Phatr_bicluster_0103 Residual: 0.38
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_0103 0.38 Phaeodactylum tricornutum
Displaying 1 - 24 of 24
PHATRDRAFT_11356 chromodomain helicase dna binding protein 7

PHATRDRAFT_11356 - chromodomain helicase dna binding protein 7

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11356
PHATRDRAFT_11409 structure specific recognition protein 1 (PH1_SSRP1-like)

PHATRDRAFT_11409 - structure specific recognition protein 1 (PH1_SSRP1-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11409
PHATRDRAFT_12813 chloroplast ferredoxin nadp(+) reductase (PLN03116)

PHATRDRAFT_12813 - chloroplast ferredoxin nadp(+) reductase (PLN03116)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12813
PHATRDRAFT_12972 isopentenyl pyrophosphate:dimethylallyl pyrophosphate isomerase (IPP_Isomerase)

PHATRDRAFT_12972 - isopentenyl pyrophosphate:dimethylallyl pyrophosphate isomerase (IPP_Isomerase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12972
PHATRDRAFT_13073 plastid beta-ketoacyl-acp reductase protein precursor (BKR_SDR_c)

PHATRDRAFT_13073 - plastid beta-ketoacyl-acp reductase protein precursor (BKR_SDR_c)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13073
PHATRDRAFT_14192 thioredoxin reductase (TRX_reduct)

PHATRDRAFT_14192 - thioredoxin reductase (TRX_reduct)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14192
PHATRDRAFT_17184 arginine methyltransferase pam1 (AdoMet_MTases)

PHATRDRAFT_17184 - arginine methyltransferase pam1 (AdoMet_MTases)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17184
PHATRDRAFT_25956 phosphoadenosine phosphosulfate reductase (PAPS_reductase)

PHATRDRAFT_25956 - phosphoadenosine phosphosulfate reductase (PAPS_reductase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25956
PHATRDRAFT_292 class vii unconventional myosin (MYSc)

PHATRDRAFT_292 - class vii unconventional myosin (MYSc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_292
PHATRDRAFT_31469 tr4 orphan receptor associated protein tra16

PHATRDRAFT_31469 - tr4 orphan receptor associated protein tra16

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31469
PHATRDRAFT_31846 ac068923_16prolyl 4-alpha subunit (2OG-FeII_Oxy_3 superfamily)

PHATRDRAFT_31846 - ac068923_16prolyl 4-alpha subunit (2OG-FeII_Oxy_3 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31846
PHATRDRAFT_33842

PHATRDRAFT_33842 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33842
PHATRDRAFT_37105

PHATRDRAFT_37105 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37105
PHATRDRAFT_37368

PHATRDRAFT_37368 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37368
PHATRDRAFT_38283

PHATRDRAFT_38283 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38283
PHATRDRAFT_432 myosin subfamily xi heavy chain (MYSc)

PHATRDRAFT_432 - myosin subfamily xi heavy chain (MYSc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_432
PHATRDRAFT_44147 gaf domain (DUF2453)

PHATRDRAFT_44147 - gaf domain (DUF2453)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44147
PHATRDRAFT_46621

PHATRDRAFT_46621 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46621
PHATRDRAFT_48145 permease of the drug metabolite transportersuperfamily (RhaT)

PHATRDRAFT_48145 - permease of the drug metabolite transportersuperfamily (RhaT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48145
PHATRDRAFT_49417 leucine carboxyl (LCM)

PHATRDRAFT_49417 - leucine carboxyl (LCM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49417
PHATRDRAFT_49957 proteophosphoglycan ppg1

PHATRDRAFT_49957 - proteophosphoglycan ppg1

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49957
PHATRDRAFT_54310 chd gene family protein containinghelicaseand dna-binding domain (SNF2_N)

PHATRDRAFT_54310 - chd gene family protein containinghelicaseand dna-binding domain (SNF2_N)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54310
PHATRDRAFT_8670 oligopeptidase a (Dcp)

PHATRDRAFT_8670 - oligopeptidase a (Dcp)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8670
PHATRDRAFT_9409 chaperone regulator (DnaJ)

PHATRDRAFT_9409 - chaperone regulator (DnaJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9409
GO ID Go Term p-value q-value Cluster
GO:0006118 electron transport 0.0210062 1 Phatr_bicluster_0103
GO:0008299 isoprenoid biosynthesis 0.0242101 1 Phatr_bicluster_0103
GO:0006633 fatty acid biosynthesis 0.0347981 1 Phatr_bicluster_0103
GO:0019538 protein metabolism 0.0936787 1 Phatr_bicluster_0103
GO:0006508 proteolysis and peptidolysis 0.120633 1 Phatr_bicluster_0103
GO:0008152 metabolism 0.187614 1 Phatr_bicluster_0103
GO:0006457 protein folding 0.275986 1 Phatr_bicluster_0103
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