30965
PHATRDRAFT_39052 pentatricopeptiderepeat-containing protein (PPR_2)

PHATRDRAFT_39052 - pentatricopeptiderepeat-containing protein (PPR_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39052
PHATRDRAFT_39714 dead (asp-glu-ala-asp) box polypeptide 28 (DEXDc superfamily)

PHATRDRAFT_39714 - dead (asp-glu-ala-asp) box polypeptide 28 (DEXDc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39714
PHATRDRAFT_41234

PHATRDRAFT_41234 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41234
PHATRDRAFT_44096 rna methylase (COG0116)

PHATRDRAFT_44096 - rna methylase (COG0116)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44096
PHATRDRAFT_44242 u3 snornp protein utp4 (WD40 superfamily)

PHATRDRAFT_44242 - u3 snornp protein utp4 (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44242
PHATRDRAFT_47514 elongation protein 4 homolog (PAXNEB superfamily)

PHATRDRAFT_47514 - elongation protein 4 homolog (PAXNEB superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47514
PHATRDRAFT_48486 histone tail methylase containing set domain (SET)

PHATRDRAFT_48486 - histone tail methylase containing set domain (SET)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48486
GO ID Go Term p-value q-value Cluster
GO:0006354 RNA elongation 0.00739277 1 Phatr_bicluster_0154
GO:0006396 RNA processing 0.00787469 1 Phatr_bicluster_0154
GO:0006446 regulation of translational initiation 0.00984608 1 Phatr_bicluster_0154
GO:0006306 DNA methylation 0.0483639 1 Phatr_bicluster_0154
GO:0006412 protein biosynthesis 0.0573335 1 Phatr_bicluster_0154
GO:0006413 translational initiation 0.0577801 1 Phatr_bicluster_0154
GO:0006810 transport 0.38354 1 Phatr_bicluster_0154
GO:0006355 regulation of transcription, DNA-dependent 0.426896 1 Phatr_bicluster_0154
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