Organism : Pseudomonas aeruginosa | Module List :
PA5332 crc

catabolite repression control protein (NCBI)

CircVis
Functional Annotations (5)
Function System
Exonuclease III cog/ cog
DNA repair go/ biological_process
exodeoxyribonuclease III activity go/ molecular_function
Base excision repair kegg/ kegg pathway
xth tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA5332
(Mouseover regulator name to see its description)

PA5332 is regulated by 43 influences and regulates 0 modules.
Regulators for PA5332 crc (43)
Regulator Module Operator
PA0424 352 tf
PA0456 352 tf
PA0610 352 tf
PA0905 352 tf
PA1335 352 tf
PA1520 352 tf
PA1853 352 tf
PA2047 352 tf
PA2076 352 tf
PA2692 352 tf
PA2885 352 tf
PA4052 352 tf
PA4451 352 tf
PA4600 352 tf
PA4745 352 tf
PA4764 352 tf
PA4853 352 tf
PA5337 352 tf
PA5438 352 tf
PA0125 41 tf
PA0306 41 tf
PA0424 41 tf
PA0455 41 tf
PA0456 41 tf
PA0961 41 tf
PA1269 41 tf
PA1455 41 tf
PA1504 41 tf
PA1864 41 tf
PA2123 41 tf
PA2534 41 tf
PA2586 41 tf
PA2692 41 tf
PA3034 41 tf
PA3266 41 tf
PA3285 41 tf
PA3341 41 tf
PA3364 41 tf
PA4451 41 tf
PA4764 41 tf
PA5337 41 tf
PA5356 41 tf
PA5525 41 tf

Warning: PA5332 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
2914 2.10e-01 tA.AaTgcccGgttt
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2915 1.40e+01 Aat.AcAc..aGcCg.atgAAata
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3528 5.20e+01 ATTaTgGgGGccatt
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3529 4.40e+00 ATGAATTTAGCTAAACCGTTTGA
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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 PA5332

PA5332 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Exonuclease III cog/ cog
DNA repair go/ biological_process
exodeoxyribonuclease III activity go/ molecular_function
Base excision repair kegg/ kegg pathway
xth tigr/ tigrfam
Module neighborhood information for PA5332

PA5332 has total of 27 gene neighbors in modules 41, 352
Gene neighbors (27)
Gene Common Name Description Module membership
PA0837 slyD peptidyl-prolyl cis-trans isomerase SlyD (NCBI) 6, 41
PA1117 PA1117 hypothetical protein (NCBI) 41, 296
PA1160 PA1160 hypothetical protein (NCBI) 41, 281
PA1440 PA1440 hypothetical protein (NCBI) 41, 251
PA1564 PA1564 hypothetical protein (NCBI) 41, 261
PA1741 PA1741 hypothetical protein (NCBI) 41, 455
PA1996 ppiC1 peptidyl-prolyl cis-trans isomerase C1 (NCBI) 41, 338
PA2045 PA2045 hypothetical protein (NCBI) 41, 100
PA3009 PA3009 hypothetical protein (NCBI) 41, 224
PA3034 PA3034 probable transcriptional regulator (NCBI) 41, 220
PA3109 PA3109 hypothetical protein (NCBI) 41, 126
PA3285 PA3285 probable sigma-70 factor, ECF subfamily (NCBI) 41, 195
PA3341 PA3341 probable transcriptional regulator (NCBI) 41, 224
PA3742 rplS 50S ribosomal protein L19 (NCBI) 352, 506
PA3755 PA3755 hypothetical protein (NCBI) 41, 57
PA3756 PA3756 hypothetical protein (NCBI) 41, 57
PA4007 proA gamma-glutamyl phosphate reductase (NCBI) 352, 440
PA4565 proB gamma-glutamyl kinase (NCBI) 224, 352
PA4566 obg GTP-binding protein Obg (NCBI) 352, 424
PA4567 rpmA 50S ribosomal protein L27 (NCBI) 210, 352
PA4963 PA4963 hypothetical protein (NCBI) 41, 251
PA5062 PA5062 hypothetical protein (NCBI) 41, 170
PA5276 lppL Lipopeptide LppL precursor (NCBI) 41, 228
PA5330 PA5330 hypothetical protein (NCBI) 212, 352
PA5331 pyrE orotate phosphoribosyltransferase (NCBI) 41, 352
PA5332 crc catabolite repression control protein (NCBI) 41, 352
PA5337 rpoZ DNA-directed RNA polymerase omega subunit (NCBI) 223, 352
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 PA5332
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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