Organism : Pseudomonas aeruginosa | Module List :
PA0547

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (7)
Function System
Methylase involved in ubiquinone/menaquinone biosynthesis cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
methyltransferase activity go/ molecular_function
lipid biosynthetic process go/ biological_process
cyclopropane-fatty-acyl-phospholipid synthase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0547
(Mouseover regulator name to see its description)

PA0547 is regulated by 31 influences and regulates 27 modules.
Regulators for PA0547 (31)
Regulator Module Operator
PA0547 19 tf
PA0652 19 tf
PA1159 19 tf
PA1283 19 tf
PA1570 19 tf
PA2376 19 tf
PA3124 19 tf
PA4238 19 tf
PA4270 19 tf
PA4451 19 tf
PA4853 19 tf
PA5116 19 tf
PA5337 19 tf
PA0547 436 tf
PA0652 436 tf
PA1159 436 tf
PA1351 436 tf
PA1998 436 tf
PA2054 436 tf
PA2121 436 tf
PA2737 436 tf
PA2849 436 tf
PA2897 436 tf
PA3002 436 tf
PA3007 436 tf
PA4169 436 tf
PA4269 436 tf
PA4462 436 tf
PA4755 436 tf
PA4984 436 tf
PA5253 436 tf

Warning: PA0547 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
2874 1.90e+02 AAAAaagt
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2875 7.00e+03 gGAaaGCcCtctcaagCaGGcct
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3692 1.30e+00 ATgAATaGgaAAaA
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3693 4.50e+01 TGTTTcaAa
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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 PA0547

PA0547 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Methylase involved in ubiquinone/menaquinone biosynthesis cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
methyltransferase activity go/ molecular_function
lipid biosynthetic process go/ biological_process
cyclopropane-fatty-acyl-phospholipid synthase activity go/ molecular_function
Module neighborhood information for PA0547

PA0547 has total of 28 gene neighbors in modules 19, 436
Gene neighbors (28)
Gene Common Name Description Module membership
PA0139 ahpC alkyl hydroperoxide reductase subunit C (NCBI) 224, 436
PA0423 PA0423 hypothetical protein (NCBI) 9, 436
PA0430 metF 5,10-methylenetetrahydrofolate reductase (NCBI) 19, 274
PA0431 PA0431 hypothetical protein (NCBI) 19, 274
PA0432 sahH S-adenosyl-L-homocysteine hydrolase (NCBI) 19, 327
PA0449 PA0449 hypothetical protein (NCBI) 2, 436
PA0546 metK S-adenosylmethionine synthetase (NCBI) 19, 436
PA0547 PA0547 probable transcriptional regulator (NCBI) 19, 436
PA0548 tktA transketolase (NCBI) 433, 436
PA0888 aotJ arginine/ornithine binding protein AotJ (NCBI) 182, 436
PA1554 PA1554 probable cytochrome oxidase subunit (cbb3-type) (NCBI) 19, 259
PA1581 sdhC succinate dehydrogenase (C subunit) (NCBI) 19, 467
PA1582 sdhD succinate dehydrogenase (D subunit) (NCBI) 19, 467
PA1770 ppsA phosphoenolpyruvate synthase (NCBI) 435, 436
PA1777 oprF Major porin and structural outer membrane porin OprF precursor (NCBI) 182, 436
PA1830 PA1830 hypothetical protein (NCBI) 342, 436
PA1969 PA1969 hypothetical protein (NCBI) 6, 436
PA2575 PA2575 hypothetical protein (NCBI) 436, 462
PA2623 icd isocitrate dehydrogenase (NCBI) 15, 436
PA2707 PA2707 hypothetical protein (NCBI) 436, 551
PA3302 PA3302 hypothetical protein (NCBI) 42, 436
PA4241 rpsM 30S ribosomal protein S13 (NCBI) 19, 417
PA4242 rpmJ 50S ribosomal protein L36 (NCBI) 19, 417
PA4265 tufA elongation factor Tu (NCBI) 19, 539
PA4268 rpsL 30S ribosomal protein S12 (NCBI) 19, 539
PA4336 PA4336 hypothetical protein (NCBI) 381, 436
PA4366 sodB superoxide dismutase (NCBI) 244, 436
PA4755 greA transcription elongation factor GreA (NCBI) 436, 477
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 PA0547
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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