Organism : Pseudomonas aeruginosa | Module List :
PA0079

hypothetical protein (NCBI)

CircVis
Functional Annotations (2)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
VI_chp_4 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0079
(Mouseover regulator name to see its description)

PA0079 is regulated by 76 influences and regulates 0 modules.
Regulators for PA0079 (76)
Regulator Module Operator
PA0610 66 tf
PA0708 66 tf
PA0876 66 tf
PA1050 66 tf
PA1182 66 tf
PA1223 66 tf
PA1526 66 tf
PA1544 66 tf
PA1633 66 tf
PA1663 66 tf
PA1713 66 tf
PA1760 66 tf
PA1912 66 tf
PA2010 66 tf
PA2196 66 tf
PA2258 66 tf
PA2276 66 tf
PA2417 66 tf
PA2426 66 tf
PA2511 66 tf
PA2622 66 tf
PA2718 66 tf
PA2877 66 tf
PA2885 66 tf
PA2897 66 tf
PA3711 66 tf
PA3965 66 tf
PA4074 66 tf
PA4080 66 tf
PA4296 66 tf
PA4354 66 tf
PA4436 66 tf
PA4462 66 tf
PA4493 66 tf
PA4508 66 tf
PA4769 66 tf
PA4890 66 tf
PA5059 66 tf
PA5166 66 tf
PA5324 66 tf
PA5342 66 tf
PA5438 66 tf
PA5483 66 tf
PA5550 66 tf
PA0218 431 tf
PA0448 431 tf
PA0610 431 tf
PA0876 431 tf
PA1015 431 tf
PA1223 431 tf
PA1241 431 tf
PA1351 431 tf
PA1413 431 tf
PA1526 431 tf
PA1544 431 tf
PA1633 431 tf
PA1663 431 tf
PA1760 431 tf
PA2354 431 tf
PA2359 431 tf
PA2426 431 tf
PA2622 431 tf
PA2897 431 tf
PA3571 431 tf
PA3845 431 tf
PA4080 431 tf
PA4296 431 tf
PA4354 431 tf
PA4436 431 tf
PA4462 431 tf
PA4596 431 tf
PA4769 431 tf
PA5166 431 tf
PA5283 431 tf
PA5483 431 tf
PA5550 431 tf

Warning: PA0079 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
2964 1.10e+03 Cg.Cgga.cgCGg.GgAt.TC
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2965 8.80e+02 TAtca.c.GtT
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3682 5.60e+01 AtCagGCagaaGgCcaTcacGA
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3683 3.00e+03 AaggaTTTt
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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 PA0079

PA0079 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
VI_chp_4 tigr/ tigrfam
Module neighborhood information for PA0079

PA0079 has total of 34 gene neighbors in modules 66, 431
Gene neighbors (34)
Gene Common Name Description Module membership
PA0070 PA0070 hypothetical protein (NCBI) 431, 495
PA0071 PA0071 hypothetical protein (NCBI) 66, 487
PA0072 PA0072 hypothetical protein (NCBI) 66, 487
PA0073 PA0073 probable ATP-binding component of ABC transporter (NCBI) 66, 487
PA0074 ppkA serine/threonine protein kinase PpkA (NCBI) 66, 487
PA0075 PA0075 probable phosphoprotein phosphatase (NCBI) 66, 495
PA0076 PA0076 hypothetical protein (NCBI) 66, 487
PA0078 PA0078 hypothetical protein (NCBI) 66, 431
PA0079 PA0079 hypothetical protein (NCBI) 66, 431
PA0080 PA0080 hypothetical protein (NCBI) 66, 431
PA0081 PA0081 hypothetical protein (NCBI) 66, 431
PA0082 PA0082 hypothetical protein (NCBI) 265, 431
PA0083 PA0083 hypothetical protein (NCBI) 431, 495
PA0084 PA0084 hypothetical protein (NCBI) 431, 495
PA0085 PA0085 hypothetical protein (NCBI) 431, 495
PA0092 PA0092 hypothetical protein (NCBI) 55, 431
PA0093 PA0093 hypothetical protein (NCBI) 55, 431
PA0094 PA0094 hypothetical protein (NCBI) 55, 431
PA0095 PA0095 hypothetical protein (NCBI) 55, 431
PA0096 PA0096 hypothetical protein (NCBI) 55, 431
PA0097 PA0097 hypothetical protein (NCBI) 55, 431
PA0098 PA0098 3-oxoacyl-(acyl carrier protein) synthase (NCBI) 55, 431
PA0099 PA0099 hypothetical protein (NCBI) 55, 431
PA0563 PA0563 hypothetical protein (NCBI) 265, 431
PA2684 PA2684 hypothetical protein (NCBI) 66, 76
PA2685 PA2685 hypothetical protein (NCBI) 45, 431
PA4487 PA4487 hypothetical protein (NCBI) 66, 76
PA4488 PA4488 hypothetical protein (NCBI) 62, 66
PA4489 PA4489 hypothetical protein (NCBI) 66, 76
PA4490 PA4490 hypothetical protein (NCBI) 66, 76
PA4491 PA4491 hypothetical protein (NCBI) 66, 76
PA4492 PA4492 hypothetical protein (NCBI) 66, 76
PA5113 PA5113 hypothetical protein (NCBI) 66, 76
PA5114 PA5114 hypothetical protein (NCBI) 11, 66
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 PA0079
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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