Organism : Pseudomonas aeruginosa | Module List :
PA1461 motD

flagellar motor protein (NCBI)

CircVis
Functional Annotations (4)
Function System
Flagellar motor protein cog/ cog
cell outer membrane go/ cellular_component
Bacterial chemotaxis kegg/ kegg pathway
Flagellar assembly kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA1461
(Mouseover regulator name to see its description)

PA1461 is regulated by 46 influences and regulates 0 modules.
Regulators for PA1461 motD (46)
Regulator Module Operator
PA0034 522 tf
PA0179 522 tf
PA0225 522 tf
PA0289 522 tf
PA0491 522 tf
PA0707 522 tf
PA0893 522 tf
PA1097 522 tf
PA1229 522 tf
PA1430 522 tf
PA1526 522 tf
PA2586 522 tf
PA2588 522 tf
PA2879 522 tf
PA3002 522 tf
PA3599 522 tf
PA3689 522 tf
PA4547 522 tf
PA5344 522 tf
PA0121 129 tf
PA0133 129 tf
PA0479 129 tf
PA0707 129 tf
PA0797 129 tf
PA0828 129 tf
PA0890 129 tf
PA0893 129 tf
PA0942 129 tf
PA1097 129 tf
PA1099 129 tf
PA1283 129 tf
PA1455 129 tf
PA1526 129 tf
PA1776 129 tf
PA2115 129 tf
PA2316 129 tf
PA2510 129 tf
PA2586 129 tf
PA3879 129 tf
PA3973 129 tf
PA4052 129 tf
PA4057 129 tf
PA4275 129 tf
PA4547 129 tf
PA5125 129 tf
PA5301 129 tf

Warning: PA1461 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
3088 5.30e+02 caaAaAAtccgcgGC
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3089 2.00e+04 TaTAAT
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3858 6.10e+01 GtAAcagcctgt.TTacaCttcCC
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3859 4.50e+03 TGGATAAaA
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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 PA1461

PA1461 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Flagellar motor protein cog/ cog
cell outer membrane go/ cellular_component
Bacterial chemotaxis kegg/ kegg pathway
Flagellar assembly kegg/ kegg pathway
Module neighborhood information for PA1461

PA1461 has total of 38 gene neighbors in modules 129, 522
Gene neighbors (38)
Gene Common Name Description Module membership
PA0387 PA0387 putative deoxyribonucleotide triphosphate pyrophosphatase (NCBI) 129, 464
PA0388 PA0388 hypothetical protein (NCBI) 129, 464
PA0598 PA0598 hypothetical protein (NCBI) 452, 522
PA0769 PA0769 hypothetical protein (NCBI) 129, 202
PA0770 rnc ribonuclease III (NCBI) 129, 202
PA0771 era GTP-binding protein Era (NCBI) 129, 259
PA1103 PA1103 flagellar assembly protein (NCBI) 129, 242
PA1104 fliI flagellum-specific ATP synthase (NCBI) 129, 296
PA1442 PA1442 flagellar protein (NCBI) 129, 296
PA1443 fliM flagellar motor switch protein (NCBI) 129, 296
PA1444 fliN flagellar motor switch protein (NCBI) 129, 296
PA1445 fliO flagellar protein FliO (NCBI) 129, 296
PA1446 fliP flagellar biosynthesis protein (NCBI) 129, 296
PA1447 fliQ flagellar biosynthesis protein (NCBI) 129, 296
PA1456 cheY two-component response regulator CheY (NCBI) 129, 242
PA1457 cheZ chemotaxis protein CheZ (NCBI) 129, 242
PA1460 motC flagellar motor protein (NCBI) 129, 522
PA1461 motD flagellar motor protein (NCBI) 129, 522
PA1462 PA1462 probable plasmid partitioning protein (NCBI) 129, 242
PA1465 PA1465 hypothetical protein (NCBI) 129, 242
PA1473 PA1473 hypothetical protein (NCBI) 3, 522
PA1526 PA1526 probable transcriptional regulator (NCBI) 62, 522
PA1527 PA1527 hypothetical protein (NCBI) 202, 522
PA2231 pslA probable glycosyl transferase (NCBI) 300, 522
PA2232 pslB probable phosphomannose isomerase/GDP-mannose pyrophosphorylase (NCBI) 300, 522
PA2233 pslC probable glycosyl transferase (NCBI) 300, 522
PA2234 pslD probable exopolysaccharide transporter (NCBI) 300, 522
PA2235 pslE hypothetical protein (NCBI) 300, 522
PA2236 pslF hypothetical protein (NCBI) 300, 522
PA2237 pslG probable glycosyl hydrolase (NCBI) 300, 522
PA2238 pslH hypothetical protein (NCBI) 300, 522
PA2239 pslI probable transferase (NCBI) 300, 522
PA2240 pslJ hypothetical protein (NCBI) 300, 522
PA2241 pslK hypothetical protein (NCBI) 289, 522
PA2242 pslL hypothetical protein (NCBI) 300, 522
PA2631 PA2631 probable acetyl transferase (NCBI) 129, 464
PA3020 PA3020 probable soluble lytic transglycosylase (NCBI) 62, 522
PA5492 PA5492 GTP-binding protein (NCBI) 129, 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 PA1461
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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