Phatr_bicluster_0254 Residual: 0.23
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_0254 0.23 Phaeodactylum tricornutum
Displaying 1 - 28 of 28
PHATRDRAFT_12280 sarcosine-dimethylglycine methyltransferase (AdoMet_MTases)

PHATRDRAFT_12280 - sarcosine-dimethylglycine methyltransferase (AdoMet_MTases)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12280
PHATRDRAFT_13791 y838_chlff upf0082 protein cf0838 (Transcrip_reg)

PHATRDRAFT_13791 - y838_chlff upf0082 protein cf0838 (Transcrip_reg)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13791
PHATRDRAFT_18398 atp synthase gamma subunit (F1-ATPase_gamma)

PHATRDRAFT_18398 - atp synthase gamma subunit (F1-ATPase_gamma)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18398
PHATRDRAFT_21316 dna topoisomerase iv subunit b (gyrB)

PHATRDRAFT_21316 - dna topoisomerase iv subunit b (gyrB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21316
PHATRDRAFT_31465 atp synthase alpha subunit mitochondrial (RecA-like_NTPases superfamily)

PHATRDRAFT_31465 - atp synthase alpha subunit mitochondrial (RecA-like_NTPases superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31465
PHATRDRAFT_33840 nhp6_debha non-histone chromosomal protein 6 (HMGB-UBF_HMG-box)

PHATRDRAFT_33840 - nhp6_debha non-histone chromosomal protein 6 (HMGB-UBF_HMG-box)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33840
PHATRDRAFT_34902 conserved hypothetical (Methyltransf_24)

PHATRDRAFT_34902 - conserved hypothetical (Methyltransf_24)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34902
PHATRDRAFT_34995 hsp10 homolog (cpn10)

PHATRDRAFT_34995 - hsp10 homolog (cpn10)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34995
PHATRDRAFT_35562 related arylesterase (SGNH_hydrolase)

PHATRDRAFT_35562 - related arylesterase (SGNH_hydrolase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35562
PHATRDRAFT_36392 (DUF1014 superfamily)

PHATRDRAFT_36392 - (DUF1014 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36392
PHATRDRAFT_40200 gtp-binding protein (PRK13796)

PHATRDRAFT_40200 - gtp-binding protein (PRK13796)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40200
PHATRDRAFT_42808 cell cycle checkpoint protein hrad1 (PCNA superfamily)

PHATRDRAFT_42808 - cell cycle checkpoint protein hrad1 (PCNA superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42808
PHATRDRAFT_43034 cyclin e2 (COG5024)

PHATRDRAFT_43034 - cyclin e2 (COG5024)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43034
PHATRDRAFT_43037

PHATRDRAFT_43037 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43037
PHATRDRAFT_43146

PHATRDRAFT_43146 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43146
PHATRDRAFT_43438 tap42-like protein (TAP42 superfamily)

PHATRDRAFT_43438 - tap42-like protein (TAP42 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43438
PHATRDRAFT_43658 translocation protein

PHATRDRAFT_43658 - translocation protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43658
PHATRDRAFT_45124

PHATRDRAFT_45124 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45124
PHATRDRAFT_45297

PHATRDRAFT_45297 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45297
PHATRDRAFT_45503 transmembrane protein

PHATRDRAFT_45503 - transmembrane protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45503
PHATRDRAFT_45927

PHATRDRAFT_45927 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45927
PHATRDRAFT_46105 isopenicillin n-epimerase (AAT_I superfamily)

PHATRDRAFT_46105 - isopenicillin n-epimerase (AAT_I superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46105
PHATRDRAFT_46566 heat shock protein

PHATRDRAFT_46566 - heat shock protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46566
PHATRDRAFT_46687 mina protein (Cupin_8 superfamily)

PHATRDRAFT_46687 - mina protein (Cupin_8 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46687
PHATRDRAFT_46908 integral membrane protein (PI-PLCc_GDPD_SF superfamily)

PHATRDRAFT_46908 - integral membrane protein (PI-PLCc_GDPD_SF superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46908
PHATRDRAFT_47134

PHATRDRAFT_47134 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47134
PHATRDRAFT_49264

PHATRDRAFT_49264 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49264
PHATRDRAFT_8511

PHATRDRAFT_8511 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8511
GO ID Go Term p-value q-value Cluster
GO:0006304 DNA modification 0.0135166 1 Phatr_bicluster_0254
GO:0006265 DNA topological change 0.0242101 1 Phatr_bicluster_0254
GO:0006259 DNA metabolism 0.032161 1 Phatr_bicluster_0254
GO:0000074 regulation of cell cycle 0.0886914 1 Phatr_bicluster_0254
GO:0015986 ATP synthesis coupled proton transport 0.096163 1 Phatr_bicluster_0254
GO:0007242 intracellular signaling cascade 0.108492 1 Phatr_bicluster_0254
GO:0007165 signal transduction 0.120668 1 Phatr_bicluster_0254
GO:0006418 tRNA aminoacylation for protein translation 0.132692 1 Phatr_bicluster_0254
GO:0006457 protein folding 0.275986 1 Phatr_bicluster_0254
GO:0006810 transport 0.412691 1 Phatr_bicluster_0254
Log in to post comments