Phatr_bicluster_0061 Residual: 0.31
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_0061 0.31 Phaeodactylum tricornutum
Displaying 1 - 46 of 46
PHATRDRAFT_11777 mgc79074 protein (MPP_PP1_PPKL)

PHATRDRAFT_11777 - mgc79074 protein (MPP_PP1_PPKL)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11777
PHATRDRAFT_12031 formyltetrahydrofolate deformylase (purU)

PHATRDRAFT_12031 - formyltetrahydrofolate deformylase (purU)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12031
PHATRDRAFT_12313 glycosyl hydrolase family 3 c terminal domain containingexpressed (Glyco_hydro_3 superfamily)

PHATRDRAFT_12313 - glycosyl hydrolase family 3 c terminal domain containingexpressed (Glyco_hydro_3 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12313
PHATRDRAFT_12762 glutamate n-acetyltransferase (DmpA_OAT superfamily)

PHATRDRAFT_12762 - glutamate n-acetyltransferase (DmpA_OAT superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12762
PHATRDRAFT_13244 cytochrome c peroxidase (plant_peroxidase_like superfamily)

PHATRDRAFT_13244 - cytochrome c peroxidase (plant_peroxidase_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13244
PHATRDRAFT_16130 protein kinase c inhibitor (PKCI_related)

PHATRDRAFT_16130 - protein kinase c inhibitor (PKCI_related)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16130
PHATRDRAFT_17187 cyanate lyase (PRK02866)

PHATRDRAFT_17187 - cyanate lyase (PRK02866)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17187
PHATRDRAFT_17344 (COG2252)

PHATRDRAFT_17344 - (COG2252)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17344
PHATRDRAFT_20318 domain family (PRK07411)

PHATRDRAFT_20318 - domain family (PRK07411)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20318
PHATRDRAFT_22974 acetyl-coenzyme a synthetase (Ac_CoA_lig_AcsA)

PHATRDRAFT_22974 - acetyl-coenzyme a synthetase (Ac_CoA_lig_AcsA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22974
PHATRDRAFT_27889 pirin-family protein (COG1741)

PHATRDRAFT_27889 - pirin-family protein (COG1741)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27889
PHATRDRAFT_3183 ac007932_21-aminocyclopropane-1-carboxylate deaminase from pseudomonas gb (Trp-synth-beta_II superfamily)

PHATRDRAFT_3183 - ac007932_21-aminocyclopropane-1-carboxylate deaminase from pseudomonas gb (Trp-synth-beta_II superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3183
PHATRDRAFT_33623 tld family protein (TLD)

PHATRDRAFT_33623 - tld family protein (TLD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33623
PHATRDRAFT_34896 transcriptional regulatorfamily (TENA_THI-4 superfamily)

PHATRDRAFT_34896 - transcriptional regulatorfamily (TENA_THI-4 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34896
PHATRDRAFT_38821 outward-rectifying potassium channel kco1 (Ion_trans_2)

PHATRDRAFT_38821 - outward-rectifying potassium channel kco1 (Ion_trans_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38821
PHATRDRAFT_38946 cysteine desulfurase (csdA)

PHATRDRAFT_38946 - cysteine desulfurase (csdA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38946
PHATRDRAFT_41029

PHATRDRAFT_41029 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41029
PHATRDRAFT_43731 caffeic acid o-methyltransferase (Methyltransf_2 superfamily)

PHATRDRAFT_43731 - caffeic acid o-methyltransferase (Methyltransf_2 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43731
PHATRDRAFT_44321 polyhydroxyalkanoate depolymerase precursor (Transglut_core)

PHATRDRAFT_44321 - polyhydroxyalkanoate depolymerase precursor (Transglut_core)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44321
PHATRDRAFT_44484

PHATRDRAFT_44484 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44484
PHATRDRAFT_44585 peptidylprolyl isomeraselike (cyclophilin superfamily)

PHATRDRAFT_44585 - peptidylprolyl isomeraselike (cyclophilin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44585
PHATRDRAFT_44679 (RHOD superfamily)

PHATRDRAFT_44679 - (RHOD superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44679
PHATRDRAFT_44980 acyltransferase family protein (Acyl_transf_3)

PHATRDRAFT_44980 - acyltransferase family protein (Acyl_transf_3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44980
PHATRDRAFT_45195 extracellular solute-bindingfamily 3 (PBPb)

PHATRDRAFT_45195 - extracellular solute-bindingfamily 3 (PBPb)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45195
PHATRDRAFT_45373

PHATRDRAFT_45373 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45373
PHATRDRAFT_45549

PHATRDRAFT_45549 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45549
PHATRDRAFT_45601 synaptobrevin like 1 (Synaptobrevin)

PHATRDRAFT_45601 - synaptobrevin like 1 (Synaptobrevin)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45601
PHATRDRAFT_46653

PHATRDRAFT_46653 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46653
PHATRDRAFT_46728 lactoylglutathione lyase (MMCE)

PHATRDRAFT_46728 - lactoylglutathione lyase (MMCE)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46728
PHATRDRAFT_46881

PHATRDRAFT_46881 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46881
PHATRDRAFT_48233 isoprenylcysteine carboxyl methyltransferase (PEMT superfamily)

PHATRDRAFT_48233 - isoprenylcysteine carboxyl methyltransferase (PEMT superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48233
PHATRDRAFT_48703 ribulose--bisphosphate carboxylase oxygenase small subunit n-methyltransferase i

PHATRDRAFT_48703 - ribulose--bisphosphate carboxylase oxygenase small subunit n-methyltransferase i

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48703
PHATRDRAFT_48946 d-isomer specific 2-hydroxyacidnad-binding (2-Hacid_dh_1)

PHATRDRAFT_48946 - d-isomer specific 2-hydroxyacidnad-binding (2-Hacid_dh_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48946
PHATRDRAFT_49174

PHATRDRAFT_49174 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49174
PHATRDRAFT_49239

PHATRDRAFT_49239 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49239
PHATRDRAFT_49353

PHATRDRAFT_49353 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49353
PHATRDRAFT_49634 cyclic amp receptor protein (CAP_ED)

PHATRDRAFT_49634 - cyclic amp receptor protein (CAP_ED)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49634
PHATRDRAFT_49690

PHATRDRAFT_49690 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49690
PHATRDRAFT_49774

PHATRDRAFT_49774 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49774
PHATRDRAFT_49781 tetratricopeptide tpr_2 repeat protein

PHATRDRAFT_49781 - tetratricopeptide tpr_2 repeat protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49781
PHATRDRAFT_50342

PHATRDRAFT_50342 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50342
PHATRDRAFT_50498 (C2)

PHATRDRAFT_50498 - (C2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50498
PHATRDRAFT_52286 tryptophanbeta subunit (Trp-synth_B)

PHATRDRAFT_52286 - tryptophanbeta subunit (Trp-synth_B)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52286
PHATRDRAFT_54981 ammonium transporter (amt)

PHATRDRAFT_54981 - ammonium transporter (amt)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54981
PHATRDRAFT_7235 membrane protein (DUF2214 superfamily)

PHATRDRAFT_7235 - membrane protein (DUF2214 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7235
PHATRDRAFT_9137 molybdopterin synthase small subunit mocs2a (MoaE)

PHATRDRAFT_9137 - molybdopterin synthase small subunit mocs2a (MoaE)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9137
GO ID Go Term p-value q-value Cluster
GO:0009439 cyanate metabolism 0.00493949 1 Phatr_bicluster_0061
GO:0006189 'de novo' IMP biosynthesis 0.0244666 1 Phatr_bicluster_0061
GO:0006777 Mo-molybdopterin cofactor biosynthesis 0.0292912 1 Phatr_bicluster_0061
GO:0006526 arginine biosynthesis 0.0340932 1 Phatr_bicluster_0061
GO:0006564 L-serine biosynthesis 0.0388725 1 Phatr_bicluster_0061
GO:0016192 vesicle-mediated transport 0.0624342 1 Phatr_bicluster_0061
GO:0006810 transport 0.0652367 1 Phatr_bicluster_0061
GO:0006813 potassium ion transport 0.0945003 1 Phatr_bicluster_0061
GO:0006979 response to oxidative stress 0.112353 1 Phatr_bicluster_0061
GO:0008152 metabolism 0.173524 1 Phatr_bicluster_0061
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