Organism : Pseudomonas aeruginosa | Module List :
PA3482 metG

methionyl-tRNA synthetase (NCBI)

CircVis
Functional Annotations (9)
Function System
Methionyl-tRNA synthetase cog/ cog
tRNA binding go/ molecular_function
methionine-tRNA ligase activity go/ molecular_function
ATP binding go/ molecular_function
cytoplasm go/ cellular_component
methionyl-tRNA aminoacylation go/ biological_process
Selenocompound metabolism kegg/ kegg pathway
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
metG tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3482
(Mouseover regulator name to see its description)

PA3482 is regulated by 33 influences and regulates 0 modules.
Regulators for PA3482 metG (33)
Regulator Module Operator
PA0393 18 tf
PA0576 18 tf
PA0893 18 tf
PA1526 18 tf
PA3002 18 tf
PA3711 18 tf
PA3804 18 tf
PA4057 18 tf
PA4269 18 tf
PA4530 18 tf
PA5344 18 tf
PA5562 18 tf
PA0393 198 tf
PA0576 198 tf
PA0893 198 tf
PA0961 198 tf
PA1759 198 tf
PA1776 198 tf
PA1826 198 tf
PA2312 198 tf
PA3002 198 tf
PA3563 198 tf
PA3804 198 tf
PA4052 198 tf
PA4094 198 tf
PA4269 198 tf
PA4270 198 tf
PA4755 198 tf
PA4769 198 tf
PA4853 198 tf
PA5116 198 tf
PA5337 198 tf
PA5344 198 tf

Warning: PA3482 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
2872 2.70e-03 acATaATAaCaacTcttC.cTcgA
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2873 7.70e-02 AcctaCctTTCAtGtGt
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3224 1.30e-02 agacaa.acct.tctagaAcAAGg
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3225 1.60e-01 CgGgCAtggTa.aCGAgtcGc
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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 PA3482

PA3482 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Methionyl-tRNA synthetase cog/ cog
tRNA binding go/ molecular_function
methionine-tRNA ligase activity go/ molecular_function
ATP binding go/ molecular_function
cytoplasm go/ cellular_component
methionyl-tRNA aminoacylation go/ biological_process
Selenocompound metabolism kegg/ kegg pathway
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
metG tigr/ tigrfam
Module neighborhood information for PA3482

PA3482 has total of 37 gene neighbors in modules 18, 198
Gene neighbors (37)
Gene Common Name Description Module membership
PA0374 ftsE cell division protein FtsE (NCBI) 18, 552
PA0375 ftsX cell division protein FtsX (NCBI) 18, 478
PA0392 PA0392 hypothetical protein (NCBI) 18, 499
PA0590 apaH diadenosinetetraphosphatase (NCBI) 18, 464
PA1611 PA1611 probable sensor/response regulator hybrid (NCBI) 198, 480
PA1612 PA1612 hypothetical protein (NCBI) 198, 480
PA1614 gpsA NAD(P)H-dependent glycerol-3-phosphate dehydrogenase (NCBI) 165, 198
PA1615 PA1615 probable lipase (NCBI) 42, 198
PA1616 PA1616 hypothetical protein (NCBI) 198, 383
PA2627 PA2627 hypothetical protein (NCBI) 198, 395
PA2973 PA2973 probable peptidase (NCBI) 18, 261
PA3002 mfd transcription-repair coupling protein Mfd (NCBI) 18, 43
PA3108 purF amidophosphoribosyltransferase (NCBI) 198, 350
PA3166 pheA chorismate mutase (NCBI) 18, 403
PA3171 ubiG 3-demethylubiquinone-9 3-methyltransferase (NCBI) 198, 293
PA3199 PA3199 hypothetical protein (NCBI) 18, 390
PA3200 PA3200 hypothetical protein (NCBI) 18, 31
PA3201 PA3201 putative intracellular septation protein (NCBI) 18, 398
PA3202 PA3202 hypothetical protein (NCBI) 18, 513
PA3482 metG methionyl-tRNA synthetase (NCBI) 18, 198
PA3625 surE stationary phase survival protein SurE (NCBI) 18, 228
PA3637 pyrG CTP synthetase (NCBI) 198, 433
PA3989 holA DNA polymerase III subunit delta (NCBI) 18, 81
PA4428 sspA stringent starvation protein A (NCBI) 198, 427
PA4430 PA4430 probable cytochrome b (NCBI) 29, 198
PA4431 PA4431 probable iron-sulfur protein (NCBI) 29, 198
PA5142 hisH1 glutamine amidotransferase (NCBI) 198, 544
PA5161 rmlB dTDP-D-glucose 4,6-dehydratase (NCBI) 198, 293
PA5223 ubiH 2-octaprenyl-6-methoxyphenyl hydroxylase (NCBI) 18, 81
PA5263 argH argininosuccinate lyase (NCBI) 198, 263
PA5278 dapF diaminopimelate epimerase (NCBI) 42, 198
PA5345 recG ATP-dependent DNA helicase RecG (NCBI) 198, 480
PA5498 PA5498 probable adhesin (NCBI) 18, 276
PA5499 np20 transcriptional regulator np20 (NCBI) 18, 276
PA5500 znuC zinc transport protein ZnuC (NCBI) 18, 276
PA5501 znuB permease of ABC zinc transporter ZnuB (NCBI) 18, 276
PA5502 PA5502 hypothetical protein (NCBI) 18, 276
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 PA3482
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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