Organism : Pseudomonas aeruginosa | Module List :
PA2320 gntR

transcriptional regulator GntR (NCBI)

CircVis
Functional Annotations (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2320
(Mouseover regulator name to see its description)

PA2320 is regulated by 38 influences and regulates 20 modules.
Regulators for PA2320 gntR (38)
Regulator Module Operator
PA1099 358 tf
PA1663 358 tf
PA1945 358 tf
PA2320 358 tf
PA2713 358 tf
PA3184 358 tf
PA3458 358 tf
PA3583 358 tf
PA4703 358 tf
PA4769 358 tf
PA5239 358 tf
PA5301 358 tf
PA5506 358 tf
PA0416 505 tf
PA0512 505 tf
PA0816 505 tf
PA1099 505 tf
PA1138 505 tf
PA1283 505 tf
PA1663 505 tf
PA1713 505 tf
PA1912 505 tf
PA1945 505 tf
PA2050 505 tf
PA2259 505 tf
PA2320 505 tf
PA2484 505 tf
PA2692 505 tf
PA2846 505 tf
PA2879 505 tf
PA3197 505 tf
PA3458 505 tf
PA3583 505 tf
PA4135 505 tf
PA4227 505 tf
PA4296 505 tf
PA4462 505 tf
PA5059 505 tf

Warning: PA2320 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
3540 1.10e-22 atT.ttct.attacaacaaat.ta
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3541 6.80e-05 ATTTtttCCAG..cGcaAaG.ta
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3824 3.50e-10 atttttT.tgtttagAAaatAat
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3825 8.70e-09 AcAACaAtAagaaaGaGacGaCc
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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 PA2320

PA2320 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for PA2320

PA2320 has total of 36 gene neighbors in modules 358, 505
Gene neighbors (36)
Gene Common Name Description Module membership
PA0035 trpA tryptophan synthase alpha chain (NCBI) 2, 505
PA0036 trpB tryptophan synthase subunit beta (NCBI) 2, 505
PA2264 PA2264 hypothetical protein (NCBI) 290, 505
PA2265 PA2265 gluconate dehydrogenase (NCBI) 290, 505
PA2266 PA2266 probable cytochrome c precursor (NCBI) 290, 505
PA2320 gntR transcriptional regulator GntR (NCBI) 358, 505
PA2321 PA2321 gluconokinase (NCBI) 358, 505
PA2322 PA2322 gluconate permease (NCBI) 358, 505
PA2323 PA2323 probable glyceraldehyde-3-phosphate dehydrogenase (NCBI) 191, 505
PA2481 PA2481 hypothetical protein (NCBI) 358, 505
PA2482 PA2482 probable cytochrome c (NCBI) 358, 505
PA2483 PA2483 hypothetical protein (NCBI) 257, 505
PA2637 nuoA NADH dehydrogenase alpha subunit (NCBI) 82, 358
PA3181 PA3181 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase (NCBI) 358, 505
PA3182 pgl 6-phosphogluconolactonase (NCBI) 358, 505
PA3183 zwf glucose-6-phosphate 1-dehydrogenase (NCBI) 358, 505
PA3184 PA3184 probable transcriptional regulator (NCBI) 358, 537
PA3192 gltR two-component response regulator GltR (NCBI) 478, 505
PA3193 glk glucokinase (NCBI) 358, 505
PA3194 edd phosphogluconate dehydratase (NCBI) 358, 505
PA3195 gapA glyceraldehyde 3-phosphate dehydrogenase (NCBI) 358, 505
PA3579 PA3579 probable carbohydrate kinase (NCBI) 358, 374
PA3580 PA3580 hypothetical protein (NCBI) 358, 374
PA3581 glpF glycerol uptake facilitator protein (NCBI) 358, 505
PA3582 glpK glycerol kinase (NCBI) 358, 505
PA3583 glpR glycerol-3-phosphate regulon repressor (NCBI) 100, 358
PA3584 glpD glycerol-3-phosphate dehydrogenase (NCBI) 358, 505
PA4810 fdnI nitrate-inducible formate dehydrogenase, gamma subunit (NCBI) 381, 505
PA4811 fdnH nitrate-inducible formate dehydrogenase, beta subunit (NCBI) 381, 505
PA4812 fdnG formate dehydrogenase-O (NCBI) 381, 505
PA5235 glpT glycerol-3-phosphate transporter (NCBI) 99, 358
PA5506 PA5506 hypothetical protein (NCBI) 138, 358
PA5507 PA5507 hypothetical protein (NCBI) 138, 358
PA5508 PA5508 probable glutamine synthetase (NCBI) 138, 358
PA5509 PA5509 hypothetical protein (NCBI) 138, 358
PA5510 PA5510 probable transporter (NCBI) 138, 358
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 PA2320
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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