Organism : Pseudomonas aeruginosa | Module List :
PA4759 dapB

dihydrodipicolinate reductase (NCBI)

CircVis
Functional Annotations (9)
Function System
Dihydrodipicolinate reductase cog/ cog
cytoplasm go/ cellular_component
dihydrodipicolinate reductase activity go/ molecular_function
lysine biosynthetic process via diaminopimelate go/ biological_process
Lysine biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
dapB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4759
(Mouseover regulator name to see its description)

PA4759 is regulated by 47 influences and regulates 0 modules.
Regulators for PA4759 dapB (47)
Regulator Module Operator
PA0393 509 tf
PA0424 509 tf
PA0576 509 tf
PA0611 509 tf
PA0905 509 tf
PA1153 509 tf
PA1264 509 tf
PA1399 509 tf
PA1776 509 tf
PA1949 509 tf
PA2076 509 tf
PA2383 509 tf
PA2468 509 tf
PA2497 509 tf
PA2622 509 tf
PA2713 509 tf
PA3126 509 tf
PA3184 509 tf
PA3225 509 tf
PA3322 509 tf
PA3420 509 tf
PA3508 509 tf
PA3899 509 tf
PA4147 509 tf
PA4196 509 tf
PA4269 509 tf
PA4279 509 tf
PA4755 509 tf
PA4784 509 tf
PA4890 509 tf
PA5324 509 tf
PA5356 509 tf
PA5365 509 tf
PA5382 509 tf
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

Warning: PA4759 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
3610 2.10e-02 TTGAAcaGccG.aaacCGcCCCta
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3611 8.50e+03 GGTTTCCA
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3832 2.10e+02 gcTTGaac
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3833 4.60e+03 cgTGGAaA
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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 PA4759

PA4759 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Dihydrodipicolinate reductase cog/ cog
cytoplasm go/ cellular_component
dihydrodipicolinate reductase activity go/ molecular_function
lysine biosynthetic process via diaminopimelate go/ biological_process
Lysine biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
dapB tigr/ tigrfam
Module neighborhood information for PA4759

PA4759 has total of 28 gene neighbors in modules 393, 509
Gene neighbors (28)
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
PA0425 mexA Resistance-Nodulation-Cell Division (RND) multidrug efflux membrane fusion protein MexA precursor (NCBI) 224, 509
PA0426 mexB Resistance-Nodulation-Cell Division (RND) multidrug efflux transporter MexB (NCBI) 47, 509
PA0427 oprM Major intrinsic multiple antibiotic resistance efflux outer membrane protein OprM precursor (NCBI) 47, 509
PA0506 PA0506 probable acyl-CoA dehydrogenase (NCBI) 342, 509
PA0779 PA0779 probable ATP-dependent protease (NCBI) 393, 509
PA1596 htpG heat shock protein 90 (NCBI) 393, 509
PA1597 PA1597 hypothetical protein (NCBI) 393, 509
PA1803 lon Lon protease (NCBI) 393, 464
PA2830 htpX heat shock protein HtpX (NCBI) 393, 524
PA3013 foaB acetyl-CoA acetyltransferase (NCBI) 342, 509
PA3014 faoA fatty-acid oxidation complex alpha-subunit (NCBI) 342, 509
PA3126 ibpA heat-shock protein IbpA (NCBI) 10, 393
PA4061 PA4061 probable thioredoxin (NCBI) 393, 509
PA4385 groEL chaperonin GroEL (NCBI) 393, 509
PA4386 groES co-chaperonin GroES (NCBI) 393, 509
PA4387 PA4387 hypothetical protein (NCBI) 393, 509
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
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
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 PA4759
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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