Organism : Pseudomonas aeruginosa | Module List :
PA4414 murD

UDP-N-acetylmuramoyl-L-alanyl-D-glutamatesynthetase (NCBI)

CircVis
Functional Annotations (12)
Function System
UDP-N-acetylmuramoylalanine-D-glutamate ligase cog/ cog
ATP binding go/ molecular_function
cytoplasm go/ cellular_component
regulation of cell shape go/ biological_process
UDP-N-acetylmuramoylalanine-D-glutamate ligase activity go/ molecular_function
peptidoglycan biosynthetic process go/ biological_process
phosphopantetheine binding go/ molecular_function
cell division go/ biological_process
D-Glutamine and D-glutamate metabolism kegg/ kegg pathway
Peptidoglycan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
murD tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4414
(Mouseover regulator name to see its description)

PA4414 is regulated by 70 influences and regulates 0 modules.
Regulators for PA4414 murD (70)
Regulator Module Operator
PA0120 216 tf
PA0762 216 tf
PA0815 216 tf
PA0876 216 tf
PA0893 216 tf
PA1003 216 tf
PA1097 216 tf
PA1128 216 tf
PA1201 216 tf
PA1455 216 tf
PA1484 216 tf
PA1504 216 tf
PA1526 216 tf
PA1850 216 tf
PA1978 216 tf
PA2020 216 tf
PA2032 216 tf
PA2206 216 tf
PA2492 216 tf
PA2511 216 tf
PA2556 216 tf
PA2601 216 tf
PA2718 216 tf
PA2885 216 tf
PA2957 216 tf
PA3124 216 tf
PA3225 216 tf
PA3266 216 tf
PA3398 216 tf
PA3458 216 tf
PA3804 216 tf
PA4147 216 tf
PA4182 216 tf
PA4493 216 tf
PA4530 216 tf
PA4787 216 tf
PA5562 216 tf
PA0034 67 tf
PA0367 67 tf
PA0475 67 tf
PA0762 67 tf
PA0780 67 tf
PA0815 67 tf
PA0893 67 tf
PA1145 67 tf
PA1201 67 tf
PA1315 67 tf
PA1374 67 tf
PA1759 67 tf
PA1853 67 tf
PA1978 67 tf
PA2020 67 tf
PA2096 67 tf
PA2100 67 tf
PA2206 67 tf
PA2277 67 tf
PA2556 67 tf
PA2718 67 tf
PA3002 67 tf
PA3124 67 tf
PA3220 67 tf
PA3225 67 tf
PA3458 67 tf
PA3804 67 tf
PA4182 67 tf
PA4315 67 tf
PA4493 67 tf
PA4530 67 tf
PA4787 67 tf
PA5562 67 tf

Warning: PA4414 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
2966 1.90e+01 TGTaAc..TTTtTgAc..CT
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2967 3.20e+02 TCAATtG
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3260 4.30e-03 TTCatCACgtgAaAtAAATCgtCA
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3261 4.30e-03 AAAAtaCCTTcCActgCGaAatTT
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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 PA4414

PA4414 is enriched for 12 functions in 3 categories.
Enrichment Table (12)
Function System
UDP-N-acetylmuramoylalanine-D-glutamate ligase cog/ cog
ATP binding go/ molecular_function
cytoplasm go/ cellular_component
regulation of cell shape go/ biological_process
UDP-N-acetylmuramoylalanine-D-glutamate ligase activity go/ molecular_function
peptidoglycan biosynthetic process go/ biological_process
phosphopantetheine binding go/ molecular_function
cell division go/ biological_process
D-Glutamine and D-glutamate metabolism kegg/ kegg pathway
Peptidoglycan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
murD tigr/ tigrfam
Module neighborhood information for PA4414

PA4414 has total of 23 gene neighbors in modules 67, 216
Gene neighbors (23)
Gene Common Name Description Module membership
PA4407 ftsZ cell division protein FtsZ (NCBI) 15, 216
PA4408 ftsA cell division protein FtsA (NCBI) 67, 216
PA4409 ftsQ cell division protein FtsQ (NCBI) 67, 216
PA4410 ddlB D-alanylalanine synthetase (NCBI) 67, 216
PA4411 murC UDP-N-acetylmuramate--L-alanine ligase (NCBI) 67, 216
PA4412 murG N-acetylglucosaminyl transferase (NCBI) 67, 216
PA4413 ftsW cell division protein FtsW (NCBI) 67, 216
PA4414 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamatesynthetase (NCBI) 67, 216
PA4415 mraY phospho-N-acetylmuramoyl-pentapeptide-transferase (NCBI) 67, 216
PA4416 murF UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanyl ligase (NCBI) 67, 216
PA4417 murE UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase (NCBI) 67, 216
PA4418 ftsI penicillin-binding protein 3 (NCBI) 67, 216
PA4419 ftsL cell division protein FtsL (NCBI) 67, 216
PA4420 mraW S-adenosyl-methyltransferase (NCBI) 67, 216
PA4421 PA4421 hypothetical protein (NCBI) 67, 216
PA4530 PA4530 zinc-binding protein (NCBI) 67, 82
PA4749 glmM phosphoglucosamine mutase (NCBI) 67, 341
PA4750 folP dihydropteroate synthase (NCBI) 67, 341
PA4916 PA4916 hypothetical protein (NCBI) 216, 278
PA4917 PA4917 hypothetical protein (NCBI) 216, 278
PA4918 PA4918 hypothetical protein (NCBI) 216, 278
PA4919 pncB1 nicotinate phosphoribosyltransferase (NCBI) 216, 278
PA4920 nadE NAD(+) synthetase (NCBI) 216, 278
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 PA4414
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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