Organism : Pseudomonas aeruginosa | Module List :
PA2996 nqrD

Na+-translocating NADH:uniquinone oxidoreductase subunit Nqr4 (NCBI)

CircVis
Functional Annotations (6)
Function System
Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrD cog/ cog
electron transport go/ biological_process
Gram-negative-bacterium-type cell wall go/ cellular_component
membrane go/ cellular_component
oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor go/ molecular_function
nqrD tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2996
(Mouseover regulator name to see its description)

PA2996 is regulated by 27 influences and regulates 0 modules.
Regulators for PA2996 nqrD (27)
Regulator Module Operator
PA0393 403 tf
PA0762 403 tf
PA0890 403 tf
PA0893 403 tf
PA1328 403 tf
PA1484 403 tf
PA2489 403 tf
PA2758 403 tf
PA3002 403 tf
PA3804 403 tf
PA3948 403 tf
PA4269 403 tf
PA4270 403 tf
PA4878 403 tf
PA5562 403 tf
PA0890 427 tf
PA1484 427 tf
PA2897 427 tf
PA3002 427 tf
PA3804 427 tf
PA4269 427 tf
PA4270 427 tf
PA4703 427 tf
PA5239 427 tf
PA5356 427 tf
PA5550 427 tf
PA5562 427 tf

Warning: PA2996 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
3630 1.90e+03 TgTAtAAT
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3631 2.50e+03 GaTCA.TTcCG
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3674 5.80e-04 tTAc.aTgCgc.gcctTTt.t
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3675 1.00e+02 TcaGGaTaaaAcgT
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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 PA2996

PA2996 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrD cog/ cog
electron transport go/ biological_process
Gram-negative-bacterium-type cell wall go/ cellular_component
membrane go/ cellular_component
oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor go/ molecular_function
nqrD tigr/ tigrfam
Module neighborhood information for PA2996

PA2996 has total of 21 gene neighbors in modules 403, 427
Gene neighbors (21)
Gene Common Name Description Module membership
PA0955 PA0955 hypothetical protein (NCBI) 160, 427
PA1479 ccmE cytochrome C-type biogenesis protein CcmE (NCBI) 403, 421
PA1480 ccmF cytochrome C-type biogenesis protein CcmF (NCBI) 403, 421
PA1481 ccmG cytochrome C biogenesis protein CcmG (NCBI) 403, 421
PA2044 PA2044 hypothetical protein (NCBI) 82, 427
PA2993 PA2993 hypothetical protein (NCBI) 403, 427
PA2994 nqrF Na(+)-translocating NADH-quinone reductase subunit F (NCBI) 43, 427
PA2995 nqrE Na(+)-translocating NADH-quinone reductase subunit E (NCBI) 403, 427
PA2996 nqrD Na+-translocating NADH:uniquinone oxidoreductase subunit Nqr4 (NCBI) 403, 427
PA2997 nqrC Na(+)-translocating NADH-quinone reductase subunit C (NCBI) 403, 427
PA3164 PA3164 still frameshift 3-PHOSPHOSHIKIMATE 1-CARBOXYVINYLTRANSFERASE prephenate dehydrogenase (NCBI) 174, 427
PA3166 pheA chorismate mutase (NCBI) 18, 403
PA3167 serC phosphoserine aminotransferase (NCBI) 329, 403
PA3636 kdsA 2-dehydro-3-deoxyphosphooctonate aldolase (NCBI) 403, 427
PA4234 uvrA excinuclease ABC subunit A (NCBI) 131, 427
PA4428 sspA stringent starvation protein A (NCBI) 198, 427
PA4558 PA4558 probable peptidyl-prolyl cis-trans isomerase, FkbP-type (NCBI) 150, 403
PA4855 purD phosphoribosylamine--glycine ligase (NCBI) 90, 427
PA5008 PA5008 hypothetical protein (NCBI) 403, 421
PA5009 waaP lipopolysaccharide kinase WaaP (NCBI) 403, 426
PA5553 atpC ATP synthase subunit epsilon (NCBI) 155, 427
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 PA2996
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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