Organism : Pseudomonas aeruginosa | Module List :
PA3925

probable acyl-CoA thiolase (NCBI)

CircVis
Functional Annotations (19)
Function System
Acetyl-CoA acetyltransferase cog/ cog
acetyl-CoA C-acetyltransferase activity go/ molecular_function
Fatty acid metabolism kegg/ kegg pathway
Synthesis and degradation of ketone bodies kegg/ kegg pathway
Valine leucine and isoleucine degradation kegg/ kegg pathway
Lysine degradation kegg/ kegg pathway
Benzoate degradation kegg/ kegg pathway
Tryptophan metabolism kegg/ kegg pathway
Pyruvate metabolism kegg/ kegg pathway
Glyoxylate and dicarboxylate metabolism kegg/ kegg pathway
Propanoate metabolism kegg/ kegg pathway
Butanoate metabolism kegg/ kegg pathway
Carbon fixation pathways in prokaryotes kegg/ kegg pathway
Terpenoid backbone biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
Two-component system kegg/ kegg pathway
AcCoA-C-Actrans tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3925
(Mouseover regulator name to see its description)

PA3925 is regulated by 41 influences and regulates 0 modules.
Regulators for PA3925 (41)
Regulator Module Operator
PA0424 224 tf
PA0456 224 tf
PA1269 224 tf
PA1544 224 tf
PA1776 224 tf
PA2849 224 tf
PA2899 224 tf
PA3002 224 tf
PA3034 224 tf
PA3126 224 tf
PA3341 224 tf
PA3423 224 tf
PA3815 224 tf
PA4745 224 tf
PA5253 224 tf
PA5337 224 tf
PA5374 224 tf
PA0181 342 tf
PA0367 342 tf
PA0576 342 tf
PA0873 342 tf
PA1067 342 tf
PA1241 342 tf
PA1776 342 tf
PA2320 342 tf
PA2387 342 tf
PA2737 342 tf
PA2825 342 tf
PA2849 342 tf
PA3006 342 tf
PA3699 342 tf
PA3714 342 tf
PA3965 342 tf
PA4080 342 tf
PA4135 342 tf
PA4169 342 tf
PA4182 342 tf
PA4270 342 tf
PA4493 342 tf
PA5085 342 tf
PA5253 342 tf

Warning: PA3925 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
3276 3.90e-07 ta.TccttttgacTaaTTt.cta.
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3277 4.30e-01 aTaGagtgagaacgTTTCa
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3510 7.90e-01 TCAAacAaacttTTG.tTt
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3511 2.80e+03 gtgACcgaaAagggtc.TccgGt
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Motif Help

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.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for PA3925

PA3925 is enriched for 19 functions in 3 categories.
Enrichment Table (19)
Function System
Acetyl-CoA acetyltransferase cog/ cog
acetyl-CoA C-acetyltransferase activity go/ molecular_function
Fatty acid metabolism kegg/ kegg pathway
Synthesis and degradation of ketone bodies kegg/ kegg pathway
Valine leucine and isoleucine degradation kegg/ kegg pathway
Lysine degradation kegg/ kegg pathway
Benzoate degradation kegg/ kegg pathway
Tryptophan metabolism kegg/ kegg pathway
Pyruvate metabolism kegg/ kegg pathway
Glyoxylate and dicarboxylate metabolism kegg/ kegg pathway
Propanoate metabolism kegg/ kegg pathway
Butanoate metabolism kegg/ kegg pathway
Carbon fixation pathways in prokaryotes kegg/ kegg pathway
Terpenoid backbone biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
Two-component system kegg/ kegg pathway
AcCoA-C-Actrans tigr/ tigrfam
Module neighborhood information for PA3925

PA3925 has total of 51 gene neighbors in modules 224, 342
Gene neighbors (51)
Gene Common Name Description Module membership
PA0139 ahpC alkyl hydroperoxide reductase subunit C (NCBI) 224, 436
PA0140 ahpF alkyl hydroperoxide reductase subunit F (NCBI) 152, 224
PA0160 PA0160 hypothetical protein (NCBI) 100, 224
PA0195 pntA putative NAD(P) transhydrogenase subunit alpha 1 (NCBI) 9, 342
PA0196 pntB pyridine nucleotide transhydrogenase, beta subunit (NCBI) 9, 342
PA0424 mexR multidrug resistance operon repressor MexR (NCBI) 224, 460
PA0425 mexA Resistance-Nodulation-Cell Division (RND) multidrug efflux membrane fusion protein MexA precursor (NCBI) 224, 509
PA0482 glcB malate synthase (NCBI) 264, 342
PA0506 PA0506 probable acyl-CoA dehydrogenase (NCBI) 342, 509
PA1092 fliC flagellin type B (NCBI) 342, 347
PA1093 PA1093 hypothetical protein (NCBI) 342, 347
PA1094 fliD flagellar capping protein FliD (NCBI) 342, 347
PA1095 PA1095 flagellar protein FliS (NCBI) 342, 347
PA1096 PA1096 hypothetical protein (NCBI) 342, 347
PA1244 PA1244 hypothetical protein (NCBI) 11, 342
PA1642 selD selenophosphate synthetase (NCBI) 224, 551
PA1643 PA1643 hypothetical protein (NCBI) 224, 551
PA1772 PA1772 ribonuclease activity regulator protein RraA (NCBI) 342, 551
PA1830 PA1830 hypothetical protein (NCBI) 342, 436
PA1835 PA1835 hypothetical protein (NCBI) 224, 264
PA1847 PA1847 hypothetical protein (NCBI) 224, 409
PA1852 PA1852 hypothetical protein (NCBI) 117, 224
PA2634 PA2634 isocitrate lyase (NCBI) 264, 342
PA2854 PA2854 hypothetical protein (NCBI) 6, 224
PA2951 etfA electron transfer flavoprotein alpha-subunit (NCBI) 264, 342
PA2952 etfB electron transfer flavoprotein beta-subunit (NCBI) 342, 462
PA2953 PA2953 electron transfer flavoprotein-ubiquinone oxidoreductase (NCBI) 342, 477
PA3009 PA3009 hypothetical protein (NCBI) 41, 224
PA3013 foaB acetyl-CoA acetyltransferase (NCBI) 342, 509
PA3014 faoA fatty-acid oxidation complex alpha-subunit (NCBI) 342, 509
PA3203 PA3203 hypothetical protein (NCBI) 316, 342
PA3204 PA3204 probable two-component response regulator (NCBI) 316, 342
PA3205 PA3205 hypothetical protein (NCBI) 189, 342
PA3341 PA3341 probable transcriptional regulator (NCBI) 41, 224
PA3431 PA3431 hypothetical protein (NCBI) 224, 261
PA3432 PA3432 hypothetical protein (NCBI) 224, 261
PA3575 PA3575 hypothetical protein (NCBI) 9, 224
PA3578 PA3578 hypothetical protein (NCBI) 224, 321
PA3719 PA3719 hypothetical protein (NCBI) 189, 224
PA3720 PA3720 hypothetical protein (NCBI) 189, 224
PA3925 PA3925 probable acyl-CoA thiolase (NCBI) 224, 342
PA4163 PA4163 amidase (NCBI) 42, 342
PA4164 PA4164 hypothetical protein (NCBI) 42, 342
PA4176 ppiC2 peptidyl-prolyl cis-trans isomerase C2 (NCBI) 42, 342
PA4180 PA4180 hypothetical protein (NCBI) 42, 342
PA4360 PA4360 hypothetical protein (NCBI) 165, 224
PA4565 proB gamma-glutamyl kinase (NCBI) 224, 352
PA4697 PA4697 hypothetical protein (NCBI) 2, 224
PA4870 PA4870 hypothetical protein (NCBI) 209, 224
PA5446 PA5446 hypothetical protein (NCBI) 224, 376
PA5527 PA5527 hypothetical protein (NCBI) 212, 224
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for PA3925
Please add your comments for this gene by using the form below. Your comments will be publicly available.

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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend