Organism : Pseudomonas aeruginosa | Module List :
PA1684

probable oxidase (NCBI)

CircVis
Functional Annotations (5)
Function System
Uncharacterized conserved protein, contains double-stranded beta-helix domain cog/ cog
acireductone dioxygenase (Ni2+-requiring) activity go/ molecular_function
acireductone dioxygenase [iron(II)-requiring] activity go/ molecular_function
Cysteine and methionine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA1684
(Mouseover regulator name to see its description)

PA1684 is regulated by 46 influences and regulates 0 modules.
Regulators for PA1684 (46)
Regulator Module Operator
PA0125 378 tf
PA0163 378 tf
PA0167 378 tf
PA0289 378 tf
PA0763 378 tf
PA1335 378 tf
PA1619 378 tf
PA1754 378 tf
PA1760 378 tf
PA2047 378 tf
PA2312 378 tf
PA2737 378 tf
PA3034 378 tf
PA3045 378 tf
PA3622 378 tf
PA3804 378 tf
PA3895 378 tf
PA3921 378 tf
PA3995 378 tf
PA4269 378 tf
PA4462 378 tf
PA4581 378 tf
PA5166 378 tf
PA5253 378 tf
PA5483 378 tf
PA0121 214 tf
PA0393 214 tf
PA0455 214 tf
PA0487 214 tf
PA0890 214 tf
PA1898 214 tf
PA2054 214 tf
PA2879 214 tf
PA2957 214 tf
PA3002 214 tf
PA3285 214 tf
PA3604 214 tf
PA3804 214 tf
PA4238 214 tf
PA4451 214 tf
PA4600 214 tf
PA4806 214 tf
PA5239 214 tf
PA5483 214 tf
PA5550 214 tf
PA5562 214 tf

Warning: PA1684 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
3256 3.40e+00 ctT.ccccac.tCcT
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3257 2.10e+03 gTaGaATg.ccggCa
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3580 5.50e+02 caGtcTtTTtC
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3581 3.80e+03 AAg.cgCTATCAt
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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 PA1684

PA1684 is enriched for 5 functions in 3 categories.
Module neighborhood information for PA1684

PA1684 has total of 36 gene neighbors in modules 214, 378
Gene neighbors (36)
Gene Common Name Description Module membership
PA0467 PA0467 hypothetical protein (NCBI) 127, 378
PA0948 PA0948 hypothetical protein (NCBI) 214, 229
PA0949 wrbA Trp repressor binding protein WrbA (NCBI) 77, 214
PA0950 PA0950 probable arsenate reductase (NCBI) 77, 214
PA0956 proS prolyl-tRNA synthetase (NCBI) 214, 433
PA1040 PA1040 hypothetical protein (NCBI) 338, 378
PA1307 PA1307 hypothetical protein (NCBI) 378, 513
PA1543 apt adenine phosphoribosyltransferase (NCBI) 86, 214
PA1681 aroC chorismate synthase (NCBI) 214, 395
PA1682 PA1682 probable MFS metabolite transporter (NCBI) 214, 253
PA1683 PA1683 hypothetical protein (NCBI) 214, 511
PA1684 PA1684 probable oxidase (NCBI) 214, 378
PA2530 PA2530 hypothetical protein (NCBI) 378, 540
PA2710 PA2710 hypothetical protein (NCBI) 203, 378
PA3052 PA3052 hypothetical protein (NCBI) 10, 378
PA3053 PA3053 probable hydrolytic enzyme (NCBI) 7, 378
PA3168 gyrA DNA gyrase subunit A (NCBI) 214, 395
PA3214 PA3214 hypothetical protein (NCBI) 81, 378
PA3856 PA3856 hypothetical protein (NCBI) 378, 443
PA3944 PA3944 hypothetical protein (NCBI) 378, 443
PA3970 amn AMP nucleosidase (NCBI) 378, 523
PA4027 PA4027 hypothetical protein (NCBI) 185, 378
PA4115 PA4115 hypothetical protein (NCBI) 378, 523
PA4367 PA4367 hypothetical protein (NCBI) 378, 464
PA4457 PA4457 hypothetical protein (NCBI) 131, 214
PA4727 pcnB poly(A) polymerase (NCBI) 214, 270
PA5064 PA5064 hypothetical protein (NCBI) 214, 433
PA5239 rho transcription termination factor Rho (NCBI) 131, 214
PA5322 algC phosphomannomutase AlgC (NCBI) 91, 214
PA5323 argB acetylglutamate kinase (NCBI) 91, 214
PA5487 PA5487 hypothetical protein (NCBI) 91, 378
PA5488 PA5488 hypothetical protein (NCBI) 378, 488
PA5521 PA5521 probable short-chain dehydrogenase (NCBI) 28, 378
PA5563 soj chromosome partitioning protein Soj (NCBI) 131, 214
PA5564 gidB glucose-inhibited division protein B (NCBI) 131, 214
PA5565 gidA glucose-inhibited division protein A (NCBI) 131, 214
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 PA1684
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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