Organism : Pseudomonas aeruginosa | Module List :
PA4074

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (5)
Function System
DNA-binding HTH domain-containing proteins cog/ cog
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 PA4074
(Mouseover regulator name to see its description)

PA4074 is regulated by 28 influences and regulates 14 modules.
Regulators for PA4074 (28)
Regulator Module Operator
PA0032 171 tf
PA0701 171 tf
PA1399 171 tf
PA2093 171 tf
PA3381 171 tf
PA3596 171 tf
PA3776 171 tf
PA3830 171 tf
PA4238 171 tf
PA0207 445 tf
PA0393 445 tf
PA0491 445 tf
PA0701 445 tf
PA0828 445 tf
PA1067 445 tf
PA1347 445 tf
PA1980 445 tf
PA2050 445 tf
PA2227 445 tf
PA2547 445 tf
PA2704 445 tf
PA2737 445 tf
PA3045 445 tf
PA3133 445 tf
PA3381 445 tf
PA3420 445 tf
PA3594 445 tf
PA4806 445 tf

Warning: PA4074 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
3170 3.00e+03 cAgCGcCAgCG
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3171 7.50e+03 ATATTTTTaAT
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3710 4.00e+01 TATcgGTGaAtAATcTGA
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3711 3.70e+02 cTGGTtGAgcGCcTgGaacatCtC
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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 PA4074

PA4074 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
DNA-binding HTH domain-containing proteins cog/ cog
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 PA4074

PA4074 has total of 46 gene neighbors in modules 171, 445
Gene neighbors (46)
Gene Common Name Description Module membership
PA0145 PA0145 hypothetical protein (NCBI) 171, 333
PA0251 PA0251 hypothetical protein (NCBI) 324, 445
PA0327 PA0327 hypothetical protein (NCBI) 171, 189
PA0435 PA0435 hypothetical protein (NCBI) 156, 445
PA0442 PA0442 hypothetical protein (NCBI) 171, 340
PA0475 PA0475 probable transcriptional regulator (NCBI) 171, 443
PA0561 PA0561 hypothetical protein (NCBI) 157, 445
PA0957 PA0957 hypothetical protein (NCBI) 33, 171
PA0977 PA0977 hypothetical protein (NCBI) 324, 445
PA1133 PA1133 hypothetical protein (NCBI) 171, 241
PA1368 PA1368 hypothetical protein (NCBI) 320, 445
PA1909 PA1909 hypothetical protein (NCBI) 171, 486
PA1935 PA1935 hypothetical protein (NCBI) 324, 445
PA1936 PA1936 hypothetical protein (NCBI) 295, 445
PA2036 PA2036 hypothetical protein (NCBI) 231, 445
PA2546 PA2546 probable ring-cleaving dioxygenase (NCBI) 171, 526
PA2704 PA2704 probable transcriptional regulator (NCBI) 445, 497
PA2763 PA2763 hypothetical protein (NCBI) 335, 445
PA2772 PA2772 hypothetical protein (NCBI) 156, 171
PA2773 PA2773 hypothetical protein (NCBI) 229, 445
PA3051 PA3051 hypothetical protein (NCBI) 26, 171
PA3122 PA3122 probable transcriptional regulator (NCBI) 171, 477
PA3316 PA3316 probable permease of ABC transporter (NCBI) 171, 387
PA3358 PA3358 hypothetical protein (NCBI) 171, 241
PA3365 PA3365 probable chaperone (NCBI) 34, 171
PA3404 PA3404 probable outer membrane protein precursor (NCBI) 132, 171
PA3405 hasE metalloprotease secretion protein (NCBI) 132, 171
PA3462 PA3462 probable sensor/response regulator hybrid (NCBI) 171, 345
PA3501 PA3501 hypothetical protein (NCBI) 254, 445
PA3682 PA3682 hypothetical protein (NCBI) 171, 498
PA3868 PA3868 hypothetical protein (NCBI) 197, 445
PA3885 PA3885 hypothetical protein (NCBI) 197, 445
PA3933 PA3933 probable choline transporter (NCBI) 291, 445
PA3953 PA3953 hypothetical protein (NCBI) 171, 489
PA4074 PA4074 probable transcriptional regulator (NCBI) 171, 445
PA4091 hpaA 4-hydroxyphenylacetate 3-monooxygenase large chain (NCBI) 171, 483
PA4179 PA4179 probable porin (NCBI) 206, 445
PA4346 PA4346 hypothetical protein (NCBI) 171, 483
PA4802 PA4802 hypothetical protein (NCBI) 337, 445
PA4806 PA4806 probable transcriptional regulator (NCBI) 445, 546
PA5023 PA5023 hypothetical protein (NCBI) 31, 171
PA5026 PA5026 hypothetical protein (NCBI) 53, 171
PA5103 PA5103 hypothetical protein (NCBI) 171, 196
PA5309 PA5309 probable oxidoreductase (NCBI) 335, 445
PA5386 PA5386 3-hydroxybutyryl-CoA dehydrogenase (NCBI) 171, 534
PA5532 PA5532 hypothetical protein (NCBI) 23, 445
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 PA4074
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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