Organism : Pseudomonas aeruginosa | Module List :
PA5125 ntrC

two-component response regulator NtrC (NCBI)

CircVis
Functional Annotations (13)
Function System
Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
nitrogen fixation go/ biological_process
nucleoside-triphosphatase activity go/ molecular_function
detection of stimulus involved in sensory perception go/ biological_process
Two-component system kegg/ kegg pathway
ntrC tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA5125
(Mouseover regulator name to see its description)

PA5125 is regulated by 38 influences and regulates 26 modules.
Regulators for PA5125 ntrC (38)
Regulator Module Operator
PA0279 464 tf
PA0393 464 tf
PA0436 464 tf
PA0707 464 tf
PA0893 464 tf
PA0905 464 tf
PA1484 464 tf
PA1754 464 tf
PA2586 464 tf
PA3002 464 tf
PA3563 464 tf
PA3721 464 tf
PA3879 464 tf
PA4270 464 tf
PA4547 464 tf
PA5125 464 tf
PA5166 464 tf
PA5324 464 tf
PA0191 203 tf
PA0289 203 tf
PA0393 203 tf
PA0784 203 tf
PA0831 203 tf
PA1050 203 tf
PA1138 203 tf
PA1754 203 tf
PA1760 203 tf
PA2047 203 tf
PA2718 203 tf
PA2921 203 tf
PA3124 203 tf
PA3321 203 tf
PA3410 203 tf
PA3458 203 tf
PA3622 203 tf
PA4547 203 tf
PA5125 203 tf
PA5261 203 tf
Regulated by PA5125 (26)
Module Residual Genes
13 0.42 12
29 0.34 10
47 0.47 14
91 0.52 20
116 0.27 15
120 0.48 21
129 0.47 21
155 0.32 9
167 0.45 13
179 0.47 15
193 0.49 22
202 0.56 21
203 0.58 24
217 0.32 11
242 0.44 16
275 0.37 15
364 0.48 23
390 0.51 20
417 0.27 12
419 0.32 11
452 0.59 23
464 0.52 17
484 0.27 12
490 0.52 19
506 0.32 9
539 0.28 12
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
3234 1.40e+00 agAAgAaccGc
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3235 1.50e+03 AaAccatg.a.A.Gga.aTct
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3744 2.00e+01 TtTtcgTt..aA
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3745 1.20e+02 TaGGtA.AgCT
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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 PA5125

PA5125 is enriched for 13 functions in 3 categories.
Enrichment Table (13)
Function System
Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
nitrogen fixation go/ biological_process
nucleoside-triphosphatase activity go/ molecular_function
detection of stimulus involved in sensory perception go/ biological_process
Two-component system kegg/ kegg pathway
ntrC tigr/ tigrfam
Module neighborhood information for PA5125

PA5125 has total of 40 gene neighbors in modules 203, 464
Gene neighbors (40)
Gene Common Name Description Module membership
PA0286 PA0286 probable fatty acid desaturase (NCBI) 203, 368
PA0387 PA0387 putative deoxyribonucleotide triphosphate pyrophosphatase (NCBI) 129, 464
PA0388 PA0388 hypothetical protein (NCBI) 129, 464
PA0589 glpE thiosulfate sulfurtransferase (NCBI) 202, 464
PA0590 apaH diadenosinetetraphosphatase (NCBI) 18, 464
PA0591 PA0591 hypothetical protein (NCBI) 202, 464
PA1061 PA1061 hypothetical protein (NCBI) 203, 511
PA1062 PA1062 hypothetical protein (NCBI) 203, 511
PA1063 PA1063 hypothetical protein (NCBI) 203, 443
PA1191 PA1191 hypothetical protein (NCBI) 153, 203
PA1754 cysB transcriptional regulator CysB (NCBI) 203, 488
PA1802 clpX ATP-dependent protease ATP-binding subunit (NCBI) 57, 464
PA1803 lon Lon protease (NCBI) 393, 464
PA2080 kynU kynureninase (NCBI) 179, 464
PA2631 PA2631 probable acetyl transferase (NCBI) 129, 464
PA2632 PA2632 hypothetical protein (NCBI) 390, 464
PA2633 PA2633 hypothetical protein (NCBI) 390, 464
PA2710 PA2710 hypothetical protein (NCBI) 203, 378
PA2723 PA2723 hypothetical protein (NCBI) 203, 469
PA3198 PA3198 hypothetical protein (NCBI) 203, 390
PA3343 PA3343 hypothetical protein (NCBI) 203, 443
PA3786 PA3786 hypothetical protein (NCBI) 10, 203
PA3851 PA3851 hypothetical protein (NCBI) 163, 203
PA3852 PA3852 hypothetical protein (NCBI) 163, 203
PA3882 PA3882 hypothetical protein (NCBI) 203, 381
PA4200 PA4200 hypothetical protein (NCBI) 3, 203
PA4236 katA catalase (NCBI) 203, 488
PA4367 PA4367 hypothetical protein (NCBI) 378, 464
PA4735 PA4735 hypothetical protein (NCBI) 57, 203
PA4736 PA4736 hypothetical protein (NCBI) 57, 203
PA4737 PA4737 hypothetical protein (NCBI) 57, 203
PA4947 amiB N-acetylmuramoyl-L-alanine amidase (NCBI) 81, 464
PA5025 metY O-acetylhomoserine sulfhydrylase (NCBI) 203, 389
PA5124 ntrB two-component sensor NtrB (NCBI) 203, 499
PA5125 ntrC two-component response regulator NtrC (NCBI) 203, 464
PA5162 rmlD dTDP-4-dehydrorhamnose reductase (NCBI) 179, 464
PA5163 rmlA glucose-1-phosphate thymidylyltransferase (NCBI) 179, 464
PA5164 rmlC dTDP-4-dehydrorhamnose 3,5-epimerase (NCBI) 179, 464
PA5229 PA5229 hypothetical protein (NCBI) 3, 203
PA5271 PA5271 hypothetical protein (NCBI) 203, 405
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 PA5125
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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