Organism : Pseudomonas aeruginosa | Module List :
PA0331 ilvA1

threonine dehydratase, biosynthetic (NCBI)

CircVis
Functional Annotations (9)
Function System
Threonine dehydratase cog/ cog
L-threonine ammonia-lyase activity go/ molecular_function
isoleucine biosynthetic process go/ biological_process
pyridoxal phosphate binding go/ molecular_function
Glycine serine and threonine metabolism kegg/ kegg pathway
Valine leucine and isoleucine biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
ilvA_2Cterm tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0331
(Mouseover regulator name to see its description)

PA0331 is regulated by 37 influences and regulates 0 modules.
Regulators for PA0331 ilvA1 (37)
Regulator Module Operator
PA0120 312 tf
PA0155 312 tf
PA0455 312 tf
PA0515 312 tf
PA0601 312 tf
PA0815 312 tf
PA0876 312 tf
PA1109 312 tf
PA1422 312 tf
PA1504 312 tf
PA2115 312 tf
PA3002 312 tf
PA3027 312 tf
PA3126 312 tf
PA3583 312 tf
PA3804 312 tf
PA3921 312 tf
PA4021 312 tf
PA4052 312 tf
PA4269 312 tf
PA4279 312 tf
PA4787 312 tf
PA4806 312 tf
PA4890 312 tf
PA5166 312 tf
PA5389 312 tf
PA5550 312 tf
PA5562 312 tf
PA0961 103 tf
PA3269 103 tf
PA3604 103 tf
PA4057 103 tf
PA4275 103 tf
PA4451 103 tf
PA4745 103 tf
PA5239 103 tf
PA5550 103 tf

Warning: PA0331 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
3038 2.00e+02 AAACGGAGGCATTGGGTAGATAAT
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3039 2.50e+02 GtCG.CGaagAAc.C.atcgGC
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3450 5.40e+00 cgcTAtAaTtgc.cgCTTt
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3451 2.40e+02 CAtGgattTcTCC.tG
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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 PA0331

PA0331 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Threonine dehydratase cog/ cog
L-threonine ammonia-lyase activity go/ molecular_function
isoleucine biosynthetic process go/ biological_process
pyridoxal phosphate binding go/ molecular_function
Glycine serine and threonine metabolism kegg/ kegg pathway
Valine leucine and isoleucine biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
ilvA_2Cterm tigr/ tigrfam
Module neighborhood information for PA0331

PA0331 has total of 32 gene neighbors in modules 103, 312
Gene neighbors (32)
Gene Common Name Description Module membership
PA0331 ilvA1 threonine dehydratase, biosynthetic (NCBI) 103, 312
PA0354 PA0354 hypothetical protein (NCBI) 312, 451
PA0733 PA0733 probable pseudouridylate synthase (NCBI) 103, 451
PA0734 PA0734 hypothetical protein (NCBI) 103, 451
PA0932 cysM cysteine synthase B (NCBI) 103, 195
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
PA2865 PA2865 probable glycosylase (NCBI) 103, 181
PA2866 mttC secretion protein MttC (NCBI) 86, 103
PA2955 PA2955 hypothetical protein (NCBI) 103, 371
PA2965 fabF1 3-oxoacyl-(acyl carrier protein) synthase (NCBI) 274, 312
PA2988 PA2988 hypothetical protein (NCBI) 103, 306
PA3169 PA3169 translation initiation factor IF-2B subunit alpha (NCBI) 312, 395
PA3269 PA3269 probable transcriptional regulator (NCBI) 103, 187
PA3527 pyrC dihydroorotase (NCBI) 113, 312
PA3620 mutS DNA mismatch repair protein (NCBI) 312, 360
PA3631 PA3631 hypothetical protein (NCBI) 225, 312
PA3633 ispD 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (NCBI) 312, 396
PA3673 plsB glycerol-3-phosphate acyltransferase (NCBI) 312, 480
PA3737 dsbC thiol:disulfide interchange protein DsbC (NCBI) 103, 251
PA3861 rhl ATP-dependent RNA helicase RhlB (RefSeq) 237, 312
PA4001 sltB1 soluble lytic transglycosylase B (NCBI) 103, 341
PA4291 PA4291 hypothetical protein (NCBI) 100, 103
PA4678 rimI peptide n-acetyltransferase RimI (NCBI) 103, 387
PA4679 PA4679 hypothetical protein (NCBI) 103, 374
PA4700 mrcB penicillin-binding protein 1B (NCBI) 103, 249
PA4997 msbA transport protein MsbA (NCBI) 103, 451
PA5133 PA5133 hypothetical protein (NCBI) 103, 306
PA5244 PA5244 hypothetical protein (NCBI) 103, 306
PA5320 dfp bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase (NCBI) 207, 312
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 PA0331
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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