Organism : Pseudomonas aeruginosa | Module List :
PA1949 rbsR

ribose operon repressor RbsR (NCBI)

CircVis
Functional Annotations (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA1949
(Mouseover regulator name to see its description)

PA1949 is regulated by 27 influences and regulates 23 modules.
Regulators for PA1949 rbsR (27)
Regulator Module Operator
PA0376 88 tf
PA0436 88 tf
PA0942 88 tf
PA1949 88 tf
PA2622 88 tf
PA3124 88 tf
PA3458 88 tf
PA4853 88 tf
PA5253 88 tf
PA5255 88 tf
PA5261 88 tf
PA5288 88 tf
PA0179 248 tf
PA0815 248 tf
PA1309 248 tf
PA1949 248 tf
PA2220 248 tf
PA2897 248 tf
PA4021 248 tf
PA4182 248 tf
PA4238 248 tf
PA4499 248 tf
PA4703 248 tf
PA4787 248 tf
PA5255 248 tf
PA5261 248 tf
PA5288 248 tf

Warning: PA1949 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
3008 1.70e-05 aAtCcgga.AaaTTC.gccaAt
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3009 1.70e-04 AGggtTTTtCCcaGcctTcgcCgT
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3324 1.10e-02 Ag.aTaGcCaG
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3325 2.30e+01 TgTGCCtGtcgaAGGagC.gAC
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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 PA1949

PA1949 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for PA1949

PA1949 has total of 43 gene neighbors in modules 88, 248
Gene neighbors (43)
Gene Common Name Description Module membership
PA0250 PA0250 hypothetical protein (NCBI) 248, 397
PA0312 PA0312 hypothetical protein (NCBI) 70, 248
PA0332 PA0332 hypothetical protein (NCBI) 248, 547
PA0436 PA0436 probable transcriptional regulator (NCBI) 57, 88
PA0962 PA0962 probable dna-binding stress protein (NCBI) 88, 238
PA1053 PA1053 hypothetical protein (NCBI) 88, 376
PA1377 PA1377 hypothetical protein (NCBI) 248, 513
PA1833 PA1833 probable oxidoreductase (NCBI) 88, 405
PA1946 rbsB binding protein component precursor of ABC ribose transporter (NCBI) 88, 248
PA1947 rbsA ribose transport protein RbsA (NCBI) 88, 248
PA1948 rbsC membrane protein component of ABC ribose transporter (NCBI) 88, 248
PA1949 rbsR ribose operon repressor RbsR (NCBI) 88, 248
PA1950 rbsK ribokinase (NCBI) 88, 248
PA2560 PA2560 hypothetical protein (NCBI) 151, 248
PA2738 ihfA integration host factor subunit alpha (NCBI) 88, 513
PA2799 PA2799 hypothetical protein (NCBI) 209, 248
PA3259 PA3259 hypothetical protein (NCBI) 88, 457
PA3260 PA3260 probable transcriptional regulator (NCBI) 51, 248
PA3261 PA3261 hypothetical protein (NCBI) 248, 457
PA3354 PA3354 hypothetical protein (NCBI) 248, 457
PA3529 PA3529 probable peroxidase (NCBI) 88, 381
PA3536 PA3536 hypothetical protein (NCBI) 88, 139
PA3740 PA3740 hypothetical protein (NCBI) 159, 248
PA3796 PA3796 hypothetical protein (NCBI) 248, 547
PA3797 PA3797 hypothetical protein (NCBI) 3, 88
PA3844 PA3844 hypothetical protein (NCBI) 88, 190
PA3846 PA3846 hypothetical protein (NCBI) 63, 248
PA4012 PA4012 hypothetical protein (NCBI) 209, 248
PA4021 PA4021 probable transcriptional regulator (NCBI) 163, 248
PA4078 PA4078 probable nonribosomal peptide synthetase (NCBI) 88, 176
PA4079 PA4079 short chain dehydrogenase (NCBI) 88, 176
PA4111 PA4111 hypothetical protein (NCBI) 248, 457
PA4326 PA4326 hypothetical protein (NCBI) 248, 496
PA4511 PA4511 hypothetical protein (NCBI) 53, 88
PA4726 cbrB two-component response regulator CbrB (NCBI) 51, 88
PA4780 PA4780 hypothetical protein (NCBI) 245, 248
PA4787 PA4787 probable transcriptional regulator (NCBI) 70, 248
PA5255 algQ Alginate regulatory protein AlgQ (NCBI) 51, 248
PA5258 PA5258 hypothetical protein (NCBI) 88, 457
PA5305 PA5305 hypothetical protein (NCBI) 87, 88
PA5306 PA5306 hypothetical protein (NCBI) 57, 88
PA5307 PA5307 hypothetical protein (NCBI) 88, 345
PA5308 lrp leucine-responsive regulatory protein (NCBI) 88, 541
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 PA1949
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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