Organism : Pseudomonas aeruginosa | Module List :
PA3158 wbpB

probable oxidoreductase WpbB (NCBI)

CircVis
Functional Annotations (3)
Function System
Predicted dehydrogenases and related proteins cog/ cog
electron transport go/ biological_process
oxidoreductase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3158
(Mouseover regulator name to see its description)

PA3158 is regulated by 71 influences and regulates 0 modules.
Regulators for PA3158 wbpB (71)
Regulator Module Operator
PA0037 219 tf
PA0152 219 tf
PA0217 219 tf
PA0248 219 tf
PA0272 219 tf
PA0456 219 tf
PA0784 219 tf
PA0791 219 tf
PA0890 219 tf
PA1141 219 tf
PA1335 219 tf
PA1619 219 tf
PA1630 219 tf
PA1738 219 tf
PA2056 219 tf
PA2100 219 tf
PA2115 219 tf
PA2126 219 tf
PA2227 219 tf
PA2387 219 tf
PA2696 219 tf
PA2736 219 tf
PA2849 219 tf
PA2879 219 tf
PA3045 219 tf
PA3458 219 tf
PA3594 219 tf
PA3596 219 tf
PA3711 219 tf
PA3721 219 tf
PA3898 219 tf
PA4288 219 tf
PA4831 219 tf
PA5308 219 tf
PA5511 219 tf
PA5562 219 tf
PA0268 297 tf
PA0393 297 tf
PA0455 297 tf
PA0611 297 tf
PA0784 297 tf
PA0815 297 tf
PA0890 297 tf
PA1141 297 tf
PA1226 297 tf
PA1229 297 tf
PA1290 297 tf
PA1328 297 tf
PA1363 297 tf
PA1619 297 tf
PA1630 297 tf
PA1633 297 tf
PA1663 297 tf
PA2047 297 tf
PA2054 297 tf
PA2100 297 tf
PA2126 297 tf
PA2196 297 tf
PA2227 297 tf
PA2387 297 tf
PA2692 297 tf
PA2718 297 tf
PA2736 297 tf
PA2758 297 tf
PA2849 297 tf
PA3067 297 tf
PA3215 297 tf
PA3711 297 tf
PA3815 297 tf
PA3898 297 tf
PA3995 297 tf

Warning: PA3158 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
3266 1.00e+02 GgatcAtTCaTcAgc
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3267 4.50e+02 TTccTtAT
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3422 3.90e-07 Tta.tAaacta.gtTTTCaaa
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3423 6.00e+00 aATAA.gAAgt
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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 PA3158

PA3158 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Predicted dehydrogenases and related proteins cog/ cog
electron transport go/ biological_process
oxidoreductase activity go/ molecular_function
Module neighborhood information for PA3158

PA3158 has total of 26 gene neighbors in modules 219, 297
Gene neighbors (26)
Gene Common Name Description Module membership
PA0053 PA0053 hypothetical protein (NCBI) 297, 476
PA0643 PA0643 hypothetical protein (NCBI) 188, 297
PA0644 PA0644 hypothetical protein (NCBI) 188, 297
PA0645 PA0645 hypothetical protein (NCBI) 188, 297
PA0729 PA0729 hypothetical protein (NCBI) 168, 297
PA1150 pys2 pyocin S2 (NCBI) 11, 297
PA1151 imm2 pyocin S2 immunity protein (NCBI) 11, 297
PA1366 PA1366 hypothetical protein (NCBI) 297, 476
PA1372 PA1372 hypothetical protein (NCBI) 297, 476
PA2462 PA2462 hypothetical protein (NCBI) 62, 297
PA3142 PA3142 hypothetical protein (NCBI) 297, 476
PA3143 PA3143 hypothetical protein (NCBI) 297, 476
PA3144 PA3144 hypothetical protein (NCBI) 219, 297
PA3145 wbpL glycosyltransferase WbpL (NCBI) 219, 508
PA3146 wbpK probable NAD-dependent epimerase/dehydratase WbpK (NCBI) 219, 508
PA3147 wbpJ probable glycosyl transferase WbpJ (NCBI) 219, 508
PA3148 wbpI probable UDP-N-acetylglucosamine 2-epimerase WbpI (NCBI) 219, 485
PA3149 wbpH probable glycosyltransferase WbpH (NCBI) 219, 485
PA3151 hisF2 imidazole glycerol phosphate synthase subunit HisF (NCBI) 219, 485
PA3152 hisH2 glutamine amidotransferase (NCBI) 219, 485
PA3155 wbpE probable aminotransferase WbpE (NCBI) 219, 508
PA3156 wbpD probable acetyltransferase WbpD (NCBI) 219, 508
PA3157 PA3157 probable acetyltransferase (NCBI) 297, 476
PA3158 wbpB probable oxidoreductase WpbB (NCBI) 219, 297
PA3159 wbpA probable UDP-glucose/GDP-mannose dehydrogenase WbpA (NCBI) 219, 297
PA3160 wzz O-antigen chain length regulator (NCBI) 297, 476
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 PA3158
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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