Phatr_bicluster_0080 Residual: 0.29
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_0080 0.29 Phaeodactylum tricornutum
Displaying 1 - 32 of 32
PHATRDRAFT_11217 atp-dependent clp proteinase regulatory chain x (HslU)

PHATRDRAFT_11217 - atp-dependent clp proteinase regulatory chain x (HslU)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11217
PHATRDRAFT_11235 pentapeptide repeat

PHATRDRAFT_11235 - pentapeptide repeat

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11235
PHATRDRAFT_11733 mitochondrial creatine kinase (phosphagen_kinases superfamily)

PHATRDRAFT_11733 - mitochondrial creatine kinase (phosphagen_kinases superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11733
PHATRDRAFT_2164 adp atp translocase (PTZ00169)

PHATRDRAFT_15797 - adp atp translocase (PTZ00169)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15797
PHATRDRAFT_31434 mfs family transporter: sugar (galactose glucose) (Sugar_tr)

PHATRDRAFT_2164 - mfs family transporter: sugar (galactose glucose) (Sugar_tr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_2164
PHATRDRAFT_35196

PHATRDRAFT_31434 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31434
PHATRDRAFT_35678 imp protein (zf-UBP)

PHATRDRAFT_35196 - imp protein (zf-UBP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35196
PHATRDRAFT_37130

PHATRDRAFT_35678 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35678
PHATRDRAFT_37440 rnase h family protein (RVT_3)

PHATRDRAFT_37130 - rnase h family protein (RVT_3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37130
PHATRDRAFT_41886 chromosome 6 open reading frame 113 (Peptidase_C78 superfamily)

PHATRDRAFT_37440 - chromosome 6 open reading frame 113 (Peptidase_C78 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37440
PHATRDRAFT_42422 hydroxysteroid (17-beta) dehydrogenase 10 (NADB_Rossmann superfamily)

PHATRDRAFT_41886 - hydroxysteroid (17-beta) dehydrogenase 10 (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41886
PHATRDRAFT_42699

PHATRDRAFT_42422 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42422
PHATRDRAFT_42778 (DUF4239)

PHATRDRAFT_42699 - (DUF4239)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42699
PHATRDRAFT_42971 (GLTP superfamily)

PHATRDRAFT_42778 - (GLTP superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42778
PHATRDRAFT_44278 (Cupin_8 superfamily)

PHATRDRAFT_42971 - (Cupin_8 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42971
PHATRDRAFT_44745

PHATRDRAFT_44278 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44278
PHATRDRAFT_44900 ubiquitin specific protease 22 (Peptidase_C19 superfamily)

PHATRDRAFT_44745 - ubiquitin specific protease 22 (Peptidase_C19 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44745
PHATRDRAFT_45312 glycerophosphodiester phosphodiesterase (GDPD_GsGDE_like)

PHATRDRAFT_44900 - glycerophosphodiester phosphodiesterase (GDPD_GsGDE_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44900
PHATRDRAFT_45381 transporter protein with conserved zn ribbon c11c7

PHATRDRAFT_45312 - transporter protein with conserved zn ribbon c11c7

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45312
PHATRDRAFT_45408 ntp pyrophosphohydrolase (Nudix_Hydrolase superfamily)

PHATRDRAFT_45381 - ntp pyrophosphohydrolase (Nudix_Hydrolase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45381
PHATRDRAFT_45563 glycine cleavage system regulatory protein (GcvR)

PHATRDRAFT_45408 - glycine cleavage system regulatory protein (GcvR)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45408
PHATRDRAFT_45576 (SEC14)

PHATRDRAFT_45563 - (SEC14)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45563
PHATRDRAFT_45611 cobyrinic acid-diamide synthase family protein

PHATRDRAFT_45576 - cobyrinic acid-diamide synthase family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45576
PHATRDRAFT_45741

PHATRDRAFT_45611 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45611
PHATRDRAFT_45799

PHATRDRAFT_45741 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45741
PHATRDRAFT_45973 s3 self-incompatibility locus-linked pollenprotein

PHATRDRAFT_45799 - s3 self-incompatibility locus-linked pollenprotein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45799
PHATRDRAFT_46129 sec14 cytosolic factor family protein phosphoglyceride transfer family protein (SEC14)

PHATRDRAFT_45973 - sec14 cytosolic factor family protein phosphoglyceride transfer family protein (SEC14)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45973
PHATRDRAFT_49281

PHATRDRAFT_46129 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46129
PHATRDRAFT_54087

PHATRDRAFT_49281 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49281
PHATRDRAFT_9342

PHATRDRAFT_54087 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54087
PHATRDRAFT_9619 ubiquitin activating enzyme e1-like protein (E1_enzyme_family superfamily)

PHATRDRAFT_9342 - ubiquitin activating enzyme e1-like protein (E1_enzyme_family superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9342

PHATRDRAFT_9619 - mgdg synthase type a (PLN02605)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9619
GO ID Go Term p-value q-value Cluster
GO:0008152 metabolism 0.109996 1 Phatr_bicluster_0080
GO:0006071 glycerol metabolism 0.00788271 1 Phatr_bicluster_0080
GO:0008643 carbohydrate transport 0.0312056 1 Phatr_bicluster_0080
GO:0006810 transport 0.0513747 1 Phatr_bicluster_0080
GO:0015031 protein transport 0.0596835 1 Phatr_bicluster_0080
GO:0006511 ubiquitin-dependent protein catabolism 0.0855993 1 Phatr_bicluster_0080
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