Organism : Pseudomonas aeruginosa | Module List :
PA3563 fruR

fructose transport system repressor FruR (NCBI)

CircVis
Functional Annotations (6)
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
response to fructose stimulus go/ biological_process
fruct_sucro_rep tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3563
(Mouseover regulator name to see its description)

PA3563 is regulated by 27 influences and regulates 27 modules.
Regulators for PA3563 fruR (27)
Regulator Module Operator
PA0576 263 tf
PA0652 263 tf
PA1504 263 tf
PA3002 263 tf
PA3563 263 tf
PA3804 263 tf
PA4057 263 tf
PA4270 263 tf
PA4451 263 tf
PA4462 263 tf
PA4755 263 tf
PA4853 263 tf
PA5166 263 tf
PA5337 263 tf
PA5344 263 tf
PA0893 493 tf
PA0961 493 tf
PA1504 493 tf
PA2423 493 tf
PA3002 493 tf
PA3563 493 tf
PA4547 493 tf
PA5105 493 tf
PA5239 493 tf
PA5274 493 tf
PA5344 493 tf
PA5550 493 tf

Warning: PA3563 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
3354 1.10e+02 cTTttCcgGta
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3355 2.50e+03 tcg.ttCAGcgtacg
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3800 9.50e+03 AcCttgAaCG
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3801 6.60e+04 ACGAAGCaGAAA
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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 PA3563

PA3563 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
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
response to fructose stimulus go/ biological_process
fruct_sucro_rep tigr/ tigrfam
Module neighborhood information for PA3563

PA3563 has total of 34 gene neighbors in modules 263, 493
Gene neighbors (34)
Gene Common Name Description Module membership
PA0292 aguA agmatine deiminase (NCBI) 62, 263
PA0341 lgt prolipoprotein diacylglyceryl transferase (NCBI) 78, 493
PA0405 PA0405 hypothetical protein (NCBI) 86, 263
PA0569 PA0569 hypothetical protein (NCBI) 60, 493
PA0666 PA0666 hypothetical protein (NCBI) 174, 263
PA0667 PA0667 hypothetical protein (NCBI) 263, 435
PA0705 PA0705 probable glycosyl transferase (NCBI) 59, 263
PA0925 PA0925 hypothetical protein (NCBI) 493, 517
PA1105 fliJ flagellar protein (NCBI) 60, 493
PA1861 modC molybdenum transport protein ModC (NCBI) 31, 263
PA1862 modB molybdenum transport protein ModB (NCBI) 220, 263
PA1863 modA molybdate-binding periplasmic protein precursor ModA (NCBI) 9, 263
PA2625 PA2625 hypothetical protein (NCBI) 493, 511
PA2831 PA2831 hypothetical protein (NCBI) 100, 263
PA2947 PA2947 hypothetical protein (NCBI) 384, 493
PA2948 cobM precorrin-3 methylase (NCBI) 49, 493
PA3077 PA3077 probable two-component response regulator (NCBI) 20, 493
PA3196 PA3196 hypothetical protein (NCBI) 187, 493
PA3217 cyaB CyaB (NCBI) 478, 493
PA3301 PA3301 hypothetical protein (NCBI) 42, 263
PA3437 PA3437 short chain dehydrogenase (NCBI) 263, 511
PA3563 fruR fructose transport system repressor FruR (NCBI) 263, 493
PA3612 PA3612 hypothetical protein (NCBI) 341, 493
PA3683 PA3683 hypothetical protein (NCBI) 253, 493
PA3747 PA3747 hypothetical protein (NCBI) 315, 493
PA3748 PA3748 hypothetical protein (NCBI) 315, 493
PA3849 ndpA nucleoid-associated protein NdpA (NCBI) 59, 263
PA3992 PA3992 hypothetical protein (NCBI) 384, 493
PA4423 PA4423 hypothetical protein (NCBI) 42, 263
PA4424 PA4424 hypothetical protein (NCBI) 94, 263
PA4689 PA4689 hypothetical protein (NCBI) 420, 493
PA5135 PA5135 hypothetical protein (NCBI) 480, 493
PA5263 argH argininosuccinate lyase (NCBI) 198, 263
PA5493 polA DNA polymerase I (NCBI) 174, 263
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 PA3563
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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