Organism : Pseudomonas aeruginosa | Module List :
PA2013 gnyH

gamma-carboxygeranoyl-CoA hydratase, GnyH (NCBI)

CircVis
Functional Annotations (5)
Function System
Enoyl-CoA hydratase/carnithine racemase cog/ cog
enoyl-CoA hydratase activity go/ molecular_function
metabolic process go/ biological_process
Valine leucine and isoleucine degradation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2013
(Mouseover regulator name to see its description)

PA2013 is regulated by 60 influences and regulates 0 modules.
Regulators for PA2013 gnyH (60)
Regulator Module Operator
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
PA0191 227 tf
PA0294 227 tf
PA0708 227 tf
PA0764 227 tf
PA0797 227 tf
PA0893 227 tf
PA1241 227 tf
PA1309 227 tf
PA1759 227 tf
PA1760 227 tf
PA2016 227 tf
PA2556 227 tf
PA2622 227 tf
PA3034 227 tf
PA3094 227 tf
PA3225 227 tf
PA3458 227 tf
PA3622 227 tf
PA3898 227 tf
PA3921 227 tf
PA4094 227 tf
PA4157 227 tf
PA4269 227 tf
PA4764 227 tf
PA4787 227 tf
PA4989 227 tf
PA5085 227 tf
PA5283 227 tf
PA5337 227 tf
PA5506 227 tf

Warning: PA2013 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
3282 3.50e+02 AaAACAA
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3283 1.20e+03 AAcGcTT
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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 PA2013

PA2013 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Enoyl-CoA hydratase/carnithine racemase cog/ cog
enoyl-CoA hydratase activity go/ molecular_function
metabolic process go/ biological_process
Valine leucine and isoleucine degradation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Module neighborhood information for PA2013

PA2013 has total of 17 gene neighbors in modules 227, 502
Gene neighbors (17)
Gene Common Name Description Module membership
PA0744 PA0744 probable enoyl-CoA hydratase/isomerase (NCBI) 227, 413
PA0745 PA0745 enoyl-CoA hydratase (NCBI) 227, 413
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
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
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 PA2013
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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