Organism : Pseudomonas aeruginosa | Module List :
PA3011 topA

DNA topoisomerase I (NCBI)

CircVis
Functional Annotations (8)
Function System
Topoisomerase IA cog/ cog
DNA topoisomerase type I activity go/ molecular_function
DNA topoisomerase (ATP-hydrolyzing) activity go/ molecular_function
chromosome go/ cellular_component
DNA topological change go/ biological_process
DNA unwinding involved in replication go/ biological_process
DNA modification go/ biological_process
topA_bact tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3011
(Mouseover regulator name to see its description)

PA3011 is regulated by 34 influences and regulates 0 modules.
Regulators for PA3011 topA (34)
Regulator Module Operator
PA0890 259 tf
PA0893 259 tf
PA1159 259 tf
PA1467 259 tf
PA1504 259 tf
PA3002 259 tf
PA3804 259 tf
PA4269 259 tf
PA4270 259 tf
PA4354 259 tf
PA4462 259 tf
PA4745 259 tf
PA4755 259 tf
PA4853 259 tf
PA5562 259 tf
PA0275 421 tf
PA0393 421 tf
PA0763 421 tf
PA0893 421 tf
PA0961 421 tf
PA1109 421 tf
PA1754 421 tf
PA1912 421 tf
PA2766 421 tf
PA3002 421 tf
PA3094 421 tf
PA3583 421 tf
PA3778 421 tf
PA3804 421 tf
PA4109 421 tf
PA4269 421 tf
PA4270 421 tf
PA5550 421 tf
PA5562 421 tf

Warning: PA3011 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
3346 4.80e+01 TTtTTAt
Loader icon
3347 9.50e+02 ATtTtTtGT
Loader icon
3664 4.40e+02 TcCcttATtaT
Loader icon
3665 6.20e+02 GCtTTaTaCa
Loader icon
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 PA3011

PA3011 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Topoisomerase IA cog/ cog
DNA topoisomerase type I activity go/ molecular_function
DNA topoisomerase (ATP-hydrolyzing) activity go/ molecular_function
chromosome go/ cellular_component
DNA topological change go/ biological_process
DNA unwinding involved in replication go/ biological_process
DNA modification go/ biological_process
topA_bact tigr/ tigrfam
Module neighborhood information for PA3011

PA3011 has total of 29 gene neighbors in modules 259, 421
Gene neighbors (29)
Gene Common Name Description Module membership
PA0771 era GTP-binding protein Era (NCBI) 129, 259
PA1478 PA1478 hypothetical protein (NCBI) 43, 421
PA1479 ccmE cytochrome C-type biogenesis protein CcmE (NCBI) 403, 421
PA1480 ccmF cytochrome C-type biogenesis protein CcmF (NCBI) 403, 421
PA1481 ccmG cytochrome C biogenesis protein CcmG (NCBI) 403, 421
PA1483 cycH cytochrome c-type biogenesis protein (NCBI) 43, 421
PA1552 PA1552 probable cytochrome c (NCBI) 259, 350
PA1553 PA1553 probable cytochrome c oxidase subunit (NCBI) 259, 350
PA1554 PA1554 probable cytochrome oxidase subunit (cbb3-type) (NCBI) 19, 259
PA3011 topA DNA topoisomerase I (NCBI) 259, 421
PA3491 PA3491 electron transport complex protein RnfC (NCBI) 43, 421
PA3493 PA3493 hypothetical protein (NCBI) 396, 421
PA3494 PA3494 NADH-ubiquinone oxidoreductase (NCBI) 396, 421
PA3495 nth endonuclease III (NCBI) 43, 421
PA3644 lpxA UDP-N-acetylglucosamine acyltransferase (NCBI) 256, 259
PA3646 lpxD UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase (NCBI) 259, 262
PA3647 PA3647 probable outer membrane protein precursor (NCBI) 75, 259
PA3648 PA3648 probable outer membrane protein precursor (NCBI) 259, 262
PA3653 frr ribosome releasing factor (NCBI) 259, 453
PA3658 glnD PII uridylyl-transferase (NCBI) 396, 421
PA3659 PA3659 hypothetical protein (NCBI) 396, 421
PA4269 rpoC DNA-directed RNA polymerase beta' subunit (NCBI) 150, 259
PA4270 rpoB DNA-directed RNA polymerase beta subunit (NCBI) 150, 259
PA4740 pnp polyribonucleotide nucleotidyltransferase (NCBI) 113, 259
PA5006 PA5006 hypothetical protein (NCBI) 204, 421
PA5007 PA5007 hypothetical protein (NCBI) 204, 421
PA5008 PA5008 hypothetical protein (NCBI) 403, 421
PA5010 waaG UDP-glucose:(heptosyl) LPS alpha 1,3-glucosyltransferase WaaG (NCBI) 204, 421
PA5011 waaC heptosyltransferase I (NCBI) 204, 421
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 PA3011
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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