Organism : Pseudomonas aeruginosa | Module List :
PA3568

probable acetyl-coa synthetase (NCBI)

CircVis
Functional Annotations (5)
Function System
Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases cog/ cog
catalytic activity go/ molecular_function
metabolic process go/ biological_process
Propanoate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3568
(Mouseover regulator name to see its description)

PA3568 is regulated by 46 influences and regulates 0 modules.
Regulators for PA3568 (46)
Regulator Module Operator
PA0248 515 tf
PA1128 515 tf
PA1430 515 tf
PA1663 515 tf
PA1759 515 tf
PA1760 515 tf
PA1978 515 tf
PA1980 515 tf
PA2320 515 tf
PA2511 515 tf
PA2704 515 tf
PA2737 515 tf
PA3266 515 tf
PA3622 515 tf
PA3630 515 tf
PA3921 515 tf
PA4147 515 tf
PA4436 515 tf
PA4659 515 tf
PA4703 515 tf
PA4769 515 tf
PA4787 515 tf
PA4906 515 tf
PA4989 515 tf
PA5189 515 tf
PA5239 515 tf
PA5337 515 tf
PA5342 515 tf
PA5374 515 tf
PA5380 515 tf
PA5389 515 tf
PA1363 294 tf
PA1484 294 tf
PA1760 294 tf
PA2123 294 tf
PA3363 294 tf
PA3364 294 tf
PA3921 294 tf
PA3948 294 tf
PA4147 294 tf
PA4703 294 tf
PA4745 294 tf
PA5380 294 tf
PA5389 294 tf
PA5511 294 tf
PA5550 294 tf

Warning: PA3568 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
3416 5.00e-04 aAtAACAAtaA
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3417 2.40e+00 GGccAATCAccCTttggggTtacG
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3844 3.60e-01 AcAACaAtAA
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3845 1.10e+02 CagGAgaAacA
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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 PA3568

PA3568 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases cog/ cog
catalytic activity go/ molecular_function
metabolic process go/ biological_process
Propanoate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Module neighborhood information for PA3568

PA3568 has total of 38 gene neighbors in modules 294, 515
Gene neighbors (38)
Gene Common Name Description Module membership
PA0105 coxB cytochrome c oxidase, subunit II (NCBI) 305, 515
PA0106 coxA cytochrome c oxidase, subunit I (NCBI) 305, 515
PA0107 PA0107 cytochrome C oxidase assembly protein (NCBI) 305, 515
PA0108 coIII cytochrome c oxidase, subunit III (NCBI) 305, 515
PA0110 PA0110 hypothetical protein (NCBI) 305, 515
PA0111 PA0111 hypothetical protein (NCBI) 305, 515
PA0112 PA0112 hypothetical protein (NCBI) 305, 515
PA0113 PA0113 probable cytochrome c oxidase assembly factor (NCBI) 305, 515
PA1484 PA1484 probable transcriptional regulator (NCBI) 294, 295
PA1485 PA1485 probable amino acid permease (NCBI) 294, 394
PA1486 PA1486 hypothetical protein (NCBI) 294, 394
PA1617 PA1617 probable AMP-binding enzyme (NCBI) 294, 397
PA1621 PA1621 probable hydrolase (NCBI) 294, 546
PA1650 PA1650 probable transporter (NCBI) 163, 294
PA1736 PA1736 acetyl-CoA acetyltransferase (NCBI) 294, 483
PA1737 PA1737 probable 3-hydroxyacyl-CoA dehydrogenase (NCBI) 185, 294
PA1761 PA1761 hypothetical protein (NCBI) 252, 515
PA1997 PA1997 probable AMP-binding enzyme (NCBI) 294, 469
PA2122 PA2122 hypothetical protein (NCBI) 252, 294
PA2504 PA2504 hypothetical protein (NCBI) 133, 294
PA2711 PA2711 probable periplasmic spermidine/putrescine-binding protein (NCBI) 74, 294
PA2862 lipA lactonizing lipase precursor (NCBI) 491, 515
PA2889 PA2889 probable acyl-CoA dehydrogenase (NCBI) 294, 330
PA3216 PA3216 hypothetical protein (NCBI) 136, 294
PA3363 amiR aliphatic amidase regulator (NCBI) 34, 294
PA3364 amiC aliphatic amidase expression-regulating protein (NCBI) 34, 294
PA3366 amiE aliphatic amidase (NCBI) 34, 294
PA3568 PA3568 probable acetyl-coa synthetase (NCBI) 294, 515
PA3569 mmsB 3-hydroxyisobutyrate dehydrogenase (NCBI) 145, 515
PA3570 mmsA methylmalonate-semialdehyde dehydrogenase (NCBI) 145, 515
PA3922 PA3922 hypothetical protein (NCBI) 252, 515
PA3923 PA3923 hypothetical protein (NCBI) 252, 515
PA3924 PA3924 acyl-CoA synthase (NCBI) 252, 294
PA4913 PA4913 probable binding protein component of ABC transporter (NCBI) 133, 515
PA5213 gcvP1 glycine cleavage system protein P1 (NCBI) 294, 367
PA5389 PA5389 probable transcriptional regulator (NCBI) 136, 294
PA5543 PA5543 hypothetical protein (NCBI) 491, 515
PA5545 PA5545 hypothetical protein (NCBI) 491, 515
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 PA3568
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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