Organism : Pseudomonas aeruginosa | Module List :
PA0797

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (6)
Function System
Transcriptional regulators cog/ cog
fatty-acyl-CoA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
regulation of fatty acid metabolic process go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0797
(Mouseover regulator name to see its description)

PA0797 is regulated by 34 influences and regulates 18 modules.
Regulators for PA0797 (34)
Regulator Module Operator
PA0179 205 tf
PA0797 205 tf
PA1351 205 tf
PA1430 205 tf
PA1455 205 tf
PA1754 205 tf
PA2586 205 tf
PA2896 205 tf
PA3622 205 tf
PA4296 205 tf
PA5105 205 tf
PA5261 205 tf
PA0125 264 tf
PA0797 264 tf
PA0942 264 tf
PA1015 264 tf
PA1285 264 tf
PA1760 264 tf
PA2591 264 tf
PA2737 264 tf
PA2849 264 tf
PA3002 264 tf
PA3622 264 tf
PA3921 264 tf
PA3965 264 tf
PA4094 264 tf
PA4269 264 tf
PA4270 264 tf
PA4462 264 tf
PA4755 264 tf
PA5253 264 tf
PA5403 264 tf
PA5437 264 tf
PA5550 264 tf

Warning: PA0797 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
3238 6.10e-05 tgttTtaaTtgaataTacaTaTac
Loader icon
3239 9.10e-01 aCtTcatcGACGcctcGAaAaGGA
Loader icon
3356 7.60e+00 AatacatTg.t.Aa
Loader icon
3357 6.70e+01 ACGcTT.tCGataA
Loader icon
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 PA0797

PA0797 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Transcriptional regulators cog/ cog
fatty-acyl-CoA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
regulation of fatty acid metabolic process go/ biological_process
Module neighborhood information for PA0797

PA0797 has total of 33 gene neighbors in modules 205, 264
Gene neighbors (33)
Gene Common Name Description Module membership
PA0337 ptsP phosphoenolpyruvate-protein phosphotransferase PtsP (NCBI) 191, 264
PA0482 glcB malate synthase (NCBI) 264, 342
PA0553 PA0553 hypothetical protein (NCBI) 91, 205
PA0565 PA0565 hypothetical protein (NCBI) 153, 205
PA0793 PA0793 hypothetical protein (NCBI) 145, 264
PA0794 PA0794 probable aconitate hydratase (NCBI) 145, 264
PA0795 prpC citrate synthase 2 (NCBI) 145, 264
PA0796 prpB carboxyphosphonoenolpyruvate phosphonomutase (NCBI) 145, 264
PA0797 PA0797 probable transcriptional regulator (NCBI) 205, 264
PA0838 PA0838 probable glutathione peroxidase (NCBI) 2, 205
PA0959 PA0959 hypothetical protein (NCBI) 205, 469
PA0960 PA0960 hypothetical protein (NCBI) 205, 469
PA1430 lasR transcriptional regulator LasR (NCBI) 166, 205
PA1828 PA1828 short chain dehydrogenase (NCBI) 7, 264
PA1829 PA1829 hypothetical protein (NCBI) 7, 264
PA1835 PA1835 hypothetical protein (NCBI) 224, 264
PA2025 gor glutathione reductase (NCBI) 10, 205
PA2634 PA2634 isocitrate lyase (NCBI) 264, 342
PA2656 PA2656 probable two-component sensor (NCBI) 205, 478
PA2657 PA2657 probable two-component response regulator (NCBI) 205, 478
PA2658 PA2658 hypothetical protein (NCBI) 205, 478
PA2659 PA2659 hypothetical protein (NCBI) 205, 478
PA2779 PA2779 hypothetical protein (NCBI) 128, 205
PA2827 PA2827 methionine sulfoxide reductase B (NCBI) 205, 376
PA2951 etfA electron transfer flavoprotein alpha-subunit (NCBI) 264, 342
PA3831 pepA leucyl aminopeptidase (NCBI) 264, 540
PA3833 PA3833 hypothetical protein (NCBI) 95, 264
PA4434 PA4434 probable oxidoreductase (NCBI) 7, 264
PA4523 PA4523 hypothetical protein (NCBI) 205, 452
PA4717 PA4717 hypothetical protein (NCBI) 205, 547
PA5104 PA5104 hypothetical protein (NCBI) 205, 328
PA5105 hutC histidine utilization repressor HutC (NCBI) 205, 328
PA5106 PA5106 atrazine chlorohydrolase (NCBI) 205, 328
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 PA0797
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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