Organism : Pseudomonas aeruginosa | Module List :
PA1005

hypothetical protein (NCBI)

CircVis
Functional Annotations (6)
Function System
Putative Zn-dependent protease, contains TPR repeats cog/ cog
metalloendopeptidase activity go/ molecular_function
binding go/ molecular_function
proteolysis go/ biological_process
zinc ion binding go/ molecular_function
membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA1005
(Mouseover regulator name to see its description)

PA1005 is regulated by 51 influences and regulates 0 modules.
Regulators for PA1005 (51)
Regulator Module Operator
PA0120 361 tf
PA0167 361 tf
PA0253 361 tf
PA0367 361 tf
PA0456 361 tf
PA0780 361 tf
PA1003 361 tf
PA1099 361 tf
PA1145 361 tf
PA2047 361 tf
PA2718 361 tf
PA2758 361 tf
PA3126 361 tf
PA3622 361 tf
PA3689 361 tf
PA3714 361 tf
PA3778 361 tf
PA3921 361 tf
PA4070 361 tf
PA4094 361 tf
PA4157 361 tf
PA4462 361 tf
PA5253 361 tf
PA5261 361 tf
PA5483 361 tf
PA5550 361 tf
PA0125 380 tf
PA0167 380 tf
PA0393 380 tf
PA0890 380 tf
PA0893 380 tf
PA1300 380 tf
PA1335 380 tf
PA1397 380 tf
PA1430 380 tf
PA1760 380 tf
PA1859 380 tf
PA1945 380 tf
PA1980 380 tf
PA2577 380 tf
PA2588 380 tf
PA2591 380 tf
PA2917 380 tf
PA3002 380 tf
PA3699 380 tf
PA3714 380 tf
PA3804 380 tf
PA4270 380 tf
PA4493 380 tf
PA5253 380 tf
PA5403 380 tf

Warning: PA1005 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
3546 1.10e-04 aC.atTa.tAGaTtgcTaT
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3547 4.70e+00 AGtgAaTCAaTATgcATAGG
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3584 1.70e-01 CgcTggaaatcTttgaccgaTccc
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3585 4.00e+03 tTtcggaAatgCgacaggAA
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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 PA1005

PA1005 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Putative Zn-dependent protease, contains TPR repeats cog/ cog
metalloendopeptidase activity go/ molecular_function
binding go/ molecular_function
proteolysis go/ biological_process
zinc ion binding go/ molecular_function
membrane go/ cellular_component
Module neighborhood information for PA1005

PA1005 has total of 51 gene neighbors in modules 361, 380
Gene neighbors (51)
Gene Common Name Description Module membership
PA0305 PA0305 hypothetical protein (NCBI) 375, 380
PA0364 PA0364 probable oxidoreductase (NCBI) 361, 441
PA0365 PA0365 hypothetical protein (NCBI) 361, 441
PA0366 PA0366 probable aldehyde dehydrogenase (NCBI) 361, 441
PA0558 PA0558 hypothetical protein (NCBI) 361, 399
PA0731 PA0731 hypothetical protein (NCBI) 166, 361
PA0895 aruC N-succinylglutamate 5-semialdehyde dehydrogenase (NCBI) 122, 380
PA0896 aruF arginine/ornithine succinyltransferase AI subunit (NCBI) 191, 380
PA0897 aruG arginine/ornithine succinyltransferase AII subunit (NCBI) 191, 380
PA0898 aruD succinylglutamate 5-semialdehyde dehydrogenase (NCBI) 191, 380
PA0899 aruB succinylarginine dihydrolase (NCBI) 191, 380
PA1005 PA1005 hypothetical protein (NCBI) 361, 380
PA1106 PA1106 hypothetical protein (NCBI) 361, 441
PA1333 PA1333 hypothetical protein (NCBI) 108, 361
PA1571 PA1571 hypothetical protein (NCBI) 166, 361
PA1572 PA1572 hypothetical protein (NCBI) 361, 376
PA1752 PA1752 2-dehydropantoate 2-reductase (NCBI) 70, 361
PA1807 PA1807 probable ATP-binding component of ABC transporter (NCBI) 37, 380
PA1808 PA1808 probable permease of ABC transporter (NCBI) 37, 380
PA1809 PA1809 probable permease of ABC transporter (NCBI) 37, 380
PA1810 PA1810 probable binding protein component of ABC transporter (NCBI) 7, 380
PA1811 PA1811 probable solute-binding protein (NCBI) 49, 380
PA3056 PA3056 hypothetical protein (NCBI) 34, 361
PA3057 PA3057 hypothetical protein (NCBI) 34, 361
PA3419 PA3419 hypothetical protein (NCBI) 208, 361
PA3438 folE1 GTP cyclohydrolase I precursor (NCBI) 380, 511
PA3439 folX d-erythro-7,8-dihydroneopterin triphosphate epimerase (NCBI) 380, 511
PA3600 PA3600 hypothetical protein (NCBI) 152, 361
PA3601 PA3601 hypothetical protein (NCBI) 152, 361
PA3602 PA3602 hypothetical protein (NCBI) 189, 361
PA3687 ppc phosphoenolpyruvate carboxylase (NCBI) 361, 441
PA3693 PA3693 hypothetical protein (NCBI) 380, 511
PA3694 PA3694 hypothetical protein (NCBI) 380, 480
PA3695 PA3695 hypothetical protein (NCBI) 7, 380
PA3696 PA3696 hypothetical protein (NCBI) 7, 380
PA3795 PA3795 probable oxidoreductase (NCBI) 107, 361
PA3934 PA3934 hypothetical protein (NCBI) 268, 380
PA4204 PA4204 hypothetical protein (NCBI) 107, 361
PA4375 PA4375 probable RND efflux transporter (NCBI) 20, 380
PA4833 PA4833 hypothetical protein (NCBI) 361, 469
PA4864 ureD urease accessory protein (NCBI) 206, 380
PA4865 ureA urease gamma subunit (NCBI) 380, 540
PA4866 PA4866 hypothetical protein (NCBI) 380, 540
PA4867 ureB urease beta subunit (NCBI) 7, 380
PA4868 ureC urease alpha subunit (NCBI) 7, 380
PA4891 ureE urease accessory protein UreE (NCBI) 240, 380
PA4893 ureG urease accessory protein UreG (NCBI) 337, 380
PA4894 PA4894 hypothetical protein (NCBI) 337, 380
PA5206 argE acetylornithine deacetylase (NCBI) 141, 361
PA5317 PA5317 probable binding protein component of ABC dipeptide transporter (NCBI) 4, 380
PA5378 PA5378 hypothetical protein (NCBI) 208, 361
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 PA1005
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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