Organism : Pseudomonas aeruginosa | Module List :
PA2012 gnyA

alpha subunit of geranoyl-CoA carboxylase, GnyA (NCBI)

CircVis
Functional Annotations (7)
Function System
Acetyl/propionyl-CoA carboxylase, alpha subunit cog/ cog
ATP binding go/ molecular_function
metabolic process go/ biological_process
biotin binding go/ molecular_function
ligase activity go/ molecular_function
Valine leucine and isoleucine degradation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2012
(Mouseover regulator name to see its description)

PA2012 is regulated by 49 influences and regulates 0 modules.
Regulators for PA2012 gnyA (49)
Regulator Module Operator
PA0125 145 tf
PA0253 145 tf
PA0708 145 tf
PA0797 145 tf
PA1363 145 tf
PA1760 145 tf
PA1853 145 tf
PA2016 145 tf
PA2556 145 tf
PA2737 145 tf
PA3622 145 tf
PA4132 145 tf
PA4169 145 tf
PA4354 145 tf
PA4764 145 tf
PA5105 145 tf
PA5253 145 tf
PA5380 145 tf
PA5389 145 tf
PA0123 502 tf
PA0167 502 tf
PA0191 502 tf
PA0236 502 tf
PA0708 502 tf
PA0797 502 tf
PA1241 502 tf
PA1309 502 tf
PA1759 502 tf
PA1760 502 tf
PA2016 502 tf
PA2277 502 tf
PA2556 502 tf
PA2622 502 tf
PA3034 502 tf
PA3094 502 tf
PA3225 502 tf
PA3433 502 tf
PA3622 502 tf
PA3921 502 tf
PA4094 502 tf
PA4132 502 tf
PA4135 502 tf
PA4764 502 tf
PA4787 502 tf
PA4989 502 tf
PA5085 502 tf
PA5283 502 tf
PA5337 502 tf
PA5380 502 tf

Warning: PA2012 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
3120 5.00e-03 TaCgtc.AcgtaAAacaAaA
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3121 3.40e+00 AGAaCaAtTAaA
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3818 9.00e+01 aAaAACAAaC.tA
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3819 1.90e+03 TT.TGAT
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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 PA2012

PA2012 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Acetyl/propionyl-CoA carboxylase, alpha subunit cog/ cog
ATP binding go/ molecular_function
metabolic process go/ biological_process
biotin binding go/ molecular_function
ligase activity go/ molecular_function
Valine leucine and isoleucine degradation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Module neighborhood information for PA2012

PA2012 has total of 30 gene neighbors in modules 145, 502
Gene neighbors (30)
Gene Common Name Description Module membership
PA0129 gabP gamma-aminobutyrate permease (NCBI) 145, 239
PA0130 PA0130 probable aldehyde dehydrogenase (NCBI) 145, 191
PA0131 PA0131 hypothetical protein (NCBI) 145, 191
PA0132 PA0132 beta-alanine--pyruvate transaminase (NCBI) 145, 191
PA0746 PA0746 probable acyl-CoA dehydrogenase (NCBI) 145, 413
PA0747 PA0747 probable aldehyde dehydrogenase (NCBI) 145, 413
PA0793 PA0793 hypothetical protein (NCBI) 145, 264
PA0794 PA0794 probable aconitate hydratase (NCBI) 145, 264
PA0795 prpC citrate synthase 2 (NCBI) 145, 264
PA0796 prpB carboxyphosphonoenolpyruvate phosphonomutase (NCBI) 145, 264
PA1999 PA1999 probable CoA transferase, subunit A (NCBI) 146, 502
PA2000 PA2000 probable CoA transferase, subunit B (NCBI) 146, 502
PA2011 gnyL 3-hydroxy-gamma-carboxygeranoyl-CoA lyase, GnyL (NCBI) 145, 502
PA2012 gnyA alpha subunit of geranoyl-CoA carboxylase, GnyA (NCBI) 145, 502
PA2013 gnyH gamma-carboxygeranoyl-CoA hydratase, GnyH (NCBI) 227, 502
PA2014 gnyB beta subunit of geranoyl-CoA carboxylase, GnyB (NCBI) 227, 502
PA2015 gnyD Citronelloyl-CoA dehydrogenase, GnyD (NCBI) 145, 502
PA2016 gnyR Regulatory gene of gnyRDBHAL cluster, GnyR (NCBI) 145, 524
PA2247 bkdA1 2-oxoisovalerate dehydrogenase (alpha subunit) (NCBI) 227, 502
PA2248 bkdA2 2-oxoisovalerate dehydrogenase (beta subunit) (NCBI) 227, 502
PA2249 bkdB branched-chain alpha-keto acid dehydrogenase (lipoamide component) (NCBI) 227, 502
PA2250 lpdV dihydrolipoamide dehydrogenase (NCBI) 227, 502
PA2552 PA2552 probable acyl-CoA dehydrogenase (NCBI) 227, 502
PA2553 PA2553 probable acyl-CoA thiolase (NCBI) 227, 502
PA2554 PA2554 probable short-chain dehydrogenase (NCBI) 145, 502
PA2555 PA2555 probable AMP-binding enzyme (NCBI) 145, 502
PA2557 PA2557 acyl-CoA synthase (NCBI) 145, 239
PA3569 mmsB 3-hydroxyisobutyrate dehydrogenase (NCBI) 145, 515
PA3570 mmsA methylmalonate-semialdehyde dehydrogenase (NCBI) 145, 515
PA5100 hutU urocanate hydratase (NCBI) 145, 258
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 PA2012
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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