Organism : Pseudomonas aeruginosa | Module List :
PA3393 nosD

NosD protein (NCBI)

CircVis
Functional Annotations (5)
Function System
Nitrous oxidase accessory protein cog/ cog
copper ion binding go/ molecular_function
copper ion transport go/ biological_process
periplasmic space go/ cellular_component
para_beta_helix tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3393
(Mouseover regulator name to see its description)

PA3393 is regulated by 14 influences and regulates 0 modules.
Regulators for PA3393 nosD (14)
Regulator Module Operator
PA0512 458 tf
PA0513 458 tf
PA0514 458 tf
PA3391 458 tf
PA0564 497 tf
PA0701 497 tf
PA2050 497 tf
PA2704 497 tf
PA3133 497 tf
PA3391 497 tf
PA3420 497 tf
PA5032 497 tf
PA5293 497 tf
PA5431 497 tf

Warning: PA3393 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
3732 1.90e-06 aaTCTTGAtTcccaTCAAGCaaG
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3733 1.90e+00 CcccgCtTcCTAtgATC
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3808 1.60e-05 CCGG.AAaTgGtC.gCtaGattcT
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3809 6.40e-04 Attg..GgggAATtc
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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 PA3393

PA3393 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Nitrous oxidase accessory protein cog/ cog
copper ion binding go/ molecular_function
copper ion transport go/ biological_process
periplasmic space go/ cellular_component
para_beta_helix tigr/ tigrfam
Module neighborhood information for PA3393

PA3393 has total of 33 gene neighbors in modules 458, 497
Gene neighbors (33)
Gene Common Name Description Module membership
PA0136 PA0136 probable ATP-binding component of ABC transporter (NCBI) 481, 497
PA0138 PA0138 probable permease of ABC transporter (NCBI) 481, 497
PA0186 PA0186 probable binding protein component of ABC transporter (NCBI) 362, 497
PA0509 nirN probable c-type cytochrome (NCBI) 458, 529
PA0511 nirJ heme d1 biosynthesis protein NirJ (NCBI) 456, 458
PA0512 PA0512 hypothetical protein (NCBI) 458, 529
PA0520 nirQ regulatory protein NirQ (NCBI) 110, 458
PA0521 PA0521 probable cytochrome c oxidase subunit (NCBI) 110, 458
PA0523 norC nitric-oxide reductase subunit C (NCBI) 110, 458
PA0524 norB nitric-oxide reductase subunit B (NCBI) 110, 458
PA0525 PA0525 probable dinitrification protein NorD (NCBI) 110, 458
PA1567 PA1567 hypothetical protein (NCBI) 16, 497
PA1671 stk1 serine-threonine kinase Stk1 (NCBI) 33, 497
PA2596 PA2596 hypothetical protein (NCBI) 241, 497
PA2704 PA2704 probable transcriptional regulator (NCBI) 445, 497
PA2916 PA2916 hypothetical protein (NCBI) 333, 497
PA3125 PA3125 hypothetical protein (NCBI) 196, 497
PA3391 nosR regulatory protein NosR (NCBI) 110, 458
PA3392 nosZ nitrous-oxide reductase precurser (NCBI) 110, 458
PA3393 nosD NosD protein (NCBI) 458, 497
PA3394 nosF NosF protein (NCBI) 458, 497
PA3395 nosY NosY protein (NCBI) 36, 497
PA3396 nosL NosL protein (NCBI) 74, 497
PA4541 PA4541 hypothetical protein (NCBI) 97, 497
PA4586 PA4586 hypothetical protein (NCBI) 192, 497
PA4827 PA4827 arylamine N-acetyltransferase (NCBI) 292, 497
PA4828 PA4828 hypothetical protein (NCBI) 292, 497
PA4982 PA4982 probable two-component sensor (NCBI) 497, 507
PA5430 PA5430 hypothetical protein (NCBI) 268, 497
PA5431 PA5431 probable transcriptional regulator (NCBI) 497, 507
PA5432 PA5432 probable acetyltransferase (NCBI) 469, 497
PA5433 PA5433 hypothetical protein (NCBI) 246, 497
PA5480 PA5480 hypothetical protein (NCBI) 71, 497
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 PA3393
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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