Organism : Pseudomonas aeruginosa | Module List :
PA0610 prtN

transcriptional regulator PrtN (NCBI)

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0610
(Mouseover regulator name to see its description)

PA0610 is regulated by 50 influences and regulates 30 modules.
Regulators for PA0610 prtN (50)
Regulator Module Operator
PA0610 468 tf
PA0611 468 tf
PA0831 468 tf
PA0906 468 tf
PA1300 468 tf
PA1335 468 tf
PA3006 468 tf
PA3007 468 tf
PA4984 468 tf
PA5365 468 tf
PA0225 11 tf
PA0367 11 tf
PA0547 11 tf
PA0610 11 tf
PA0611 11 tf
PA0708 11 tf
PA0797 11 tf
PA0815 11 tf
PA0906 11 tf
PA0942 11 tf
PA1197 11 tf
PA1226 11 tf
PA1229 11 tf
PA1328 11 tf
PA1351 11 tf
PA1504 11 tf
PA1603 11 tf
PA1627 11 tf
PA1713 11 tf
PA2032 11 tf
PA2054 11 tf
PA2126 11 tf
PA2258 11 tf
PA2376 11 tf
PA2511 11 tf
PA2704 11 tf
PA2718 11 tf
PA2736 11 tf
PA2846 11 tf
PA3007 11 tf
PA3094 11 tf
PA3135 11 tf
PA3321 11 tf
PA3508 11 tf
PA3757 11 tf
PA4354 11 tf
PA4530 11 tf
PA4659 11 tf
PA4784 11 tf
PA5274 11 tf

Warning: PA0610 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
2858 3.60e+00 ttTccaatt.ctggA
Loader icon
2859 1.40e+03 cAtTgA.CGAC
Loader icon
3752 6.60e-19 attActgTATg.aaataCAgttAt
Loader icon
3753 7.60e-06 AcAgAaatgaCacGgaaAaCggAt
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 PA0610

Warning: No Functional annotations were found!

Module neighborhood information for PA0610

PA0610 has total of 59 gene neighbors in modules 11, 468
Gene neighbors (59)
Gene Common Name Description Module membership
PA0100 PA0100 hypothetical protein (NCBI) 11, 226
PA0101 PA0101 hypothetical protein (NCBI) 11, 34
PA0610 prtN transcriptional regulator PrtN (NCBI) 11, 468
PA0611 prtR transcriptional regulator PrtR (NCBI) 11, 468
PA0612 PA0612 hypothetical protein (NCBI) 11, 96
PA0613 PA0613 hypothetical protein (NCBI) 11, 468
PA0615 PA0615 hypothetical protein (NCBI) 11, 298
PA0616 PA0616 hypothetical protein (NCBI) 11, 298
PA0617 PA0617 probable bacteriophage protein (NCBI) 11, 298
PA0618 PA0618 probable bacteriophage protein (NCBI) 11, 298
PA0619 PA0619 probable bacteriophage protein (NCBI) 11, 298
PA0620 PA0620 probable bacteriophage protein (NCBI) 11, 298
PA0621 PA0621 hypothetical protein (NCBI) 11, 298
PA0622 PA0622 probable bacteriophage protein (NCBI) 11, 298
PA0623 PA0623 probable bacteriophage protein (NCBI) 11, 298
PA0624 PA0624 hypothetical protein (NCBI) 11, 298
PA0625 PA0625 hypothetical protein (NCBI) 11, 298
PA0626 PA0626 hypothetical protein (NCBI) 11, 298
PA0627 PA0627 hypothetical protein (NCBI) 11, 298
PA0628 PA0628 hypothetical protein (NCBI) 11, 298
PA0630 PA0630 hypothetical protein (NCBI) 11, 96
PA0640 PA0640 probable bacteriophage protein (NCBI) 11, 96
PA0642 PA0642 hypothetical protein (NCBI) 11, 188
PA0646 PA0646 hypothetical protein (NCBI) 11, 188
PA0647 PA0647 hypothetical protein (NCBI) 11, 188
PA0648 PA0648 hypothetical protein (NCBI) 11, 298
PA0670 PA0670 hypothetical protein (NCBI) 468, 542
PA0671 PA0671 hypothetical protein (NCBI) 468, 542
PA0906 PA0906 probable transcriptional regulator (NCBI) 11, 468
PA0907 PA0907 hypothetical protein (NCBI) 243, 468
PA0908 PA0908 hypothetical protein (NCBI) 11, 34
PA0909 PA0909 hypothetical protein (NCBI) 11, 34
PA0910 PA0910 hypothetical protein (NCBI) 11, 149
PA0922 PA0922 hypothetical protein (NCBI) 460, 468
PA0985 PA0985 pyocin S5 (NCBI) 11, 383
PA1150 pys2 pyocin S2 (NCBI) 11, 297
PA1151 imm2 pyocin S2 immunity protein (NCBI) 11, 297
PA1244 PA1244 hypothetical protein (NCBI) 11, 342
PA1471 PA1471 hypothetical protein (NCBI) 11, 166
PA2288 PA2288 hypothetical protein (NCBI) 460, 468
PA3006 psrA transcriptional regulator PsrA (NCBI) 460, 468
PA3007 lexA LexA repressor (NCBI) 460, 468
PA3008 PA3008 hypothetical protein (NCBI) 460, 468
PA3021 PA3021 hypothetical protein (NCBI) 11, 76
PA3413 PA3413 hypothetical protein (NCBI) 460, 468
PA3414 PA3414 hypothetical protein (NCBI) 460, 468
PA3616 recX RecA regulator RecX (NCBI) 460, 468
PA3617 recA recombinase A (NCBI) 460, 468
PA3730 PA3730 hypothetical protein (NCBI) 212, 468
PA3731 PA3731 hypothetical protein (NCBI) 376, 468
PA3732 PA3732 hypothetical protein (NCBI) 376, 468
PA3866 PA3866 pyocin protein (NCBI) 11, 212
PA4763 recN DNA repair protein RecN (NCBI) 460, 468
PA5114 PA5114 hypothetical protein (NCBI) 11, 66
PA5319 radC DNA repair protein RadC (NCBI) 11, 53
PA5522 PA5522 probable glutamine synthetase (NCBI) 243, 468
PA5523 PA5523 probable aminotransferase (NCBI) 243, 468
PA5524 PA5524 probable short-chain dehydrogenase (NCBI) 243, 468
PA5525 PA5525 probable transcriptional regulator (NCBI) 243, 468
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 PA0610
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