Phatr_bicluster_0079 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_0079 0.32 Phaeodactylum tricornutum
Displaying 1 - 21 of 21
PHATRDRAFT_16595 2-dehydropantoate 2-reductase (ApbA_C)

PHATRDRAFT_16595 - 2-dehydropantoate 2-reductase (ApbA_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16595
PHATRDRAFT_28723 gcn5-related n-acetyltransferasefamily protein (RimI)

PHATRDRAFT_28723 - gcn5-related n-acetyltransferasefamily protein (RimI)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28723
PHATRDRAFT_33692 (N2227 superfamily)

PHATRDRAFT_33692 - (N2227 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33692
PHATRDRAFT_33738 transmembrane protein

PHATRDRAFT_33738 - transmembrane protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33738
PHATRDRAFT_35126 kinesin motor domain containing protein

PHATRDRAFT_35126 - kinesin motor domain containing protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35126
PHATRDRAFT_40382 mosc domain containing protein (MOSC superfamily)

PHATRDRAFT_40382 - mosc domain containing protein (MOSC superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40382
PHATRDRAFT_42003 cystathionine beta-synthase (cysta_beta)

PHATRDRAFT_42003 - cystathionine beta-synthase (cysta_beta)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42003
PHATRDRAFT_42941 y6689_myxxdupf0272 protein mxan_6689 (DUF111 superfamily)

PHATRDRAFT_42941 - y6689_myxxdupf0272 protein mxan_6689 (DUF111 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42941
PHATRDRAFT_44171 (DUF2042 superfamily)

PHATRDRAFT_44171 - (DUF2042 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44171
PHATRDRAFT_44299

PHATRDRAFT_44299 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44299
PHATRDRAFT_44709

PHATRDRAFT_44709 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44709
PHATRDRAFT_45995 (ZnMc superfamily)

PHATRDRAFT_45995 - (ZnMc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45995
PHATRDRAFT_46560 ipt tig domain containing protein

PHATRDRAFT_46560 - ipt tig domain containing protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46560
PHATRDRAFT_47780 probable glycosyltransferase (ATPgrasp_TupA superfamily)

PHATRDRAFT_47780 - probable glycosyltransferase (ATPgrasp_TupA superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47780
PHATRDRAFT_47972

PHATRDRAFT_47972 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47972
PHATRDRAFT_48864 nad-dependent steroid dehydrogenase-like protein (NADB_Rossmann superfamily)

PHATRDRAFT_48864 - nad-dependent steroid dehydrogenase-like protein (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48864
PHATRDRAFT_49572 rad54b protein (SNF2_N)

PHATRDRAFT_49572 - rad54b protein (SNF2_N)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49572
PHATRDRAFT_49766 (E3_UbLigase_R4 superfamily)

PHATRDRAFT_49766 - (E3_UbLigase_R4 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49766
PHATRDRAFT_6151 beta 1 subunit of 20s proteasome (proteasome_beta)

PHATRDRAFT_6151 - beta 1 subunit of 20s proteasome (proteasome_beta)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6151
PHATRDRAFT_8773 akin10 (arabidopsis snf1 kinase homologsnf1-related protein kinase) protein kinase (S_TKc)

PHATRDRAFT_8773 - akin10 (arabidopsis snf1 kinase homologsnf1-related protein kinase) protein kinase (S_TKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8773
PHATRDRAFT_9606 (Haemolytic)

PHATRDRAFT_9606 - (Haemolytic)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9606
GO ID Go Term p-value q-value Cluster
GO:0019343 cysteine biosynthesis via cystathione 0.00172882 1 Phatr_bicluster_0079
GO:0006694 steroid biosynthesis 0.00172882 1 Phatr_bicluster_0079
GO:0006535 cysteine biosynthesis from serine 0.00517878 1 Phatr_bicluster_0079
GO:0006511 ubiquitin-dependent protein catabolism 0.0753046 1 Phatr_bicluster_0079
GO:0006468 protein amino acid phosphorylation 0.262204 1 Phatr_bicluster_0079
GO:0006508 proteolysis and peptidolysis 0.328797 1 Phatr_bicluster_0079
GO:0008152 metabolism 0.410263 1 Phatr_bicluster_0079
Log in to post comments