Organism : Pseudomonas aeruginosa | Module List :
PA1562 acnA

aconitate hydratase 1 (NCBI)

CircVis
Functional Annotations (11)
Function System
Aconitase A cog/ cog
aconitate hydratase activity go/ molecular_function
metabolic process go/ biological_process
4 iron, 4 sulfur cluster binding go/ molecular_function
Citrate cycle (TCA cycle) kegg/ kegg pathway
Glyoxylate and dicarboxylate metabolism kegg/ kegg pathway
Carbon fixation pathways in prokaryotes kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
aconitase_1 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA1562
(Mouseover regulator name to see its description)

PA1562 is regulated by 42 influences and regulates 0 modules.
Regulators for PA1562 acnA (42)
Regulator Module Operator
PA0120 399 tf
PA0248 399 tf
PA0610 399 tf
PA0611 399 tf
PA0791 399 tf
PA0877 399 tf
PA0979 399 tf
PA1099 399 tf
PA1484 399 tf
PA1504 399 tf
PA1520 399 tf
PA1760 399 tf
PA1978 399 tf
PA2047 399 tf
PA2076 399 tf
PA2718 399 tf
PA2896 399 tf
PA2921 399 tf
PA3622 399 tf
PA3714 399 tf
PA4052 399 tf
PA4745 399 tf
PA4853 399 tf
PA4890 399 tf
PA5029 399 tf
PA5253 399 tf
PA5261 399 tf
PA5431 399 tf
PA5437 399 tf
PA5483 399 tf
PA0763 107 tf
PA1099 107 tf
PA2047 107 tf
PA3604 107 tf
PA3622 107 tf
PA4275 107 tf
PA4354 107 tf
PA4890 107 tf
PA5261 107 tf
PA5382 107 tf
PA5403 107 tf
PA5483 107 tf

Warning: PA1562 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
3046 1.30e+04 TTAGGTAA
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3047 8.50e+03 AAaCcActTC
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3622 4.00e+01 GG.atttCcctGCCgc.Cc.gAG
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3623 3.90e+02 aAac.cTcaTt.gGAa
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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 PA1562

PA1562 is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
Aconitase A cog/ cog
aconitate hydratase activity go/ molecular_function
metabolic process go/ biological_process
4 iron, 4 sulfur cluster binding go/ molecular_function
Citrate cycle (TCA cycle) kegg/ kegg pathway
Glyoxylate and dicarboxylate metabolism kegg/ kegg pathway
Carbon fixation pathways in prokaryotes kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
aconitase_1 tigr/ tigrfam
Module neighborhood information for PA1562

PA1562 has total of 33 gene neighbors in modules 107, 399
Gene neighbors (33)
Gene Common Name Description Module membership
PA0231 pcaD beta-ketoadipate enol-lactone hydrolase (NCBI) 87, 399
PA0232 pcaC gamma-carboxymuconolactone decarboxylase (NCBI) 215, 399
PA0558 PA0558 hypothetical protein (NCBI) 361, 399
PA0567 PA0567 hypothetical protein (NCBI) 107, 441
PA0853 PA0853 probable oxidoreductase (NCBI) 107, 154
PA0854 fumC2 fumarate hydratase (NCBI) 107, 154
PA1115 PA1115 hypothetical protein (NCBI) 10, 399
PA1323 PA1323 hypothetical protein (NCBI) 107, 154
PA1408 PA1408 hypothetical protein (NCBI) 28, 107
PA1562 acnA aconitate hydratase 1 (NCBI) 107, 399
PA1605 PA1605 hypothetical protein (NCBI) 85, 107
PA1944 PA1944 hypothetical protein (NCBI) 107, 441
PA1985 pqqA coenzyme PQQ synthesis protein PqqA (NCBI) 233, 399
PA1986 pqqB pyrroloquinoline quinone biosynthesis protein PqqB (NCBI) 233, 399
PA1987 pqqC pyrroloquinoline quinone biosynthesis protein PqqC (NCBI) 233, 399
PA1988 pqqD pyrroloquinoline quinone biosynthesis protein PqqD (NCBI) 233, 399
PA1989 pqqE pyrroloquinoline quinone biosynthesis protein PqqE (NCBI) 233, 399
PA1990 PA1990 probable peptidase (NCBI) 382, 399
PA3459 PA3459 probable glutamine amidotransferase (NCBI) 107, 328
PA3460 PA3460 probable acetyltransferase (NCBI) 107, 328
PA3461 PA3461 hypothetical protein (NCBI) 107, 328
PA3795 PA3795 probable oxidoreductase (NCBI) 107, 361
PA3888 PA3888 probable permease of ABC transporter (NCBI) 28, 399
PA3889 PA3889 probable binding protein component of ABC transporter (NCBI) 28, 399
PA3890 PA3890 probable permease of ABC transporter (NCBI) 28, 399
PA3891 PA3891 probable ATP-binding component of ABC transporter (NCBI) 28, 399
PA4017 PA4017 hypothetical protein (NCBI) 2, 399
PA4204 PA4204 hypothetical protein (NCBI) 107, 361
PA4880 PA4880 probable bacterioferritin (NCBI) 107, 154
PA5376 PA5376 probable ATP-binding component of ABC transporter (NCBI) 87, 399
PA5377 PA5377 probable permease of ABC transporter (NCBI) 87, 399
PA5483 algB two-component response regulator AlgB (NCBI) 107, 221
PA5484 PA5484 probable two-component sensor (NCBI) 107, 221
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 PA1562
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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