Organism : Pseudomonas aeruginosa | Module List :
PA2998 nqrB

Na(+)-translocating NADH-quinone reductase subunit B (NCBI)

CircVis
Functional Annotations (8)
Function System
Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrB cog/ cog
electron transport go/ biological_process
transport go/ biological_process
Gram-negative-bacterium-type cell wall go/ cellular_component
FMN binding go/ molecular_function
integral to membrane go/ cellular_component
oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor go/ molecular_function
nqrB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2998
(Mouseover regulator name to see its description)

PA2998 is regulated by 32 influences and regulates 0 modules.
Regulators for PA2998 nqrB (32)
Regulator Module Operator
PA0455 395 tf
PA0611 395 tf
PA1826 395 tf
PA1853 395 tf
PA2047 395 tf
PA2957 395 tf
PA3002 395 tf
PA3604 395 tf
PA3948 395 tf
PA4052 395 tf
PA4057 395 tf
PA4238 395 tf
PA4269 395 tf
PA4451 395 tf
PA4703 395 tf
PA4745 395 tf
PA5337 395 tf
PA5562 395 tf
PA0763 43 tf
PA0893 43 tf
PA0961 43 tf
PA1335 43 tf
PA2383 43 tf
PA2766 43 tf
PA2859 43 tf
PA3002 43 tf
PA3804 43 tf
PA4269 43 tf
PA4270 43 tf
PA4275 43 tf
PA5356 43 tf
PA5562 43 tf

Warning: PA2998 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
2918 6.60e-01 aaagaa.GcccggcATTaTaaa
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2919 8.60e+02 AtgaTtgG.GAtttt
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3614 3.70e+02 TTTtCtG
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3615 3.00e+03 GGctcgtTaTaATC
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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 PA2998

PA2998 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrB cog/ cog
electron transport go/ biological_process
transport go/ biological_process
Gram-negative-bacterium-type cell wall go/ cellular_component
FMN binding go/ molecular_function
integral to membrane go/ cellular_component
oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor go/ molecular_function
nqrB tigr/ tigrfam
Module neighborhood information for PA2998

PA2998 has total of 28 gene neighbors in modules 43, 395
Gene neighbors (28)
Gene Common Name Description Module membership
PA1478 PA1478 hypothetical protein (NCBI) 43, 421
PA1482 ccmH cytochrome C-type biogenesis protein CcmH (NCBI) 43, 350
PA1483 cycH cytochrome c-type biogenesis protein (NCBI) 43, 421
PA1681 aroC chorismate synthase (NCBI) 214, 395
PA2626 trmU tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (NCBI) 77, 395
PA2627 PA2627 hypothetical protein (NCBI) 198, 395
PA2744 thrS threonyl-tRNA synthetase (NCBI) 278, 395
PA2992 PA2992 hypothetical protein (NCBI) 43, 552
PA2994 nqrF Na(+)-translocating NADH-quinone reductase subunit F (NCBI) 43, 427
PA2998 nqrB Na(+)-translocating NADH-quinone reductase subunit B (NCBI) 43, 395
PA2999 nqrA Na(+)-translocating NADH-quinone reductase subunit A (NCBI) 77, 395
PA3002 mfd transcription-repair coupling protein Mfd (NCBI) 18, 43
PA3134 gltX glutamyl-tRNA synthetase (NCBI) 395, 451
PA3168 gyrA DNA gyrase subunit A (NCBI) 214, 395
PA3169 PA3169 translation initiation factor IF-2B subunit alpha (NCBI) 312, 395
PA3491 PA3491 electron transport complex protein RnfC (NCBI) 43, 421
PA3492 PA3492 hypothetical protein (NCBI) 43, 396
PA3495 nth endonuclease III (NCBI) 43, 421
PA3735 thrC threonine synthase (NCBI) 43, 350
PA3769 guaA bifunctional GMP synthase/glutamine amidotransferase protein (NCBI) 43, 204
PA3806 PA3806 hypothetical protein (NCBI) 308, 395
PA4044 dxs 1-deoxy-D-xylulose-5-phosphate synthase (NCBI) 395, 451
PA4053 ribH riboflavin synthase subunit beta (NCBI) 77, 395
PA4557 lytB 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (NCBI) 43, 350
PA4559 lspA signal peptidase II (NCBI) 43, 350
PA4560 ileS isoleucyl-tRNA synthetase (NCBI) 43, 106
PA5065 ubiB ubiquinone biosynthetic protein UbiB (NCBI) 43, 387
PA5074 PA5074 probable ATP-binding component of ABC transporter (NCBI) 43, 151
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 PA2998
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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