Organism : Pseudomonas aeruginosa | Module List :
PA1173 napB

cytochrome c-type protein NapB precursor (NCBI)

CircVis
Functional Annotations (3)
Function System
Nitrate reductase cytochrome c-type subunit cog/ cog
electron transport go/ biological_process
Nitrogen metabolism kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA1173
(Mouseover regulator name to see its description)

PA1173 is regulated by 47 influences and regulates 0 modules.
Regulators for PA1173 napB (47)
Regulator Module Operator
PA0179 415 tf
PA0491 415 tf
PA1351 415 tf
PA1760 415 tf
PA1898 415 tf
PA3225 415 tf
PA3266 415 tf
PA3285 415 tf
PA3363 415 tf
PA3604 415 tf
PA3815 415 tf
PA3921 415 tf
PA4451 415 tf
PA4581 415 tf
PA4703 415 tf
PA5059 415 tf
PA0179 548 tf
PA0225 548 tf
PA0456 548 tf
PA0527 548 tf
PA0708 548 tf
PA0906 548 tf
PA1223 548 tf
PA1269 548 tf
PA1760 548 tf
PA1945 548 tf
PA2047 548 tf
PA2115 548 tf
PA2622 548 tf
PA2848 548 tf
PA2885 548 tf
PA3225 548 tf
PA3266 548 tf
PA3285 548 tf
PA3363 548 tf
PA3423 548 tf
PA3622 548 tf
PA3921 548 tf
PA4354 548 tf
PA4451 548 tf
PA4581 548 tf
PA4703 548 tf
PA4787 548 tf
PA5059 548 tf
PA5085 548 tf
PA5261 548 tf
PA5550 548 tf

Warning: PA1173 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
3654 7.60e+01 CTAgTT.tAGtA
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3655 2.00e+03 TTtgCCGgCGA
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3908 2.50e+03 ACTG.A.c.AGC.aaGagcC.tC
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3909 2.80e+03 AaTaAcTGAAA
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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 PA1173

PA1173 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Nitrate reductase cytochrome c-type subunit cog/ cog
electron transport go/ biological_process
Nitrogen metabolism kegg/ kegg pathway
Module neighborhood information for PA1173

PA1173 has total of 15 gene neighbors in modules 415, 548
Gene neighbors (15)
Gene Common Name Description Module membership
PA0173 PA0173 probable methylesterase (NCBI) 345, 415
PA0174 PA0174 hypothetical protein (NCBI) 345, 415
PA0175 PA0175 probable chemotaxis protein methyltransferase (NCBI) 415, 548
PA0176 aer2 aerotaxis transducer Aer2 (NCBI) 415, 548
PA0177 PA0177 probable purine-binding chemotaxis protein (NCBI) 415, 548
PA0178 PA0178 probable two-component sensor (NCBI) 415, 548
PA0180 PA0180 probable chemotaxis transducer (NCBI) 128, 415
PA0586 PA0586 hypothetical protein (NCBI) 413, 548
PA0587 PA0587 hypothetical protein (NCBI) 413, 548
PA0588 PA0588 hypothetical protein (NCBI) 413, 548
PA1172 napC cytochrome c-type protein NapC (NCBI) 415, 548
PA1173 napB cytochrome c-type protein NapB precursor (NCBI) 415, 548
PA1174 napA periplasmic nitrate reductase protein NapA (NCBI) 415, 548
PA1175 napD NapD protein of periplasmic nitrate reductase (NCBI) 128, 415
PA1176 napF ferredoxin protein NapF (NCBI) 128, 415
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 PA1173
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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