Organism : Pseudomonas aeruginosa | Module List :
PA2076

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2076
(Mouseover regulator name to see its description)

PA2076 is regulated by 32 influences and regulates 23 modules.
Regulators for PA2076 (32)
Regulator Module Operator
PA0116 170 tf
PA0564 170 tf
PA0961 170 tf
PA1201 170 tf
PA1422 170 tf
PA1898 170 tf
PA2076 170 tf
PA2622 170 tf
PA2896 170 tf
PA2957 170 tf
PA3027 170 tf
PA3220 170 tf
PA3604 170 tf
PA3948 170 tf
PA4451 170 tf
PA4600 170 tf
PA5029 170 tf
PA5274 170 tf
PA5342 170 tf
PA5550 170 tf
PA1335 371 tf
PA1544 371 tf
PA2076 371 tf
PA2123 371 tf
PA2591 371 tf
PA4451 371 tf
PA4745 371 tf
PA4853 371 tf
PA5293 371 tf
PA5308 371 tf
PA5337 371 tf
PA5365 371 tf

Warning: PA2076 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
3168 1.00e+05 TGaCAcTACaaAGGcaAAATA
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3169 1.10e+01 TtTtCCGAtcTT
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3566 7.40e-03 atggcAttct.c.gttaTTct
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3567 8.30e-02 CacTacAgAacTGaTaGtaGAcgG
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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 PA2076

PA2076 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for PA2076

PA2076 has total of 54 gene neighbors in modules 170, 371
Gene neighbors (54)
Gene Common Name Description Module membership
PA0063 PA0063 hypothetical protein (NCBI) 58, 170
PA0115 PA0115 hypothetical protein (NCBI) 170, 178
PA0255 PA0255 hypothetical protein (NCBI) 170, 245
PA0267 PA0267 hypothetical protein (NCBI) 170, 517
PA0356 PA0356 hypothetical protein (NCBI) 170, 374
PA0357 mutM formamidopyrimidine-DNA glycosylase (NCBI) 123, 170
PA0360 PA0360 hypothetical protein (NCBI) 170, 245
PA0385 PA0385 hypothetical protein (NCBI) 170, 181
PA0418 PA0418 hypothetical protein (NCBI) 170, 374
PA0541 PA0541 hypothetical protein (NCBI) 170, 528
PA0730 PA0730 probable transferase (NCBI) 212, 371
PA0855 PA0855 hypothetical protein (NCBI) 265, 371
PA0857 bolA morphogene protein BolA (NCBI) 6, 371
PA0902 PA0902 hypothetical protein (NCBI) 170, 384
PA0938 PA0938 hypothetical protein (NCBI) 363, 371
PA1034 PA1034 hypothetical protein (NCBI) 271, 371
PA1064 PA1064 hypothetical protein (NCBI) 123, 170
PA1069 PA1069 hypothetical protein (NCBI) 170, 487
PA1913 PA1913 hypothetical protein (NCBI) 86, 170
PA2076 PA2076 probable transcriptional regulator (NCBI) 170, 371
PA2081 kynB kynurenine formamidase KynB (NCBI) 371, 541
PA2954 PA2954 hypothetical protein (NCBI) 20, 371
PA2955 PA2955 hypothetical protein (NCBI) 103, 371
PA3027 PA3027 probable transcriptional regulator (NCBI) 170, 489
PA3220 PA3220 probable transcriptional regulator (NCBI) 20, 170
PA3264 PA3264 probable transporter (NCBI) 114, 170
PA3397 fpr ferredoxin--NADP+ reductase (NCBI) 371, 490
PA3466 PA3466 probable ATP-dependent RNA helicase (NCBI) 58, 170
PA3475 pheC cyclohexadienyl dehydratase precursor (NCBI) 170, 338
PA3603 dgkA diacylglycerol kinase (NCBI) 126, 170
PA3722 PA3722 hypothetical protein (NCBI) 371, 496
PA3798 PA3798 putative aminotransferase (NCBI) 123, 170
PA4010 PA4010 3-methyladenine DNA glycosylase (NCBI) 170, 315
PA4029 PA4029 hypothetical protein (NCBI) 170, 249
PA4030 PA4030 hypothetical protein (NCBI) 170, 249
PA4058 PA4058 hypothetical protein (NCBI) 228, 371
PA4059 PA4059 hypothetical protein (NCBI) 228, 371
PA4139 PA4139 hypothetical protein (NCBI) 9, 371
PA4307 pctC chemotactic transducer PctC (NCBI) 170, 315
PA4446 algW AlgW protein (NCBI) 232, 371
PA4626 hprA glycerate dehydrogenase (NCBI) 170, 187
PA4643 PA4643 hypothetical protein (NCBI) 170, 499
PA4683 PA4683 hypothetical protein (NCBI) 321, 371
PA5062 PA5062 hypothetical protein (NCBI) 41, 170
PA5225 PA5225 hypothetical protein (NCBI) 170, 306
PA5295 PA5295 hypothetical protein (NCBI) 170, 374
PA5342 PA5342 probable transcriptional regulator (NCBI) 170, 253
PA5343 PA5343 hypothetical protein (NCBI) 170, 253
PA5360 phoB two-component response regulator PhoB (NCBI) 371, 477
PA5361 phoR two-component sensor PhoR (NCBI) 371, 477
PA5365 phoU phosphate uptake regulatory protein PhoU (NCBI) 48, 371
PA5366 pstB ATP-binding component of ABC phosphate transporter (NCBI) 48, 371
PA5367 pstA membrane protein component of ABC phosphate transporter (NCBI) 48, 371
PA5369 PA5369 hypothetical protein (NCBI) 48, 371
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 PA2076
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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