Organism : Pseudomonas aeruginosa | Module List :
PA3760

probable phosphotransferase protein (NCBI)

CircVis
Functional Annotations (8)
Function System
Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) cog/ cog
sugar:hydrogen symporter activity go/ molecular_function
cytoplasm go/ cellular_component
phosphoenolpyruvate-protein phosphotransferase activity go/ molecular_function
phosphoenolpyruvate-dependent sugar phosphotransferase system go/ biological_process
membrane go/ cellular_component
phosphorylation go/ biological_process
PTBA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3760
(Mouseover regulator name to see its description)

PA3760 is regulated by 33 influences and regulates 0 modules.
Regulators for PA3760 (33)
Regulator Module Operator
PA0181 373 tf
PA0218 373 tf
PA1138 373 tf
PA1264 373 tf
PA2082 373 tf
PA2577 373 tf
PA2696 373 tf
PA2846 373 tf
PA3630 373 tf
PA3995 373 tf
PA4288 373 tf
PA0120 523 tf
PA0167 523 tf
PA0393 523 tf
PA0475 523 tf
PA0479 523 tf
PA0784 523 tf
PA0815 523 tf
PA0961 523 tf
PA1760 523 tf
PA2047 523 tf
PA2376 523 tf
PA2484 523 tf
PA2713 523 tf
PA2737 523 tf
PA2766 523 tf
PA3714 523 tf
PA3757 523 tf
PA3895 523 tf
PA4145 523 tf
PA4451 523 tf
PA5253 523 tf
PA5403 523 tf

Warning: PA3760 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
3570 9.00e-11 tttt.gaAtcAGtAttA.gaa.aa
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3571 1.70e-02 ga..agaacaacc.GAtTtC
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3860 2.40e+04 aTTcCTC.TtT
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3861 4.30e+04 GTTGTTctGGG.GAt
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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 PA3760

PA3760 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) cog/ cog
sugar:hydrogen symporter activity go/ molecular_function
cytoplasm go/ cellular_component
phosphoenolpyruvate-protein phosphotransferase activity go/ molecular_function
phosphoenolpyruvate-dependent sugar phosphotransferase system go/ biological_process
membrane go/ cellular_component
phosphorylation go/ biological_process
PTBA tigr/ tigrfam
Module neighborhood information for PA3760

PA3760 has total of 64 gene neighbors in modules 373, 523
Gene neighbors (64)
Gene Common Name Description Module membership
PA0117 PA0117 probable short chain dehydrogenase (NCBI) 138, 373
PA0118 PA0118 hypothetical protein (NCBI) 138, 373
PA0181 PA0181 probable transcriptional regulator (NCBI) 196, 373
PA0446 PA0446 hypothetical protein (NCBI) 141, 523
PA0447 gcdH glutaryl-CoA dehydrogenase (NCBI) 185, 523
PA0478 PA0478 probable N-acetyltransferase (NCBI) 373, 542
PA0479 PA0479 probable transcriptional regulator (NCBI) 397, 523
PA0487 PA0487 probable molybdenum transport regulator (NCBI) 220, 523
PA0507 PA0507 probable acyl-CoA dehydrogenase (NCBI) 74, 373
PA0508 PA0508 probable acyl-CoA dehydrogenase (NCBI) 20, 373
PA0657 PA0657 probable ATPase (NCBI) 443, 523
PA0700 PA0700 hypothetical protein (NCBI) 373, 532
PA0784 PA0784 probable transcriptional regulator (NCBI) 523, 551
PA0840 PA0840 probable oxidoreductase (NCBI) 523, 550
PA0841 PA0841 hypothetical protein (NCBI) 246, 373
PA0847 PA0847 hypothetical protein (NCBI) 241, 523
PA1033 PA1033 probable glutathione S-transferase (NCBI) 462, 523
PA1137 PA1137 probable oxidoreductase (NCBI) 333, 373
PA1138 PA1138 probable transcriptional regulator (NCBI) 192, 373
PA1204 PA1204 hypothetical protein (NCBI) 338, 523
PA1205 PA1205 hypothetical protein (NCBI) 258, 523
PA1292 PA1292 probable 3-mercaptopyruvate sulfurtransferase (NCBI) 462, 523
PA1362 PA1362 hypothetical protein (NCBI) 373, 432
PA1500 PA1500 probable oxidoreductase (NCBI) 236, 373
PA1501 PA1501 hypothetical protein (NCBI) 236, 373
PA1502 gcl glyoxylate carboligase (NCBI) 373, 425
PA1618 PA1618 hypothetical protein (NCBI) 397, 523
PA1747 PA1747 hypothetical protein (NCBI) 373, 432
PA1826 PA1826 probable transcriptional regulator (NCBI) 373, 463
PA2010 PA2010 probable transcriptional regulator (NCBI) 373, 450
PA2035 PA2035 acetolactate synthase II large subunit (NCBI) 397, 523
PA2082 PA2082 probable transcriptional regulator (NCBI) 373, 541
PA2120 PA2120 hypothetical protein (NCBI) 292, 373
PA2197 PA2197 hypothetical protein (NCBI) 389, 523
PA2198 PA2198 hypothetical protein (NCBI) 389, 523
PA2218 PA2218 hypothetical protein (NCBI) 373, 537
PA2577 PA2577 probable transcriptional regulator (NCBI) 397, 523
PA2665 PA2665 anaerobic nitric oxide reductase transcription regulator (NCBI) 58, 373
PA2696 PA2696 probable transcriptional regulator (NCBI) 373, 461
PA2705 PA2705 hypothetical protein (NCBI) 7, 523
PA2846 PA2846 probable transcriptional regulator (NCBI) 373, 546
PA2930 PA2930 probable transcriptional regulator (NCBI) 143, 373
PA3127 PA3127 hypothetical protein (NCBI) 10, 523
PA3427 PA3427 probable short-chain dehydrogenases (NCBI) 397, 523
PA3499 PA3499 hypothetical protein (NCBI) 373, 432
PA3630 PA3630 probable transcriptional regulator (NCBI) 340, 373
PA3757 PA3757 probable transcriptional regulator (NCBI) 397, 523
PA3758 PA3758 probable N-acetylglucosamine-6-phosphate deacetylase (NCBI) 397, 523
PA3759 PA3759 probable aminotransferase (NCBI) 295, 523
PA3760 PA3760 probable phosphotransferase protein (NCBI) 373, 523
PA3761 PA3761 probable phosphotransferase system protein (NCBI) 24, 523
PA3970 amn AMP nucleosidase (NCBI) 378, 523
PA4026 PA4026 probable acetyltransferase (NCBI) 51, 523
PA4086 cupB1 probable fimbrial subunit CupB1 (NCBI) 20, 373
PA4115 PA4115 hypothetical protein (NCBI) 378, 523
PA4282 PA4282 probable exonuclease (NCBI) 443, 523
PA4288 PA4288 probable transcriptional regulator (NCBI) 192, 373
PA4472 pmbA PmbA protein (NCBI) 28, 523
PA4798 PA4798 hypothetical protein (NCBI) 511, 523
PA4976 aspC aspartate transaminase (NCBI) 397, 523
PA5190 PA5190 probable nitroreductase (NCBI) 131, 373
PA5195 PA5195 probable heat shock protein (NCBI) 165, 523
PA5394 cls cardiolipin synthetase (NCBI) 373, 432
PA5547 PA5547 hypothetical protein (NCBI) 335, 373
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 PA3760
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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