Organism : Pseudomonas aeruginosa | Module List :
PA4201 ddlA

D-alanine-D-alanine ligase A (NCBI)

CircVis
Functional Annotations (10)
Function System
D-alanine-D-alanine ligase and related ATP-grasp enzymes cog/ cog
ATP binding go/ molecular_function
cell wall go/ cellular_component
cytoplasm go/ cellular_component
D-alanine-D-alanine ligase activity go/ molecular_function
peptidoglycan biosynthetic process go/ biological_process
D-Alanine metabolism kegg/ kegg pathway
Peptidoglycan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
D_ala_D_alaTIGR tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4201
(Mouseover regulator name to see its description)

PA4201 is regulated by 30 influences and regulates 0 modules.
Regulators for PA4201 ddlA (30)
Regulator Module Operator
PA0289 443 tf
PA0475 443 tf
PA0533 443 tf
PA0815 443 tf
PA1315 443 tf
PA1760 443 tf
PA2047 443 tf
PA2123 443 tf
PA2259 443 tf
PA3363 443 tf
PA3864 443 tf
PA4145 443 tf
PA4703 443 tf
PA5059 443 tf
PA5437 443 tf
PA0289 469 tf
PA0939 469 tf
PA0942 469 tf
PA1290 469 tf
PA1754 469 tf
PA1760 469 tf
PA2601 469 tf
PA2718 469 tf
PA2885 469 tf
PA3322 469 tf
PA4203 469 tf
PA4270 469 tf
PA4745 469 tf
PA5105 469 tf
PA5261 469 tf

Warning: PA4201 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
3706 1.30e+02 atTCcTCgTgcAtaGgcTgGa
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3707 4.00e+04 gcGgCGgCgcggcGCttGccGaG
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3754 1.70e-16 actgT.gcAAAcatttTttTAttc
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3755 1.10e-04 AAtgcaTtT.gcATcgAtactAac
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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 PA4201

PA4201 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
D-alanine-D-alanine ligase and related ATP-grasp enzymes cog/ cog
ATP binding go/ molecular_function
cell wall go/ cellular_component
cytoplasm go/ cellular_component
D-alanine-D-alanine ligase activity go/ molecular_function
peptidoglycan biosynthetic process go/ biological_process
D-Alanine metabolism kegg/ kegg pathway
Peptidoglycan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
D_ala_D_alaTIGR tigr/ tigrfam
Module neighborhood information for PA4201

PA4201 has total of 67 gene neighbors in modules 443, 469
Gene neighbors (67)
Gene Common Name Description Module membership
PA0144 PA0144 hypothetical protein (NCBI) 291, 443
PA0289 gpuR transcriptional activator GpuR (NCBI) 443, 469
PA0458 PA0458 probable major facilitator superfamily (MFS) transporter (NCBI) 3, 443
PA0475 PA0475 probable transcriptional regulator (NCBI) 171, 443
PA0657 PA0657 probable ATPase (NCBI) 443, 523
PA0704 PA0704 amidase (NCBI) 388, 443
PA0808 PA0808 hypothetical protein (NCBI) 163, 443
PA0813 PA0813 hypothetical protein (NCBI) 243, 443
PA0815 PA0815 probable transcriptional regulator (NCBI) 243, 443
PA0939 PA0939 hypothetical protein (NCBI) 243, 469
PA0940 PA0940 hypothetical protein (NCBI) 243, 469
PA0941 PA0941 hypothetical protein (NCBI) 243, 469
PA0942 PA0942 probable transcriptional regulator (NCBI) 243, 469
PA0959 PA0959 hypothetical protein (NCBI) 205, 469
PA0960 PA0960 hypothetical protein (NCBI) 205, 469
PA0990 PA0990 hypothetical protein (NCBI) 450, 469
PA1063 PA1063 hypothetical protein (NCBI) 203, 443
PA1290 PA1290 probable transcriptional regulator (NCBI) 469, 546
PA1521 PA1521 probable guanine deaminase (NCBI) 163, 443
PA1575 PA1575 hypothetical protein (NCBI) 63, 469
PA1680 PA1680 hypothetical protein (NCBI) 206, 443
PA1762 PA1762 hypothetical protein (NCBI) 443, 489
PA1763 PA1763 hypothetical protein (NCBI) 443, 483
PA1765 PA1765 hypothetical protein (NCBI) 153, 443
PA1957 PA1957 hypothetical protein (NCBI) 313, 469
PA1994 PA1994 hypothetical protein (NCBI) 292, 469
PA1995 PA1995 hypothetical protein (NCBI) 457, 469
PA1997 PA1997 probable AMP-binding enzyme (NCBI) 294, 469
PA2121 PA2121 probable transcriptional regulator (NCBI) 252, 443
PA2123 PA2123 probable transcriptional regulator (NCBI) 443, 483
PA2601 PA2601 probable transcriptional regulator (NCBI) 346, 469
PA2602 PA2602 hypothetical protein (NCBI) 346, 469
PA2603 PA2603 probable thiosulfate sulfurtransferase (NCBI) 346, 469
PA2723 PA2723 hypothetical protein (NCBI) 203, 469
PA2814 PA2814 hypothetical protein (NCBI) 136, 469
PA2816 PA2816 hypothetical protein (NCBI) 328, 469
PA2885 PA2885 probable transcriptional regulator (NCBI) 469, 541
PA3343 PA3343 hypothetical protein (NCBI) 203, 443
PA3425 PA3425 hypothetical protein (NCBI) 443, 483
PA3426 PA3426 enoyl-CoA hydratase (NCBI) 28, 443
PA3715 PA3715 hypothetical protein (NCBI) 101, 443
PA3787 PA3787 hypothetical protein (NCBI) 432, 469
PA3847 PA3847 hypothetical protein (NCBI) 397, 443
PA3856 PA3856 hypothetical protein (NCBI) 378, 443
PA3943 PA3943 hypothetical protein (NCBI) 443, 546
PA3944 PA3944 hypothetical protein (NCBI) 378, 443
PA4147 acoR transcriptional regulator AcoR (NCBI) 236, 443
PA4199 PA4199 probable acyl-CoA dehydrogenase (NCBI) 3, 443
PA4201 ddlA D-alanine-D-alanine ligase A (NCBI) 443, 469
PA4202 PA4202 hypothetical protein (NCBI) 346, 469
PA4203 PA4203 probable transcriptional regulator (NCBI) 346, 469
PA4282 PA4282 probable exonuclease (NCBI) 443, 523
PA4330 PA4330 probable enoyl-CoA hydratase/isomerase (NCBI) 192, 443
PA4331 PA4331 hypothetical protein (NCBI) 62, 443
PA4332 PA4332 hypothetical protein (NCBI) 62, 443
PA4335 PA4335 hypothetical protein (NCBI) 443, 462
PA4397 panE 2-dehydropantoate 2-reductase (NCBI) 10, 443
PA4833 PA4833 hypothetical protein (NCBI) 361, 469
PA4875 PA4875 hypothetical protein (NCBI) 397, 443
PA4983 PA4983 probable two-component response regulator (NCBI) 245, 469
PA5115 PA5115 hypothetical protein (NCBI) 469, 483
PA5272 cyaA adenylate cyclase (NCBI) 127, 443
PA5422 PA5422 hypothetical protein (NCBI) 397, 469
PA5432 PA5432 probable acetyltransferase (NCBI) 469, 497
PA5439 PA5439 probable glucose-6-phosphate dehydrogenase (NCBI) 190, 469
PA5447 wbpZ glycosyltransferase WbpZ (NCBI) 3, 469
PA5514 poxB probable beta-lactamase (NCBI) 241, 469
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 PA4201
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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