Organism : Pseudomonas aeruginosa | Module List :
PA1781 nirB

assimilatory nitrite reductase large subunit (NCBI)

CircVis
Functional Annotations (11)
Function System
NAD(P)H-nitrite reductase cog/ cog
electron transport go/ biological_process
nitrite reductase [NAD(P)H] activity go/ molecular_function
heme binding go/ molecular_function
nitrate assimilation go/ biological_process
flavin adenine dinucleotide binding go/ molecular_function
NADP binding go/ molecular_function
iron-sulfur cluster binding go/ molecular_function
Nitrogen metabolism kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
nitri_red_nirB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA1781
(Mouseover regulator name to see its description)

PA1781 is regulated by 33 influences and regulates 0 modules.
Regulators for PA1781 nirB (33)
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
PA0133 532 tf
PA0675 532 tf
PA0701 532 tf
PA0893 532 tf
PA1067 532 tf
PA1399 532 tf
PA2376 532 tf
PA2547 532 tf
PA3045 532 tf
PA3133 532 tf
PA3381 532 tf
PA3420 532 tf
PA3594 532 tf
PA3714 532 tf
PA4341 532 tf
PA5032 532 tf
PA5293 532 tf
PA5562 532 tf

Warning: PA1781 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
3596 7.50e-01 AAAgGCG
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3597 7.60e+01 ACCTTGAAGTCGACTTcAATCTTA
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3876 2.50e-11 aaTtattGtatAcaAAaaagaa
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3877 2.80e-01 AAAactaaAACAAAa
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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 PA1781

PA1781 is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
NAD(P)H-nitrite reductase cog/ cog
electron transport go/ biological_process
nitrite reductase [NAD(P)H] activity go/ molecular_function
heme binding go/ molecular_function
nitrate assimilation go/ biological_process
flavin adenine dinucleotide binding go/ molecular_function
NADP binding go/ molecular_function
iron-sulfur cluster binding go/ molecular_function
Nitrogen metabolism kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
nitri_red_nirB tigr/ tigrfam
Module neighborhood information for PA1781

PA1781 has total of 34 gene neighbors in modules 386, 532
Gene neighbors (34)
Gene Common Name Description Module membership
PA0220 PA0220 probable amino acid permease (NCBI) 425, 532
PA0325 PA0325 probable permease of ABC transporter (NCBI) 267, 532
PA0326 PA0326 probable ATP-binding component of ABC transporter (NCBI) 267, 532
PA0443 PA0443 probable transporter (NCBI) 481, 532
PA0476 PA0476 probable permease (NCBI) 235, 532
PA0690 PA0690 hypothetical protein (NCBI) 400, 532
PA0700 PA0700 hypothetical protein (NCBI) 373, 532
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
PA1498 pykF pyruvate kinase (NCBI) 180, 532
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
PA1953 PA1953 hypothetical protein (NCBI) 12, 386
PA1954 PA1954 hypothetical protein (NCBI) 105, 532
PA1956 PA1956 hypothetical protein (NCBI) 158, 532
PA2716 PA2716 probable FMN oxidoreductase (NCBI) 334, 386
PA2719 PA2719 hypothetical protein (NCBI) 190, 386
PA3218 PA3218 hypothetical protein (NCBI) 158, 532
PA3258 PA3258 hypothetical protein (NCBI) 532, 545
PA3389 PA3389 probable ring-cleaving dioxygenase (NCBI) 44, 532
PA3390 PA3390 hypothetical protein (NCBI) 44, 532
PA3773 PA3773 hypothetical protein (NCBI) 386, 486
PA3994 PA3994 probable epoxide hydrolase (NCBI) 330, 532
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
PA4901 mdlC benzoylformate decarboxylase (NCBI) 532, 538
PA4994 PA4994 probable acyl-CoA dehydrogenase (NCBI) 471, 532
PA5328 PA5328 probable cytochrome c(mono-heme type) (NCBI) 532, 545
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 PA1781
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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