Organism : Pseudomonas aeruginosa | Module List :
PA3650 dxr

1-deoxy-D-xylulose 5-phosphate reductoisomerase (NCBI)

CircVis
Functional Annotations (7)
Function System
1-deoxy-D-xylulose 5-phosphate reductoisomerase cog/ cog
isoprenoid biosynthetic process go/ biological_process
1-deoxy-D-xylulose-5-phosphate reductoisomerase activity go/ molecular_function
Terpenoid backbone biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Dxr tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3650
(Mouseover regulator name to see its description)

PA3650 is regulated by 32 influences and regulates 0 modules.
Regulators for PA3650 dxr (32)
Regulator Module Operator
PA0275 270 tf
PA0762 270 tf
PA0890 270 tf
PA0961 270 tf
PA1335 270 tf
PA1898 270 tf
PA2511 270 tf
PA2556 270 tf
PA2622 270 tf
PA3002 270 tf
PA3804 270 tf
PA4052 270 tf
PA4238 270 tf
PA4269 270 tf
PA4547 270 tf
PA5239 270 tf
PA5550 270 tf
PA5562 270 tf
PA0890 131 tf
PA1898 131 tf
PA2047 131 tf
PA2957 131 tf
PA3804 131 tf
PA3948 131 tf
PA4238 131 tf
PA4451 131 tf
PA4499 131 tf
PA4530 131 tf
PA4581 131 tf
PA5239 131 tf
PA5550 131 tf
PA5562 131 tf

Warning: PA3650 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
3092 5.60e-05 AaaAtA
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3093 2.70e-01 CAgtaaaGcctgAcAGaa.aActA
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3368 5.60e-01 AaaCgAaA
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3369 3.20e+03 tGaaaAAgctG
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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 PA3650

PA3650 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
1-deoxy-D-xylulose 5-phosphate reductoisomerase cog/ cog
isoprenoid biosynthetic process go/ biological_process
1-deoxy-D-xylulose-5-phosphate reductoisomerase activity go/ molecular_function
Terpenoid backbone biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Dxr tigr/ tigrfam
Module neighborhood information for PA3650

PA3650 has total of 36 gene neighbors in modules 131, 270
Gene neighbors (36)
Gene Common Name Description Module membership
PA0783 putP sodium/proline symporter PutP (NCBI) 131, 315
PA2630 PA2630 hypothetical protein (NCBI) 225, 270
PA3632 PA3632 hypothetical protein (NCBI) 174, 270
PA3640 dnaE DNA polymerase III subunit alpha (NCBI) 270, 552
PA3642 rnhB ribonuclease HII (NCBI) 131, 277
PA3643 lpxB lipid-A-disaccharide synthase (NCBI) 270, 277
PA3650 dxr 1-deoxy-D-xylulose 5-phosphate reductoisomerase (NCBI) 131, 270
PA3652 uppS undecaprenyl pyrophosphate synthetase (NCBI) 270, 353
PA3799 engA GTP-binding protein EngA (NCBI) 270, 353
PA3800 PA3800 hypothetical protein (NCBI) 270, 329
PA3804 PA3804 hypothetical protein (NCBI) 270, 329
PA3820 secF protein export protein SecF (NCBI) 270, 277
PA3827 PA3827 hypothetical protein (NCBI) 131, 353
PA4234 uvrA excinuclease ABC subunit A (NCBI) 131, 427
PA4250 rpsN 30S ribosomal protein S14 (NCBI) 131, 329
PA4427 sspB stringent starvation protein B (NCBI) 131, 212
PA4449 hisG ATP phosphoribosyltransferase (NCBI) 270, 510
PA4457 PA4457 hypothetical protein (NCBI) 131, 214
PA4498 PA4498 probable metallopeptidase (NCBI) 131, 517
PA4499 PA4499 probable transcriptional regulator (NCBI) 131, 212
PA4696 ilvI acetolactate synthase III large subunit (NCBI) 131, 543
PA4727 pcnB poly(A) polymerase (NCBI) 214, 270
PA4757 PA4757 hypothetical protein (NCBI) 270, 453
PA5001 PA5001 hypothetical protein (NCBI) 270, 353
PA5002 PA5002 hypothetical protein (NCBI) 270, 353
PA5003 PA5003 hypothetical protein (NCBI) 174, 270
PA5052 PA5052 hypothetical protein (NCBI) 225, 270
PA5190 PA5190 probable nitroreductase (NCBI) 131, 373
PA5239 rho transcription termination factor Rho (NCBI) 131, 214
PA5549 glmS D-fructose-6-phosphate amidotransferase (NCBI) 270, 353
PA5552 glmU glucosamine-1-phosphate acetyltransferase/N-acetylglucosamine-1-phosphate uridyltransferase (NCBI) 270, 389
PA5561 atpI ATP synthase subunit I (NCBI) 131, 354
PA5562 spoOJ chromosome partitioning protein Spo0J (NCBI) 82, 131
PA5563 soj chromosome partitioning protein Soj (NCBI) 131, 214
PA5564 gidB glucose-inhibited division protein B (NCBI) 131, 214
PA5565 gidA glucose-inhibited division protein A (NCBI) 131, 214
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 PA3650
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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