Organism : Pseudomonas aeruginosa | Module List :
PA2696

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (6)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA 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
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2696
(Mouseover regulator name to see its description)

PA2696 is regulated by 28 influences and regulates 21 modules.
Regulators for PA2696 (28)
Regulator Module Operator
PA0181 373 tf
PA0218 373 tf
PA1138 373 tf
PA1264 373 tf
PA2082 373 tf
PA2577 373 tf
PA2696 373 tf
PA2846 373 tf
PA3630 373 tf
PA3995 373 tf
PA4288 373 tf
PA0207 461 tf
PA0547 461 tf
PA0942 461 tf
PA1351 461 tf
PA1399 461 tf
PA1484 461 tf
PA1603 461 tf
PA1850 461 tf
PA1859 461 tf
PA2376 461 tf
PA2696 461 tf
PA2713 461 tf
PA3565 461 tf
PA3815 461 tf
PA4703 461 tf
PA4745 461 tf
PA5344 461 tf
Regulated by PA2696 (21)
Module Residual Genes
80 0.43 20
89 0.39 15
104 0.52 27
106 0.43 15
109 0.51 22
190 0.57 25
201 0.42 20
204 0.47 18
219 0.27 12
260 0.44 12
288 0.43 19
289 0.48 20
302 0.44 18
357 0.40 17
373 0.52 32
400 0.41 15
439 0.44 19
461 0.50 27
483 0.49 32
516 0.45 17
534 0.45 16
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
3570 9.00e-11 tttt.gaAtcAGtAttA.gaa.aa
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3571 1.70e-02 ga..agaacaacc.GAtTtC
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3738 1.00e+01 gc.atca..aAaaagaccgTCa
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3739 5.30e+02 ttCGcggC.gtgAT.ATcGAc
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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 PA2696

PA2696 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA 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
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for PA2696

PA2696 has total of 58 gene neighbors in modules 373, 461
Gene neighbors (58)
Gene Common Name Description Module membership
PA0029 PA0029 probable sulfate transporter (NCBI) 201, 461
PA0031 betC choline sulfatase (NCBI) 340, 461
PA0117 PA0117 probable short chain dehydrogenase (NCBI) 138, 373
PA0118 PA0118 hypothetical protein (NCBI) 138, 373
PA0181 PA0181 probable transcriptional regulator (NCBI) 196, 373
PA0249 PA0249 probable acetyltransferase (NCBI) 53, 461
PA0478 PA0478 probable N-acetyltransferase (NCBI) 373, 542
PA0507 PA0507 probable acyl-CoA dehydrogenase (NCBI) 74, 373
PA0508 PA0508 probable acyl-CoA dehydrogenase (NCBI) 20, 373
PA0700 PA0700 hypothetical protein (NCBI) 373, 532
PA0841 PA0841 hypothetical protein (NCBI) 246, 373
PA0894 PA0894 hypothetical protein (NCBI) 30, 461
PA1137 PA1137 probable oxidoreductase (NCBI) 333, 373
PA1138 PA1138 probable transcriptional regulator (NCBI) 192, 373
PA1188 PA1188 hypothetical protein (NCBI) 345, 461
PA1362 PA1362 hypothetical protein (NCBI) 373, 432
PA1448 fliR flagellar biosynthesis protein (NCBI) 296, 461
PA1449 flhB flagellar biosynthesis protein (NCBI) 461, 537
PA1500 PA1500 probable oxidoreductase (NCBI) 236, 373
PA1501 PA1501 hypothetical protein (NCBI) 236, 373
PA1502 gcl glyoxylate carboligase (NCBI) 373, 425
PA1649 PA1649 short chain dehydrogenase (NCBI) 84, 461
PA1747 PA1747 hypothetical protein (NCBI) 373, 432
PA1826 PA1826 probable transcriptional regulator (NCBI) 373, 463
PA1851 PA1851 hypothetical protein (NCBI) 79, 461
PA2010 PA2010 probable transcriptional regulator (NCBI) 373, 450
PA2048 PA2048 hypothetical protein (NCBI) 136, 461
PA2082 PA2082 probable transcriptional regulator (NCBI) 373, 541
PA2120 PA2120 hypothetical protein (NCBI) 292, 373
PA2128 cupA1 fimbrial subunit CupA1 (NCBI) 9, 461
PA2218 PA2218 hypothetical protein (NCBI) 373, 537
PA2282 PA2282 hypothetical protein (NCBI) 289, 461
PA2576 PA2576 hypothetical protein (NCBI) 359, 461
PA2578 PA2578 probable acetyltransferase (NCBI) 359, 461
PA2580 PA2580 hypothetical protein (NCBI) 53, 461
PA2665 PA2665 anaerobic nitric oxide reductase transcription regulator (NCBI) 58, 373
PA2696 PA2696 probable transcriptional regulator (NCBI) 373, 461
PA2722 PA2722 hypothetical protein (NCBI) 84, 461
PA2819 PA2819 hypothetical protein (NCBI) 401, 461
PA2846 PA2846 probable transcriptional regulator (NCBI) 373, 546
PA2869 PA2869 hypothetical protein (NCBI) 190, 461
PA2870 PA2870 hypothetical protein (NCBI) 190, 461
PA2930 PA2930 probable transcriptional regulator (NCBI) 143, 373
PA2958 PA2958 hypothetical protein (NCBI) 136, 461
PA3499 PA3499 hypothetical protein (NCBI) 373, 432
PA3565 PA3565 probable transcriptional regulator (NCBI) 190, 461
PA3630 PA3630 probable transcriptional regulator (NCBI) 340, 373
PA3760 PA3760 probable phosphotransferase protein (NCBI) 373, 523
PA4086 cupB1 probable fimbrial subunit CupB1 (NCBI) 20, 373
PA4288 PA4288 probable transcriptional regulator (NCBI) 192, 373
PA4353 PA4353 hypothetical protein (NCBI) 108, 461
PA4521 PA4521 hypothetical protein (NCBI) 53, 461
PA4522 ampD beta-lactamase expression regulator AmpD (NCBI) 283, 461
PA5190 PA5190 probable nitroreductase (NCBI) 131, 373
PA5310 PA5310 hypothetical protein (NCBI) 295, 461
PA5394 cls cardiolipin synthetase (NCBI) 373, 432
PA5409 PA5409 hypothetical protein (NCBI) 405, 461
PA5547 PA5547 hypothetical protein (NCBI) 335, 373
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 PA2696
Please add your comments for this gene by using the form below. Your comments will be publicly available.

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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