Organism : Pseudomonas aeruginosa | Module List :
PA1779

assimilatory nitrate reductase (NCBI)

CircVis
Functional Annotations (7)
Function System
Anaerobic dehydrogenases, typically selenocysteine-containing cog/ cog
electron transport go/ biological_process
nitrate reductase activity go/ molecular_function
nitrate reductase complex go/ cellular_component
molybdenum ion binding go/ molecular_function
Nitrogen metabolism kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA1779
(Mouseover regulator name to see its description)

PA1779 is regulated by 37 influences and regulates 0 modules.
Regulators for PA1779 (37)
Regulator Module Operator
PA0564 386 tf
PA0701 386 tf
PA1145 386 tf
PA1351 386 tf
PA1980 386 tf
PA2376 386 tf
PA2547 386 tf
PA2586 386 tf
PA3045 386 tf
PA3133 386 tf
PA3381 386 tf
PA3420 386 tf
PA3711 386 tf
PA3771 386 tf
PA5032 386 tf
PA0159 344 tf
PA0163 344 tf
PA0191 344 tf
PA0652 344 tf
PA1380 344 tf
PA1836 344 tf
PA1853 344 tf
PA2047 344 tf
PA2050 344 tf
PA2276 344 tf
PA2316 344 tf
PA2492 344 tf
PA3045 344 tf
PA3266 344 tf
PA3711 344 tf
PA3815 344 tf
PA3830 344 tf
PA4354 344 tf
PA5166 344 tf
PA5253 344 tf
PA5437 344 tf
PA5562 344 tf

Warning: PA1779 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
3514 2.80e-03 cgCCGAttAtcGAcAtga
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3515 2.10e-01 GaA.TCcATCcgtCtTtTTCC
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3596 7.50e-01 AAAgGCG
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3597 7.60e+01 ACCTTGAAGTCGACTTcAATCTTA
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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 PA1779

PA1779 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Anaerobic dehydrogenases, typically selenocysteine-containing cog/ cog
electron transport go/ biological_process
nitrate reductase activity go/ molecular_function
nitrate reductase complex go/ cellular_component
molybdenum ion binding go/ molecular_function
Nitrogen metabolism kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
Module neighborhood information for PA1779

PA1779 has total of 35 gene neighbors in modules 344, 386
Gene neighbors (35)
Gene Common Name Description Module membership
PA0163 PA0163 probable transcriptional regulator (NCBI) 344, 438
PA0885 PA0885 probable C4-dicarboxylate transporter (NCBI) 386, 428
PA1238 PA1238 probable outer membrane component of multidrug efflux pump (NCBI) 177, 386
PA1351 PA1351 probable sigma-70 factor, ECF subfamily (NCBI) 292, 386
PA1360 PA1360 hypothetical protein (NCBI) 247, 344
PA1450 PA1450 hypothetical protein (NCBI) 266, 344
PA1540 PA1540 hypothetical protein (NCBI) 344, 412
PA1541 PA1541 probable drug efflux transporter (NCBI) 344, 412
PA1577 PA1577 hypothetical protein (NCBI) 236, 344
PA1778 cobA uroporphyrin-III C-methyltransferase (NCBI) 344, 386
PA1779 PA1779 assimilatory nitrate reductase (NCBI) 344, 386
PA1780 nirD assimilatory nitrite reductase small subunit (NCBI) 311, 386
PA1781 nirB assimilatory nitrite reductase large subunit (NCBI) 386, 532
PA1785 PA1785 hypothetical protein (NCBI) 311, 386
PA1790 PA1790 hypothetical protein (NCBI) 135, 344
PA1836 PA1836 probable transcriptional regulator (NCBI) 44, 344
PA1953 PA1953 hypothetical protein (NCBI) 12, 386
PA2243 pslM hypothetical protein (NCBI) 24, 344
PA2314 PA2314 probable major facilitator superfamily (MFS) transporter (NCBI) 304, 344
PA2315 PA2315 hypothetical protein (NCBI) 135, 344
PA2316 PA2316 probable transcriptional regulator (NCBI) 135, 344
PA2716 PA2716 probable FMN oxidoreductase (NCBI) 334, 386
PA2719 PA2719 hypothetical protein (NCBI) 190, 386
PA2847 PA2847 hypothetical protein (NCBI) 44, 344
PA2956 PA2956 hypothetical protein (NCBI) 344, 422
PA3663 PA3663 hypothetical protein (NCBI) 335, 344
PA3773 PA3773 hypothetical protein (NCBI) 386, 486
PA4612 PA4612 hypothetical protein (NCBI) 152, 344
PA4635 PA4635 hypothetical protein (NCBI) 344, 412
PA4861 PA4861 probable ATP-binding component of ABC transporter (NCBI) 177, 386
PA4862 PA4862 probable ATP-binding component of ABC transporter (NCBI) 386, 507
PA4882 PA4882 hypothetical protein (NCBI) 148, 386
PA4883 PA4883 hypothetical protein (NCBI) 148, 386
PA5468 PA5468 probable citrate transporter (NCBI) 344, 375
PA5469 PA5469 hypothetical protein (NCBI) 344, 375
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 PA1779
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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