Organism : Pseudomonas aeruginosa | Module List :
PA3699

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (5)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3699
(Mouseover regulator name to see its description)

PA3699 is regulated by 51 influences and regulates 17 modules.
Regulators for PA3699 (51)
Regulator Module Operator
PA0056 7 tf
PA0125 7 tf
PA0167 7 tf
PA0253 7 tf
PA0393 7 tf
PA0527 7 tf
PA1015 7 tf
PA1099 7 tf
PA1269 7 tf
PA1335 7 tf
PA1754 7 tf
PA1760 7 tf
PA2047 7 tf
PA2376 7 tf
PA2591 7 tf
PA2849 7 tf
PA3341 7 tf
PA3699 7 tf
PA3714 7 tf
PA3778 7 tf
PA3864 7 tf
PA3895 7 tf
PA3921 7 tf
PA4147 7 tf
PA4157 7 tf
PA4182 7 tf
PA4288 7 tf
PA4462 7 tf
PA4493 7 tf
PA5116 7 tf
PA5253 7 tf
PA5437 7 tf
PA5483 7 tf
PA0167 123 tf
PA0393 123 tf
PA0477 123 tf
PA1128 123 tf
PA1300 123 tf
PA1422 123 tf
PA2093 123 tf
PA2885 123 tf
PA2896 123 tf
PA2957 123 tf
PA3215 123 tf
PA3604 123 tf
PA3699 123 tf
PA4451 123 tf
PA4703 123 tf
PA4745 123 tf
PA4755 123 tf
PA5344 123 tf

Warning: PA3699 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
2850 1.90e+03 GaTCtGCcGGCaGaT
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2851 6.00e+03 A.GCaaCaGtA
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3076 3.80e+02 cgG.a.a.aatgcgCGgg..TTt
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3077 2.60e+01 cggC.TGCaatGaAt
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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 PA3699

PA3699 is enriched for 5 functions in 3 categories.
Module neighborhood information for PA3699

PA3699 has total of 48 gene neighbors in modules 7, 123
Gene neighbors (48)
Gene Common Name Description Module membership
PA0023 qor quinone oxidoreductase (NCBI) 7, 462
PA0357 mutM formamidopyrimidine-DNA glycosylase (NCBI) 123, 170
PA0660 PA0660 hypothetical protein (NCBI) 7, 381
PA0750 ung uracil-DNA glycosylase (NCBI) 123, 384
PA0759 PA0759 hypothetical protein (NCBI) 123, 338
PA0946 PA0946 hypothetical protein (NCBI) 123, 220
PA1064 PA1064 hypothetical protein (NCBI) 123, 170
PA1534 recR recombination protein RecR (NCBI) 123, 478
PA1613 PA1613 hypothetical protein (NCBI) 123, 268
PA1806 fabI NADH-dependent enoyl-ACP reductase (NCBI) 7, 37
PA1810 PA1810 probable binding protein component of ABC transporter (NCBI) 7, 380
PA1828 PA1828 short chain dehydrogenase (NCBI) 7, 264
PA1829 PA1829 hypothetical protein (NCBI) 7, 264
PA2705 PA2705 hypothetical protein (NCBI) 7, 523
PA2765 PA2765 hypothetical protein (NCBI) 123, 306
PA2811 PA2811 probable permease of ABC-2 transporter (NCBI) 7, 37
PA2812 PA2812 probable ATP-binding component of ABC transporter (NCBI) 7, 37
PA3029 moaB2 molybdopterin biosynthetic protein B2 (NCBI) 7, 540
PA3043 PA3043 deoxyguanosinetriphosphate triphosphohydrolase (NCBI) 7, 462
PA3053 PA3053 probable hydrolytic enzyme (NCBI) 7, 378
PA3117 asd aspartate-semialdehyde dehydrogenase (NCBI) 123, 281
PA3213 PA3213 hypothetical protein (NCBI) 7, 81
PA3238 PA3238 hypothetical protein (NCBI) 7, 341
PA3239 PA3239 hypothetical protein (NCBI) 7, 341
PA3455 PA3455 hypothetical protein (NCBI) 7, 405
PA3471 PA3471 probable malic enzyme (NCBI) 7, 462
PA3686 adk adenylate kinase (NCBI) 123, 286
PA3695 PA3695 hypothetical protein (NCBI) 7, 380
PA3696 PA3696 hypothetical protein (NCBI) 7, 380
PA3697 PA3697 hypothetical protein (NCBI) 7, 87
PA3699 PA3699 probable transcriptional regulator (NCBI) 7, 123
PA3736 hom homoserine dehydrogenase (NCBI) 123, 260
PA3798 PA3798 putative aminotransferase (NCBI) 123, 170
PA3848 PA3848 hypothetical protein (NCBI) 7, 141
PA4042 xseB exodeoxyribonuclease VII small subunit (NCBI) 123, 178
PA4043 ispA geranyltranstransferase (NCBI) 123, 178
PA4340 PA4340 hypothetical protein (NCBI) 70, 123
PA4389 speA arginine decarboxylase (ADC) (NCBI) 123, 541
PA4434 PA4434 probable oxidoreductase (NCBI) 7, 264
PA4440 PA4440 hypothetical protein (NCBI) 123, 315
PA4632 PA4632 hypothetical protein (NCBI) 55, 123
PA4676 PA4676 probable carbonic anhydrase (NCBI) 123, 477
PA4867 ureB urease beta subunit (NCBI) 7, 380
PA4868 ureC urease alpha subunit (NCBI) 7, 380
PA5080 PA5080 prolyl aminopeptidase (NCBI) 123, 462
PA5237 PA5237 hypothetical protein (NCBI) 123, 281
PA5241 ppx exopolyphosphatase (NCBI) 123, 499
PA5344 PA5344 probable transcriptional regulator (NCBI) 123, 540
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 PA3699
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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