Organism : Pseudomonas aeruginosa | Module List :
PA0019 def

peptide deformylase (NCBI)

CircVis
Functional Annotations (5)
Function System
N-formylmethionyl-tRNA deformylase cog/ cog
iron ion binding go/ molecular_function
translation go/ biological_process
peptide deformylase activity go/ molecular_function
pept_deformyl tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0019
(Mouseover regulator name to see its description)

PA0019 is regulated by 39 influences and regulates 0 modules.
Regulators for PA0019 def (39)
Regulator Module Operator
PA0547 274 tf
PA0652 274 tf
PA0815 274 tf
PA0906 274 tf
PA1109 274 tf
PA1269 274 tf
PA1399 274 tf
PA1504 274 tf
PA1864 274 tf
PA2736 274 tf
PA2766 274 tf
PA3002 274 tf
PA3045 274 tf
PA3689 274 tf
PA3895 274 tf
PA3965 274 tf
PA4052 274 tf
PA4269 274 tf
PA4270 274 tf
PA4787 274 tf
PA4853 274 tf
PA4984 274 tf
PA5261 274 tf
PA5438 274 tf
PA5562 274 tf
PA0167 223 tf
PA0576 223 tf
PA0652 223 tf
PA0961 223 tf
PA1520 223 tf
PA1539 223 tf
PA3965 223 tf
PA4238 223 tf
PA4462 223 tf
PA4755 223 tf
PA4853 223 tf
PA5253 223 tf
PA5337 223 tf
PA5344 223 tf

Warning: PA0019 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
3274 1.70e-02 t.aAaggccGGCATTcTAaC
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3275 7.60e+02 AAaatT
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3376 4.60e+02 TcCtT.CatctaTTaatG.C
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3377 4.40e+03 GcgtTTtttAtCgatacc.ca
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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 PA0019

PA0019 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
N-formylmethionyl-tRNA deformylase cog/ cog
iron ion binding go/ molecular_function
translation go/ biological_process
peptide deformylase activity go/ molecular_function
pept_deformyl tigr/ tigrfam
Module neighborhood information for PA0019

PA0019 has total of 29 gene neighbors in modules 223, 274
Gene neighbors (29)
Gene Common Name Description Module membership
PA0001 dnaA chromosomal replication initiation protein (NCBI) 8, 274
PA0003 recF recombination protein F (NCBI) 274, 442
PA0004 gyrB DNA gyrase subunit B (NCBI) 274, 293
PA0008 glyS glycyl-tRNA synthetase beta subunit (NCBI) 274, 453
PA0016 trkA potassium uptake protein TrkA (NCBI) 174, 274
PA0017 PA0017 hypothetical protein (NCBI) 174, 274
PA0018 fmt methionyl-tRNA formyltransferase (NCBI) 174, 274
PA0019 def peptide deformylase (NCBI) 223, 274
PA0429 PA0429 hypothetical protein (NCBI) 274, 480
PA0430 metF 5,10-methylenetetrahydrofolate reductase (NCBI) 19, 274
PA0431 PA0431 hypothetical protein (NCBI) 19, 274
PA1317 cyoA cytochrome o ubiquinol oxidase subunit II (NCBI) 274, 312
PA1318 cyoB cytochrome o ubiquinol oxidase subunit I (NCBI) 274, 312
PA1319 cyoC cytochrome o ubiquinol oxidase subunit III (NCBI) 274, 312
PA1320 cyoD cytochrome o ubiquinol oxidase subunit IV (NCBI) 274, 312
PA1801 clpP ATP-dependent Clp protease proteolytic subunit (NCBI) 223, 271
PA1805 ppiD peptidyl-prolyl cis-trans isomerase D (NCBI) 223, 237
PA2963 PA2963 hypothetical protein (NCBI) 1, 274
PA2965 fabF1 3-oxoacyl-(acyl carrier protein) synthase (NCBI) 274, 312
PA3139 PA3139 probable amino acid aminotransferase (NCBI) 256, 274
PA3262 PA3262 probable peptidyl-prolyl cis-trans isomerase, FkbP-type (NCBI) 223, 273
PA4425 gmhA phosphoheptose isomerase (NCBI) 144, 223
PA4426 PA4426 hypothetical protein (NCBI) 223, 435
PA4460 PA4460 hypothetical protein (NCBI) 223, 262
PA4462 rpoN RNA polymerase sigma-54 factor (NCBI) 75, 223
PA5013 ilvE branched-chain amino acid aminotransferase (NCBI) 186, 223
PA5063 ubiE ubiquinone/menaquinone biosynthesis methyltransferase (NCBI) 223, 433
PA5128 secB export protein SecB (NCBI) 223, 435
PA5337 rpoZ DNA-directed RNA polymerase omega subunit (NCBI) 223, 352
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 PA0019
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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