Organism : Pseudomonas aeruginosa | Module List :
PA0764 mucB

negative regulator for alginate biosynthesis MucB (NCBI)

CircVis
Functional Annotations (1)
Function System
Negative regulator of sigma E activity cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0764
(Mouseover regulator name to see its description)

PA0764 is regulated by 43 influences and regulates 14 modules.
Regulators for PA0764 mucB (43)
Regulator Module Operator
PA0167 273 tf
PA0376 273 tf
PA0652 273 tf
PA0762 273 tf
PA0763 273 tf
PA0764 273 tf
PA0765 273 tf
PA1099 273 tf
PA1544 273 tf
PA1570 273 tf
PA1607 273 tf
PA1663 273 tf
PA1754 273 tf
PA2849 273 tf
PA2957 273 tf
PA3006 273 tf
PA3845 273 tf
PA3921 273 tf
PA3973 273 tf
PA4755 273 tf
PA4984 273 tf
PA5179 273 tf
PA5253 273 tf
PA5308 273 tf
PA5344 273 tf
PA5483 273 tf
PA0376 551 tf
PA0762 551 tf
PA0763 551 tf
PA0765 551 tf
PA0784 551 tf
PA1097 551 tf
PA1520 551 tf
PA2016 551 tf
PA2047 551 tf
PA2577 551 tf
PA2586 551 tf
PA2622 551 tf
PA2737 551 tf
PA4315 551 tf
PA4493 551 tf
PA5253 551 tf
PA5483 551 tf

Warning: PA0764 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
3374 6.00e-01 GAAcTctccCgaga
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3375 1.30e+03 GAatTaCtGAA
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3914 2.00e+00 tTgttagaa.ggacaatTct
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3915 1.50e+03 GAAtTcagAcTgaa.AaaT
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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 PA0764

PA0764 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Negative regulator of sigma E activity cog/ cog
Module neighborhood information for PA0764

PA0764 has total of 36 gene neighbors in modules 273, 551
Gene neighbors (36)
Gene Common Name Description Module membership
PA0102 PA0102 probable carbonic anhydrase (NCBI) 95, 273
PA0309 PA0309 hypothetical protein (NCBI) 221, 551
PA0555 fda fructose-bisphosphate aldolase (NCBI) 237, 273
PA0655 PA0655 hypothetical protein (NCBI) 452, 551
PA0764 mucB negative regulator for alginate biosynthesis MucB (NCBI) 273, 551
PA0765 mucC positive regulator for alginate biosynthesis MucC (NCBI) 273, 551
PA0766 mucD serine protease MucD precursor (NCBI) 273, 551
PA0784 PA0784 probable transcriptional regulator (NCBI) 523, 551
PA0833 PA0833 hypothetical protein (NCBI) 147, 273
PA0856 PA0856 hypothetical protein (NCBI) 6, 273
PA0943 PA0943 hypothetical protein (NCBI) 237, 273
PA1048 PA1048 probable outer membrane protein precursor (NCBI) 95, 273
PA1097 fleQ transcriptional regulator FleQ (NCBI) 437, 551
PA1198 PA1198 hypothetical protein (NCBI) 68, 551
PA1199 PA1199 probable lipoprotein (NCBI) 68, 551
PA1200 PA1200 hypothetical protein (NCBI) 68, 551
PA1376 aceK bifunctional isocitrate dehydrogenase kinase/phosphatase protein (NCBI) 513, 551
PA1642 selD selenophosphate synthetase (NCBI) 224, 551
PA1643 PA1643 hypothetical protein (NCBI) 224, 551
PA1772 PA1772 ribonuclease activity regulator protein RraA (NCBI) 342, 551
PA2023 galU UTP--glucose-1-phosphate uridylyltransferase (NCBI) 6, 273
PA2707 PA2707 hypothetical protein (NCBI) 436, 551
PA2796 tal transaldolase (NCBI) 95, 273
PA2820 PA2820 hypothetical protein (NCBI) 397, 551
PA2821 PA2821 probable glutathione S-transferase (NCBI) 397, 551
PA3031 PA3031 hypothetical protein (NCBI) 273, 525
PA3262 PA3262 probable peptidyl-prolyl cis-trans isomerase, FkbP-type (NCBI) 223, 273
PA3857 pcs phosphatidylcholine synthase (NCBI) 95, 273
PA4315 mvaT transcriptional regulator MvaT, P16 subunit (NCBI) 525, 551
PA4441 PA4441 hypothetical protein (NCBI) 237, 273
PA4495 PA4495 hypothetical protein (NCBI) 525, 551
PA4793 PA4793 hypothetical protein (NCBI) 513, 551
PA4972 PA4972 hypothetical protein (NCBI) 273, 551
PA5078 PA5078 hypothetical protein (NCBI) 237, 273
PA5191 PA5191 hypothetical protein (NCBI) 159, 551
PA5227 PA5227 hypothetical protein (NCBI) 499, 551
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 PA0764
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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