Organism : Pseudomonas aeruginosa | Module List :
PA4042 xseB

exodeoxyribonuclease VII small subunit (NCBI)

CircVis
Functional Annotations (6)
Function System
Exonuclease VII small subunit cog/ cog
DNA catabolic process go/ biological_process
exodeoxyribonuclease VII activity go/ molecular_function
exodeoxyribonuclease VII complex go/ cellular_component
Mismatch repair kegg/ kegg pathway
xseB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4042
(Mouseover regulator name to see its description)

PA4042 is regulated by 36 influences and regulates 0 modules.
Regulators for PA4042 xseB (36)
Regulator Module Operator
PA0167 178 tf
PA0564 178 tf
PA0961 178 tf
PA1015 178 tf
PA1526 178 tf
PA2115 178 tf
PA2246 178 tf
PA2957 178 tf
PA3027 178 tf
PA3322 178 tf
PA3604 178 tf
PA3804 178 tf
PA4275 178 tf
PA4451 178 tf
PA4764 178 tf
PA5105 178 tf
PA5274 178 tf
PA5344 178 tf
PA0167 123 tf
PA0393 123 tf
PA0477 123 tf
PA1128 123 tf
PA1300 123 tf
PA1422 123 tf
PA2093 123 tf
PA2885 123 tf
PA2896 123 tf
PA2957 123 tf
PA3215 123 tf
PA3604 123 tf
PA3699 123 tf
PA4451 123 tf
PA4703 123 tf
PA4745 123 tf
PA4755 123 tf
PA5344 123 tf

Warning: PA4042 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
3076 3.80e+02 cgG.a.a.aatgcgCGgg..TTt
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3077 2.60e+01 cggC.TGCaatGaAt
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3184 6.80e+00 gtccgccaccgt.GCAatGgc
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3185 3.70e+02 gGtcATGGCaTGgaGCGAga
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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 PA4042

PA4042 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Exonuclease VII small subunit cog/ cog
DNA catabolic process go/ biological_process
exodeoxyribonuclease VII activity go/ molecular_function
exodeoxyribonuclease VII complex go/ cellular_component
Mismatch repair kegg/ kegg pathway
xseB tigr/ tigrfam
Module neighborhood information for PA4042

PA4042 has total of 41 gene neighbors in modules 123, 178
Gene neighbors (41)
Gene Common Name Description Module membership
PA0115 PA0115 hypothetical protein (NCBI) 170, 178
PA0357 mutM formamidopyrimidine-DNA glycosylase (NCBI) 123, 170
PA0363 coaD phosphopantetheine adenylyltransferase (NCBI) 72, 178
PA0750 ung uracil-DNA glycosylase (NCBI) 123, 384
PA0759 PA0759 hypothetical protein (NCBI) 123, 338
PA0946 PA0946 hypothetical protein (NCBI) 123, 220
PA1064 PA1064 hypothetical protein (NCBI) 123, 170
PA1532 dnaX DNA polymerase III subunits gamma and tau (NCBI) 94, 178
PA1534 recR recombination protein RecR (NCBI) 123, 478
PA1613 PA1613 hypothetical protein (NCBI) 123, 268
PA1674 folE2 GTP cyclohydrolase I precursor (NCBI) 122, 178
PA1734 PA1734 hypothetical protein (NCBI) 178, 266
PA1735 PA1735 hypothetical protein (NCBI) 178, 266
PA2765 PA2765 hypothetical protein (NCBI) 123, 306
PA2957 PA2957 probable transcriptional regulator (NCBI) 178, 354
PA3117 asd aspartate-semialdehyde dehydrogenase (NCBI) 123, 281
PA3131 PA3131 probable aldolase (NCBI) 178, 229
PA3243 minC septum formation inhibitor (NCBI) 178, 271
PA3245 minE cell division topological specificity factor MinE (NCBI) 178, 271
PA3639 accA acetyl-CoA carboxylase alpha subunit (NCBI) 77, 178
PA3686 adk adenylate kinase (NCBI) 123, 286
PA3699 PA3699 probable transcriptional regulator (NCBI) 7, 123
PA3736 hom homoserine dehydrogenase (NCBI) 123, 260
PA3798 PA3798 putative aminotransferase (NCBI) 123, 170
PA3822 yajC preprotein translocase subunit YajC (NCBI) 178, 271
PA4035 PA4035 hypothetical protein (NCBI) 178, 315
PA4042 xseB exodeoxyribonuclease VII small subunit (NCBI) 123, 178
PA4043 ispA geranyltranstransferase (NCBI) 123, 178
PA4340 PA4340 hypothetical protein (NCBI) 70, 123
PA4381 PA4381 probable two-component response regulator (NCBI) 178, 315
PA4389 speA arginine decarboxylase (ADC) (NCBI) 123, 541
PA4440 PA4440 hypothetical protein (NCBI) 123, 315
PA4456 PA4456 probable ATP-binding component of ABC transporter (NCBI) 178, 474
PA4632 PA4632 hypothetical protein (NCBI) 55, 123
PA4676 PA4676 probable carbonic anhydrase (NCBI) 123, 477
PA5080 PA5080 prolyl aminopeptidase (NCBI) 123, 462
PA5184 PA5184 chorismate mutase (NCBI) 178, 251
PA5237 PA5237 hypothetical protein (NCBI) 123, 281
PA5241 ppx exopolyphosphatase (NCBI) 123, 499
PA5274 rnk nucleoside diphosphate kinase regulator (NCBI) 77, 178
PA5344 PA5344 probable transcriptional regulator (NCBI) 123, 540
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 PA4042
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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