Organism : Pseudomonas aeruginosa | Module List :
PA5263 argH

argininosuccinate lyase (NCBI)

CircVis
Functional Annotations (8)
Function System
Argininosuccinate lyase cog/ cog
argininosuccinate lyase activity go/ molecular_function
arginine biosynthetic process via ornithine go/ biological_process
Alanine aspartate and glutamate metabolism kegg/ kegg pathway
Arginine and proline metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
argH tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA5263
(Mouseover regulator name to see its description)

PA5263 is regulated by 36 influences and regulates 0 modules.
Regulators for PA5263 argH (36)
Regulator Module Operator
PA0576 263 tf
PA0652 263 tf
PA1504 263 tf
PA3002 263 tf
PA3563 263 tf
PA3804 263 tf
PA4057 263 tf
PA4270 263 tf
PA4451 263 tf
PA4462 263 tf
PA4755 263 tf
PA4853 263 tf
PA5166 263 tf
PA5337 263 tf
PA5344 263 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: PA5263 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
3224 1.30e-02 agacaa.acct.tctagaAcAAGg
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3225 1.60e-01 CgGgCAtggTa.aCGAgtcGc
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3354 1.10e+02 cTTttCcgGta
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3355 2.50e+03 tcg.ttCAGcgtacg
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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 PA5263

PA5263 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Argininosuccinate lyase cog/ cog
argininosuccinate lyase activity go/ molecular_function
arginine biosynthetic process via ornithine go/ biological_process
Alanine aspartate and glutamate metabolism kegg/ kegg pathway
Arginine and proline metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
argH tigr/ tigrfam
Module neighborhood information for PA5263

PA5263 has total of 34 gene neighbors in modules 198, 263
Gene neighbors (34)
Gene Common Name Description Module membership
PA0292 aguA agmatine deiminase (NCBI) 62, 263
PA0405 PA0405 hypothetical protein (NCBI) 86, 263
PA0666 PA0666 hypothetical protein (NCBI) 174, 263
PA0667 PA0667 hypothetical protein (NCBI) 263, 435
PA0705 PA0705 probable glycosyl transferase (NCBI) 59, 263
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
PA1861 modC molybdenum transport protein ModC (NCBI) 31, 263
PA1862 modB molybdenum transport protein ModB (NCBI) 220, 263
PA1863 modA molybdate-binding periplasmic protein precursor ModA (NCBI) 9, 263
PA2627 PA2627 hypothetical protein (NCBI) 198, 395
PA2831 PA2831 hypothetical protein (NCBI) 100, 263
PA3108 purF amidophosphoribosyltransferase (NCBI) 198, 350
PA3171 ubiG 3-demethylubiquinone-9 3-methyltransferase (NCBI) 198, 293
PA3301 PA3301 hypothetical protein (NCBI) 42, 263
PA3437 PA3437 short chain dehydrogenase (NCBI) 263, 511
PA3482 metG methionyl-tRNA synthetase (NCBI) 18, 198
PA3563 fruR fructose transport system repressor FruR (NCBI) 263, 493
PA3637 pyrG CTP synthetase (NCBI) 198, 433
PA3849 ndpA nucleoid-associated protein NdpA (NCBI) 59, 263
PA4423 PA4423 hypothetical protein (NCBI) 42, 263
PA4424 PA4424 hypothetical protein (NCBI) 94, 263
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
PA5263 argH argininosuccinate lyase (NCBI) 198, 263
PA5278 dapF diaminopimelate epimerase (NCBI) 42, 198
PA5345 recG ATP-dependent DNA helicase RecG (NCBI) 198, 480
PA5493 polA DNA polymerase I (NCBI) 174, 263
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 PA5263
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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