Organism : Pseudomonas aeruginosa | Module List :
PA0883

probable acyl-CoA lyase beta chain (NCBI)

CircVis
Functional Annotations (7)
Function System
Citrate lyase beta subunit cog/ cog
cellular aromatic compound metabolic process go/ biological_process
citrate (pro-3S)-lyase activity go/ molecular_function
citrate lyase complex go/ cellular_component
Citrate cycle (TCA cycle) kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Two-component system kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0883
(Mouseover regulator name to see its description)

PA0883 is regulated by 36 influences and regulates 0 modules.
Regulators for PA0883 (36)
Regulator Module Operator
PA0056 428 tf
PA0564 428 tf
PA1067 428 tf
PA1109 428 tf
PA1223 428 tf
PA1347 428 tf
PA1980 428 tf
PA2547 428 tf
PA2704 428 tf
PA3045 428 tf
PA3133 428 tf
PA3249 428 tf
PA3381 428 tf
PA3420 428 tf
PA3771 428 tf
PA4057 428 tf
PA5032 428 tf
PA0032 526 tf
PA0491 526 tf
PA0512 526 tf
PA0564 526 tf
PA0748 526 tf
PA0877 526 tf
PA1067 526 tf
PA1223 526 tf
PA1980 526 tf
PA2547 526 tf
PA2785 526 tf
PA2838 526 tf
PA3420 526 tf
PA3630 526 tf
PA3711 526 tf
PA3771 526 tf
PA3776 526 tf
PA4989 526 tf
PA5293 526 tf

Warning: PA0883 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
3676 1.00e-02 AACAAcAAgaA
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3677 7.50e+02 TgGCGTTcccC
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3866 1.90e-07 aTagcG.AtaataAAatTatCaAA
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3867 4.90e-05 AttGgtTtCtGaaAAacaGaa
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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 PA0883

PA0883 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Citrate lyase beta subunit cog/ cog
cellular aromatic compound metabolic process go/ biological_process
citrate (pro-3S)-lyase activity go/ molecular_function
citrate lyase complex go/ cellular_component
Citrate cycle (TCA cycle) kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Two-component system kegg/ kegg pathway
Module neighborhood information for PA0883

PA0883 has total of 28 gene neighbors in modules 428, 526
Gene neighbors (28)
Gene Common Name Description Module membership
PA0135 PA0135 hypothetical protein (NCBI) 119, 428
PA0222 PA0222 hypothetical protein (NCBI) 310, 428
PA0278 PA0278 hypothetical protein (NCBI) 333, 526
PA0288 gpuA 3-guanidinopropionase (NCBI) 428, 481
PA0491 PA0491 probable transcriptional regulator (NCBI) 125, 526
PA0492 PA0492 hypothetical protein (NCBI) 125, 526
PA0493 PA0493 acetyl-CoA carboxylase (NCBI) 125, 526
PA0494 PA0494 acetyl-CoA carboxylase (NCBI) 125, 526
PA0495 PA0495 hypothetical protein (NCBI) 125, 526
PA0496 PA0496 hypothetical protein (NCBI) 125, 526
PA0877 PA0877 probable transcriptional regulator (NCBI) 243, 526
PA0878 PA0878 hypothetical protein (NCBI) 24, 526
PA0879 PA0879 probable acyl-CoA dehydrogenase (NCBI) 428, 526
PA0880 PA0880 probable ring-cleaving dioxygenase (NCBI) 428, 526
PA0881 PA0881 hypothetical protein (NCBI) 401, 526
PA0882 PA0882 hypothetical protein (NCBI) 428, 526
PA0883 PA0883 probable acyl-CoA lyase beta chain (NCBI) 428, 526
PA0884 PA0884 probable C4-dicarboxylate-binding periplasmic protein (NCBI) 428, 526
PA0885 PA0885 probable C4-dicarboxylate transporter (NCBI) 386, 428
PA0886 PA0886 probable C4-dicarboxylate transporter (NCBI) 340, 526
PA1980 PA1980 probable two-component response regulator (NCBI) 428, 434
PA2215 PA2215 hypothetical protein (NCBI) 285, 428
PA2221 PA2221 hypothetical protein (NCBI) 324, 526
PA2546 PA2546 probable ring-cleaving dioxygenase (NCBI) 171, 526
PA2807 PA2807 hypothetical protein (NCBI) 407, 428
PA3422 PA3422 hypothetical protein (NCBI) 310, 428
PA3597 PA3597 probable amino acid permease (NCBI) 334, 428
PA5325 PA5325 hypothetical protein (NCBI) 292, 428
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 PA0883
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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