Organism : Pseudomonas aeruginosa | Module List :
PA3344 recQ

ATP-dependent DNA helicase RecQ (NCBI)

CircVis
Functional Annotations (9)
Function System
Superfamily II DNA helicase cog/ cog
nucleic acid binding go/ molecular_function
ATP-dependent DNA helicase activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
DNA recombination go/ biological_process
SOS response go/ biological_process
RNA degradation kegg/ kegg pathway
recQ_fam tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3344
(Mouseover regulator name to see its description)

PA3344 is regulated by 34 influences and regulates 0 modules.
Regulators for PA3344 recQ (34)
Regulator Module Operator
PA0236 544 tf
PA1397 544 tf
PA1663 544 tf
PA1853 544 tf
PA2076 544 tf
PA2877 544 tf
PA3002 544 tf
PA3574 544 tf
PA3604 544 tf
PA3804 544 tf
PA4052 544 tf
PA4057 544 tf
PA4275 544 tf
PA4451 544 tf
PA4703 544 tf
PA4745 544 tf
PA4890 544 tf
PA5344 544 tf
PA0191 478 tf
PA0831 478 tf
PA0893 478 tf
PA1153 478 tf
PA1776 478 tf
PA1853 478 tf
PA2802 478 tf
PA2859 478 tf
PA3002 478 tf
PA3322 478 tf
PA3804 478 tf
PA3864 478 tf
PA4080 478 tf
PA4269 478 tf
PA5239 478 tf
PA5344 478 tf

Warning: PA3344 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
3772 1.40e-02 AtgaC.aGGGcgaGCcAaAtGg
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3773 3.40e-06 aTggg..AaATTccGcta.catt
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3900 1.60e+00 tgGgaAaaagggCGggcagTgta
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3901 7.60e-02 TaTAaTGCtgcgCcTttttta
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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 PA3344

PA3344 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Superfamily II DNA helicase cog/ cog
nucleic acid binding go/ molecular_function
ATP-dependent DNA helicase activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
DNA recombination go/ biological_process
SOS response go/ biological_process
RNA degradation kegg/ kegg pathway
recQ_fam tigr/ tigrfam
Module neighborhood information for PA3344

PA3344 has total of 40 gene neighbors in modules 478, 544
Gene neighbors (40)
Gene Common Name Description Module membership
PA0375 ftsX cell division protein FtsX (NCBI) 18, 478
PA0662 argC N-acetyl-gamma-glutamyl-phosphate reductase (NCBI) 72, 544
PA0663 PA0663 hypothetical protein (NCBI) 72, 544
PA0664 PA0664 hypothetical protein (NCBI) 72, 544
PA1294 rnd ribonuclease D (NCBI) 306, 544
PA1295 PA1295 hypothetical protein (NCBI) 59, 544
PA1475 ccmA heme exporter protein CcmA (NCBI) 249, 544
PA1476 ccmB heme exporter protein CcmB (NCBI) 249, 544
PA1477 ccmC heme exporter protein CcmC (NCBI) 249, 544
PA1534 recR recombination protein RecR (NCBI) 123, 478
PA1796 folD 5,10-methylene-tetrahydrofolate dehydrogenase / cyclohydrolase (NCBI) 106, 544
PA1812 mltD membrane-bound lytic murein transglycosylase D precursor (NCBI) 316, 478
PA1820 nhaB sodium/proton antiporter NhaB (NCBI) 175, 478
PA1821 PA1821 enoyl-CoA hydratase (NCBI) 228, 478
PA1822 fimL hypothetical protein (NCBI) 228, 478
PA1823 nudC NADH pyrophosphatase (NCBI) 389, 478
PA2629 purB adenylosuccinate lyase (NCBI) 106, 544
PA2656 PA2656 probable two-component sensor (NCBI) 205, 478
PA2657 PA2657 probable two-component response regulator (NCBI) 205, 478
PA2658 PA2658 hypothetical protein (NCBI) 205, 478
PA2659 PA2659 hypothetical protein (NCBI) 205, 478
PA2660 PA2660 hypothetical protein (NCBI) 478, 501
PA2661 PA2661 hypothetical protein (NCBI) 375, 478
PA3192 gltR two-component response regulator GltR (NCBI) 478, 505
PA3217 cyaB CyaB (NCBI) 478, 493
PA3314 PA3314 probable ATP-binding component of ABC transporter (NCBI) 420, 478
PA3344 recQ ATP-dependent DNA helicase RecQ (NCBI) 478, 544
PA3489 PA3489 hypothetical protein (NCBI) 232, 478
PA3574 PA3574 probable transcriptional regulator (NCBI) 143, 544
PA3701 prfB peptide chain release factor H (NCBI) 308, 544
PA3949 PA3949 hypothetical protein (NCBI) 351, 544
PA4002 rodA rod shape-determining protein (NCBI) 59, 478
PA4754 PA4754 hypothetical protein (NCBI) 453, 478
PA4939 PA4939 ATP phosphoribosyltransferase regulatory subunit (NCBI) 77, 478
PA4945 miaA tRNA delta(2)-isopentenylpyrophosphate transferase (NCBI) 306, 478
PA4946 mutL DNA mismatch repair protein (NCBI) 81, 478
PA4996 rfaE LPS biosynthesis protein RfaE (NCBI) 8, 544
PA5142 hisH1 glutamine amidotransferase (NCBI) 198, 544
PA5143 hisB imidazoleglycerol-phosphate dehydratase (NCBI) 165, 544
PA5463 PA5463 hypothetical protein (NCBI) 276, 544
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 PA3344
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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