Phatr_bicluster_0085 Residual: 0.45
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_0085 0.45 Phaeodactylum tricornutum
Displaying 1 - 30 of 30
PHATRDRAFT_1457 nls receptor (ARM)

PHATRDRAFT_1457 - nls receptor (ARM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_1457
PHATRDRAFT_14645 iojap-related protein (Oligomerization)

PHATRDRAFT_14645 - iojap-related protein (Oligomerization)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14645
PHATRDRAFT_14849 family protein (BolA superfamily)

PHATRDRAFT_14849 - family protein (BolA superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14849
PHATRDRAFT_15281 vacuolar transporter (VTC1)

PHATRDRAFT_15281 - vacuolar transporter (VTC1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15281
PHATRDRAFT_15595 tryptophanyl-trna synthetase (PRK00927)

PHATRDRAFT_15595 - tryptophanyl-trna synthetase (PRK00927)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15595
PHATRDRAFT_16262 chromatin remodeling factor chrom1 isoform 1 (SNF2_N)

PHATRDRAFT_16262 - chromatin remodeling factor chrom1 isoform 1 (SNF2_N)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16262
PHATRDRAFT_17029 rna polymerase sigma factor (Sig70-cyanoRpoD)

PHATRDRAFT_17029 - rna polymerase sigma factor (Sig70-cyanoRpoD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17029
PHATRDRAFT_17043 drug resistance atpase-1 (drug ra1) abc transporteratp-binding protein (Uup)

PHATRDRAFT_17043 - drug resistance atpase-1 (drug ra1) abc transporteratp-binding protein (Uup)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17043
PHATRDRAFT_17172 gtp-binding protein (PRK00093)

PHATRDRAFT_17172 - gtp-binding protein (PRK00093)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17172
PHATRDRAFT_18027 delta-1-pyrroline 5-carboxylase synthetase (PLN02418)

PHATRDRAFT_18027 - delta-1-pyrroline 5-carboxylase synthetase (PLN02418)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18027
PHATRDRAFT_18080 phosphoribosylamidoimidazole-succinocarboxamide synthase (SAICAR_synt_Sc)

PHATRDRAFT_18080 - phosphoribosylamidoimidazole-succinocarboxamide synthase (SAICAR_synt_Sc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18080
PHATRDRAFT_22510 delta 5 fatty acid desaturase (Delta6-FADS-like)

PHATRDRAFT_22510 - delta 5 fatty acid desaturase (Delta6-FADS-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22510
PHATRDRAFT_29004 inositol monophosphatase family protein (IMPase)

PHATRDRAFT_29004 - inositol monophosphatase family protein (IMPase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29004
PHATRDRAFT_37533

PHATRDRAFT_37533 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37533
PHATRDRAFT_38930 carbon-nitrogen hydrolase (CPA)

PHATRDRAFT_38930 - carbon-nitrogen hydrolase (CPA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38930
PHATRDRAFT_39046 at3g04650 f7o18_13 (NAD_binding_8 superfamily)

PHATRDRAFT_39046 - at3g04650 f7o18_13 (NAD_binding_8 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39046
PHATRDRAFT_43507 (CRAL_TRIO_2)

PHATRDRAFT_43507 - (CRAL_TRIO_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43507
PHATRDRAFT_45871 hepatocellular carcinoma-associated antigen 66 (U3_assoc_6 superfamily)

PHATRDRAFT_45871 - hepatocellular carcinoma-associated antigen 66 (U3_assoc_6 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45871
PHATRDRAFT_47239 solute carrier family 34 (sodium phosphate)member 1 (Na_Pi_cotrans)

PHATRDRAFT_47239 - solute carrier family 34 (sodium phosphate)member 1 (Na_Pi_cotrans)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47239
PHATRDRAFT_47489 intestinal mucin

PHATRDRAFT_47489 - intestinal mucin

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47489
PHATRDRAFT_47558 elicitin-like protein 6 precursor

PHATRDRAFT_47558 - elicitin-like protein 6 precursor

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47558
PHATRDRAFT_47588 mgc85567 protein

PHATRDRAFT_47588 - mgc85567 protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47588
PHATRDRAFT_48489

PHATRDRAFT_48489 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48489
PHATRDRAFT_48958 spou protein (SpoU_methylase)

PHATRDRAFT_48958 - spou protein (SpoU_methylase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48958
PHATRDRAFT_49488 cog3781: membrane protein (Bestrophin superfamily)

PHATRDRAFT_49488 - cog3781: membrane protein (Bestrophin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49488
PHATRDRAFT_49915

PHATRDRAFT_49915 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49915
PHATRDRAFT_50885 glycyl-trna synthetase (PRK04173)

PHATRDRAFT_50885 - glycyl-trna synthetase (PRK04173)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50885
PHATRDRAFT_51214 (gltB)

PHATRDRAFT_51214 - (gltB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51214
PHATRDRAFT_51305 carbonic anhydrase family protein (beta_CA_cladeA)

PHATRDRAFT_51305 - carbonic anhydrase family protein (beta_CA_cladeA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51305
PHATRDRAFT_54958 (SPFH_prohibitin)

PHATRDRAFT_54958 - (SPFH_prohibitin)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54958
GO ID Go Term p-value q-value Cluster
GO:0006807 nitrogen compound metabolism 0.00246558 1 Phatr_bicluster_0085
GO:0015976 carbon utilization 0.0108387 1 Phatr_bicluster_0085
GO:0006426 glycyl-tRNA aminoacylation 0.0108387 1 Phatr_bicluster_0085
GO:0006436 tryptophanyl-tRNA aminoacylation 0.0108387 1 Phatr_bicluster_0085
GO:0006164 purine nucleotide biosynthesis 0.0215652 1 Phatr_bicluster_0085
GO:0006561 proline biosynthesis 0.0268867 1 Phatr_bicluster_0085
GO:0006537 glutamate biosynthesis 0.0268867 1 Phatr_bicluster_0085
GO:0006418 tRNA aminoacylation for protein translation 0.0317216 1 Phatr_bicluster_0085
GO:0006396 RNA processing 0.0363639 1 Phatr_bicluster_0085
GO:0006817 phosphate transport 0.037447 1 Phatr_bicluster_0085
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