Organism : Pseudomonas aeruginosa | Module List :
PA0393 proC

pyrroline-5-carboxylate reductase (NCBI)

CircVis
Functional Annotations (11)
Function System
Pyrroline-5-carboxylate reductase cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
pyrroline-5-carboxylate reductase activity go/ molecular_function
electron transport go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
proline biosynthetic process go/ biological_process
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor go/ molecular_function
Arginine and proline metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
proC tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0393
(Mouseover regulator name to see its description)

PA0393 is regulated by 43 influences and regulates 80 modules.
Regulators for PA0393 proC (43)
Regulator Module Operator
PA0393 393 tf
PA0424 393 tf
PA0576 393 tf
PA0652 393 tf
PA0905 393 tf
PA1399 393 tf
PA2123 393 tf
PA2206 393 tf
PA2588 393 tf
PA3126 393 tf
PA3225 393 tf
PA4269 393 tf
PA5324 393 tf
PA0393 389 tf
PA0547 389 tf
PA0762 389 tf
PA0828 389 tf
PA0890 389 tf
PA1015 389 tf
PA1050 389 tf
PA1484 389 tf
PA1663 389 tf
PA1760 389 tf
PA1961 389 tf
PA2281 389 tf
PA2846 389 tf
PA2897 389 tf
PA3002 389 tf
PA3045 389 tf
PA3699 389 tf
PA3804 389 tf
PA3995 389 tf
PA4269 389 tf
PA4493 389 tf
PA4547 389 tf
PA4764 389 tf
PA4806 389 tf
PA4831 389 tf
PA4896 389 tf
PA5389 389 tf
PA5438 389 tf
PA5550 389 tf
PA5562 389 tf

Warning: PA0393 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
3602 5.50e+01 ct.TTttcgtc
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3603 1.00e+03 GCctccggcaAagcTga.atcc
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3610 2.10e-02 TTGAAcaGccG.aaacCGcCCCta
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3611 8.50e+03 GGTTTCCA
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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 PA0393

PA0393 is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
Pyrroline-5-carboxylate reductase cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
pyrroline-5-carboxylate reductase activity go/ molecular_function
electron transport go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
proline biosynthetic process go/ biological_process
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor go/ molecular_function
Arginine and proline metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
proC tigr/ tigrfam
Module neighborhood information for PA0393

PA0393 has total of 45 gene neighbors in modules 389, 393
Gene neighbors (45)
Gene Common Name Description Module membership
PA0067 prlC oligopeptidase A (NCBI) 293, 393
PA0393 proC pyrroline-5-carboxylate reductase (NCBI) 389, 393
PA0394 PA0394 hypothetical protein (NCBI) 393, 499
PA0779 PA0779 probable ATP-dependent protease (NCBI) 393, 509
PA1293 PA1293 hypothetical protein (NCBI) 389, 540
PA1596 htpG heat shock protein 90 (NCBI) 393, 509
PA1597 PA1597 hypothetical protein (NCBI) 393, 509
PA1803 lon Lon protease (NCBI) 393, 464
PA1823 nudC NADH pyrophosphatase (NCBI) 389, 478
PA1940 PA1940 hypothetical protein (NCBI) 234, 389
PA1941 PA1941 hypothetical protein (NCBI) 234, 389
PA2197 PA2197 hypothetical protein (NCBI) 389, 523
PA2198 PA2198 hypothetical protein (NCBI) 389, 523
PA2199 PA2199 probable dehydrogenase (NCBI) 320, 389
PA2725 PA2725 probable chaperone (NCBI) 389, 487
PA2726 PA2726 probable radical activating enzyme (NCBI) 389, 487
PA2727 PA2727 hypothetical protein (NCBI) 389, 487
PA2728 PA2728 hypothetical protein (NCBI) 389, 487
PA2729 PA2729 hypothetical protein (NCBI) 389, 487
PA2830 htpX heat shock protein HtpX (NCBI) 393, 524
PA3003 PA3003 hypothetical protein (NCBI) 389, 511
PA3126 ibpA heat-shock protein IbpA (NCBI) 10, 393
PA3173 PA3173 short chain dehydrogenase (NCBI) 179, 389
PA3299 fadD1 long-chain-fatty-acid--CoA ligase (NCBI) 293, 389
PA3789 PA3789 hypothetical protein (NCBI) 291, 389
PA3790 oprC Putative copper transport outer membrane porin OprC precursor (NCBI) 389, 462
PA4061 PA4061 probable thioredoxin (NCBI) 393, 509
PA4372 PA4372 hypothetical protein (NCBI) 98, 389
PA4385 groEL chaperonin GroEL (NCBI) 393, 509
PA4386 groES co-chaperonin GroES (NCBI) 393, 509
PA4387 PA4387 hypothetical protein (NCBI) 393, 509
PA4402 argJ bifunctional ornithine acetyltransferase/N-acetylglutamate synthase protein (NCBI) 150, 389
PA4542 clpB ClpB protein (NCBI) 393, 509
PA4751 ftsH cell division protein FtsH (NCBI) 393, 488
PA4759 dapB dihydrodipicolinate reductase (NCBI) 393, 509
PA4760 dnaJ DnaJ protein (NCBI) 393, 509
PA4761 dnaK molecular chaperone DnaK (NCBI) 393, 509
PA4762 grpE heat shock protein GrpE (NCBI) 393, 509
PA5025 metY O-acetylhomoserine sulfhydrylase (NCBI) 203, 389
PA5053 hslV ATP-dependent protease peptidase subunit (NCBI) 393, 509
PA5054 hslU ATP-dependent protease ATP-binding subunit (NCBI) 393, 509
PA5055 PA5055 hypothetical protein (NCBI) 393, 509
PA5203 gshA glutamate--cysteine ligase (NCBI) 353, 389
PA5551 PA5551 hypothetical protein (NCBI) 374, 389
PA5552 glmU glucosamine-1-phosphate acetyltransferase/N-acetylglucosamine-1-phosphate uridyltransferase (NCBI) 270, 389
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 PA0393
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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