Organism : Pseudomonas aeruginosa | Module List :
PA3417

probable pyruvate dehydrogenase E1 component, alpha subunit (NCBI)

CircVis
Functional Annotations (12)
Function System
Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit cog/ cog
pyruvate dehydrogenase (acetyl-transferring) activity go/ molecular_function
metabolic process go/ biological_process
Glycolysis / Gluconeogenesis kegg/ kegg pathway
Citrate cycle (TCA cycle) kegg/ kegg pathway
Valine leucine and isoleucine biosynthesis kegg/ kegg pathway
Pyruvate metabolism kegg/ kegg pathway
Butanoate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
PDH_E1_alph_x tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3417
(Mouseover regulator name to see its description)

PA3417 is regulated by 45 influences and regulates 0 modules.
Regulators for PA3417 (45)
Regulator Module Operator
PA0179 492 tf
PA0611 492 tf
PA0763 492 tf
PA0961 492 tf
PA1351 492 tf
PA1945 492 tf
PA2016 492 tf
PA2047 492 tf
PA2896 492 tf
PA2897 492 tf
PA3266 492 tf
PA3622 492 tf
PA3973 492 tf
PA4296 492 tf
PA4703 492 tf
PA5059 492 tf
PA5105 492 tf
PA5261 492 tf
PA5344 492 tf
PA5356 492 tf
PA5374 492 tf
PA5403 492 tf
PA5550 492 tf
PA0167 133 tf
PA0179 133 tf
PA0905 133 tf
PA1351 133 tf
PA1945 133 tf
PA2047 133 tf
PA2511 133 tf
PA2897 133 tf
PA3249 133 tf
PA3363 133 tf
PA4147 133 tf
PA4296 133 tf
PA4451 133 tf
PA4703 133 tf
PA4745 133 tf
PA5105 133 tf
PA5116 133 tf
PA5239 133 tf
PA5261 133 tf
PA5288 133 tf
PA5374 133 tf
PA5550 133 tf

Warning: PA3417 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
3096 2.70e+02 GatTTcgcTgTgaTtC
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3097 3.90e+03 TctttCTT
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3798 7.00e+03 AcTccaGgaAaGaAt
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3799 1.70e+04 TTTaCTcTCA
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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 PA3417

PA3417 is enriched for 12 functions in 3 categories.
Module neighborhood information for PA3417

PA3417 has total of 21 gene neighbors in modules 133, 492
Gene neighbors (21)
Gene Common Name Description Module membership
PA0788 PA0788 hypothetical protein (NCBI) 133, 475
PA0804 PA0804 probable oxidoreductase (NCBI) 133, 475
PA1118 PA1118 hypothetical protein (NCBI) 27, 133
PA1190 PA1190 hypothetical protein (NCBI) 133, 200
PA1327 PA1327 probable protease (NCBI) 475, 492
PA1860 PA1860 hypothetical protein (NCBI) 133, 475
PA1930 PA1930 probable chemotaxis transducer (NCBI) 492, 503
PA2071 fusA2 elongation factor G (NCBI) 64, 492
PA2174 PA2174 hypothetical protein (NCBI) 133, 153
PA2364 PA2364 hypothetical protein (NCBI) 133, 200
PA2375 PA2375 hypothetical protein (NCBI) 133, 200
PA2504 PA2504 hypothetical protein (NCBI) 133, 294
PA2572 PA2572 probable two-component response regulator (NCBI) 492, 503
PA3415 PA3415 probable dihydrolipoamide acetyltransferase (NCBI) 133, 492
PA3416 PA3416 probable pyruvate dehydrogenase E1 component, beta chain (NCBI) 133, 492
PA3417 PA3417 probable pyruvate dehydrogenase E1 component, alpha subunit (NCBI) 133, 492
PA3723 PA3723 probable FMN oxidoreductase (NCBI) 492, 503
PA4311 PA4311 hypothetical protein (NCBI) 322, 492
PA4312 PA4312 hypothetical protein (NCBI) 388, 492
PA4913 PA4913 probable binding protein component of ABC transporter (NCBI) 133, 515
PA4915 PA4915 probable chemotaxis transducer (NCBI) 128, 492
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 PA3417
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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