Phatr_bicluster_0100 Residual: 0.43
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_0100 0.43 Phaeodactylum tricornutum
Displaying 1 - 46 of 46
PHATRDRAFT_13255 hybrid sensory kinase (REC)

PHATRDRAFT_13255 - hybrid sensory kinase (REC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13255
PHATRDRAFT_16982 glutathione s-transferase (PRK11752)

PHATRDRAFT_16982 - glutathione s-transferase (PRK11752)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16982
PHATRDRAFT_17048 tcp1-chaperonin cofactor a isolog (TBCA)

PHATRDRAFT_17048 - tcp1-chaperonin cofactor a isolog (TBCA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17048
PHATRDRAFT_18572 catalase peroxidase hpi (PRK15061)

PHATRDRAFT_18572 - catalase peroxidase hpi (PRK15061)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18572
PHATRDRAFT_20677 short-chain dehydrogenase reductase sdr (NADB_Rossmann superfamily)

PHATRDRAFT_20677 - short-chain dehydrogenase reductase sdr (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20677
PHATRDRAFT_21548 (ABC_MTABC3_MDL1_MDL2)

PHATRDRAFT_21548 - (ABC_MTABC3_MDL1_MDL2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21548
PHATRDRAFT_23497 (ABC_subfamily_A)

PHATRDRAFT_23497 - (ABC_subfamily_A)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23497
PHATRDRAFT_24493 eukaryotic translation initiation factor 6 (IF6)

PHATRDRAFT_24493 - eukaryotic translation initiation factor 6 (IF6)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_24493
PHATRDRAFT_30389 ubc1p like ubiquitin-conjugating enzyme e2 fused to a uba domain (ubc+uba) (UBCc)

PHATRDRAFT_30389 - ubc1p like ubiquitin-conjugating enzyme e2 fused to a uba domain (ubc+uba) (UBCc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30389
PHATRDRAFT_30578 short chain dehydrogenase oxidoreductase (NADB_Rossmann superfamily)

PHATRDRAFT_30578 - short chain dehydrogenase oxidoreductase (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30578
PHATRDRAFT_31433 abc transporter family protein (3a01204)

PHATRDRAFT_31433 - abc transporter family protein (3a01204)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31433
PHATRDRAFT_31558

PHATRDRAFT_31558 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31558
PHATRDRAFT_33025

PHATRDRAFT_33025 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33025
PHATRDRAFT_33087

PHATRDRAFT_33087 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33087
PHATRDRAFT_36801 nitroreductase (Nitro_FMN_reductase superfamily)

PHATRDRAFT_36608 - nitroreductase (Nitro_FMN_reductase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36608
PHATRDRAFT_3787 (EBP superfamily)

PHATRDRAFT_36801 - (EBP superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36801
PHATRDRAFT_39769 allc_xenlaallantoicase (allantoate amidinohydrolase) (allantoicase)

PHATRDRAFT_3787 - allc_xenlaallantoicase (allantoate amidinohydrolase) (allantoicase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3787
PHATRDRAFT_39969

PHATRDRAFT_39769 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39769
PHATRDRAFT_42557

PHATRDRAFT_39969 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39969
PHATRDRAFT_42560 nod3isoform cra_d (LRR_RI superfamily)

PHATRDRAFT_42557 - nod3isoform cra_d (LRR_RI superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42557
PHATRDRAFT_43313

PHATRDRAFT_42560 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42560
PHATRDRAFT_43314 membrane protein (VIT1)

PHATRDRAFT_43313 - membrane protein (VIT1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43313
PHATRDRAFT_43478 membrane protein (VIT1)

PHATRDRAFT_43314 - membrane protein (VIT1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43314
PHATRDRAFT_44522 (PDZ_signaling)

PHATRDRAFT_43478 - (PDZ_signaling)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43478
PHATRDRAFT_44630 (2OG-FeII_Oxy_3)

PHATRDRAFT_44522 - (2OG-FeII_Oxy_3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44522
PHATRDRAFT_45012 carbonyl reductase (NADB_Rossmann superfamily)

PHATRDRAFT_44630 - carbonyl reductase (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44630
PHATRDRAFT_45335 ring finger protein 12 (RING)

PHATRDRAFT_45012 - ring finger protein 12 (RING)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45012
PHATRDRAFT_45852 (EFh)

PHATRDRAFT_45335 - (EFh)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45335
PHATRDRAFT_46126 aromatic amino acid transporter (Trp_Tyr_perm superfamily)

PHATRDRAFT_45852 - aromatic amino acid transporter (Trp_Tyr_perm superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45852
PHATRDRAFT_46332 tb2 hva22 family protein (TB2_DP1_HVA22)

PHATRDRAFT_46126 - tb2 hva22 family protein (TB2_DP1_HVA22)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46126
PHATRDRAFT_46707

PHATRDRAFT_46332 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46332
PHATRDRAFT_46721 short-chain dehydrogenase reductase sdr (NADB_Rossmann superfamily)

PHATRDRAFT_46707 - short-chain dehydrogenase reductase sdr (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46707
PHATRDRAFT_46867 cog0702: nucleoside-diphosphate-sugar epimerases (NADB_Rossmann superfamily)

PHATRDRAFT_46721 - cog0702: nucleoside-diphosphate-sugar epimerases (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46721
PHATRDRAFT_48319 rnd family transporter: niemann-pick type c1 diseaseprotein (Patched)

PHATRDRAFT_46867 - rnd family transporter: niemann-pick type c1 diseaseprotein (Patched)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46867
PHATRDRAFT_48793 (WLM superfamily)

PHATRDRAFT_48319 - (WLM superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48319
PHATRDRAFT_48899 ctr2 family transporter: copper ion ctr-type copper transporter (Ctr)

PHATRDRAFT_48793 - ctr2 family transporter: copper ion ctr-type copper transporter (Ctr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48793
PHATRDRAFT_49482

PHATRDRAFT_48899 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48899
PHATRDRAFT_49730

PHATRDRAFT_49482 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49482
PHATRDRAFT_50298 cog3224: uncharacterized protein conserved in bacteria (COG3224 superfamily)

PHATRDRAFT_49730 - cog3224: uncharacterized protein conserved in bacteria (COG3224 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49730
PHATRDRAFT_5142

PHATRDRAFT_50298 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50298
PHATRDRAFT_545 mitochondrial carrier (Mito_carr)

PHATRDRAFT_5142 - mitochondrial carrier (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5142
PHATRDRAFT_54974 thermostable beta-glucosidase (glycoside hydrolase family 3) (Glyco_hydro_3)

PHATRDRAFT_545 - thermostable beta-glucosidase (glycoside hydrolase family 3) (Glyco_hydro_3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_545
PHATRDRAFT_55096 alpha beta fold family protein (Abhydrolase_6)

PHATRDRAFT_54974 - alpha beta fold family protein (Abhydrolase_6)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54974
PHATRDRAFT_9171

PHATRDRAFT_55096 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55096

PHATRDRAFT_9171 - protein disulfide isomerase (PDI_a_family)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9171

PHATRDRAFT_9912 - peptide methionine sulfoxide reductase (PMSR superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9912
GO ID Go Term p-value q-value Cluster
GO:0007022 chaperonin-mediated tubulin folding 0.00518647 1 Phatr_bicluster_0100
GO:0006825 copper ion transport 0.0154826 1 Phatr_bicluster_0100
GO:0006464 protein modification 0.0413866 1 Phatr_bicluster_0100
GO:0008152 metabolism 0.0610585 1 Phatr_bicluster_0100
GO:0006979 response to oxidative stress 0.117641 1 Phatr_bicluster_0100
GO:0006413 translational initiation 0.117641 1 Phatr_bicluster_0100
GO:0000160 two-component signal transduction system (phosphorelay) 0.126825 1 Phatr_bicluster_0100
GO:0006865 amino acid transport 0.135918 1 Phatr_bicluster_0100
GO:0006512 ubiquitin cycle 0.180048 1 Phatr_bicluster_0100
GO:0006810 transport 0.260576 1 Phatr_bicluster_0100
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