Organism : Pseudomonas aeruginosa | Module List :
PA4172

probable nuclease (NCBI)

CircVis
Functional Annotations (8)
Function System
Exonuclease III cog/ cog
DNA binding go/ molecular_function
endonuclease activity go/ molecular_function
intracellular go/ cellular_component
DNA repair go/ biological_process
exodeoxyribonuclease III activity go/ molecular_function
Base excision repair kegg/ kegg pathway
exoDNase_III tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4172
(Mouseover regulator name to see its description)

PA4172 is regulated by 34 influences and regulates 0 modules.
Regulators for PA4172 (34)
Regulator Module Operator
PA0864 280 tf
PA1347 280 tf
PA1351 280 tf
PA1374 280 tf
PA2121 280 tf
PA2896 280 tf
PA3006 280 tf
PA3045 280 tf
PA3184 280 tf
PA3197 280 tf
PA3596 280 tf
PA3604 280 tf
PA3879 280 tf
PA4745 280 tf
PA4853 280 tf
PA5483 280 tf
PA0547 521 tf
PA1153 521 tf
PA1347 521 tf
PA1351 521 tf
PA2076 521 tf
PA2121 521 tf
PA2896 521 tf
PA2899 521 tf
PA3006 521 tf
PA3045 521 tf
PA3563 521 tf
PA3604 521 tf
PA3804 521 tf
PA4057 521 tf
PA4745 521 tf
PA4853 521 tf
PA5085 521 tf
PA5483 521 tf

Warning: PA4172 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
3388 4.90e-05 GaacgaGGTttCaCtGGcaGGAtC
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3389 2.90e+02 GTgCCGgCGaGgTta
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3856 3.30e-07 GggAAA.a.tCTGAac.atC
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3857 1.90e+01 gccgctggatT.cCTgca
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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 PA4172

PA4172 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Exonuclease III cog/ cog
DNA binding go/ molecular_function
endonuclease activity go/ molecular_function
intracellular go/ cellular_component
DNA repair go/ biological_process
exodeoxyribonuclease III activity go/ molecular_function
Base excision repair kegg/ kegg pathway
exoDNase_III tigr/ tigrfam
Module neighborhood information for PA4172

PA4172 has total of 46 gene neighbors in modules 280, 521
Gene neighbors (46)
Gene Common Name Description Module membership
PA1111 PA1111 hypothetical protein (NCBI) 280, 322
PA1242 PA1242 hypothetical protein (NCBI) 245, 280
PA1870 PA1870 hypothetical protein (NCBI) 187, 521
PA1921 PA1921 hypothetical protein (NCBI) 280, 450
PA1931 PA1931 probable ferredoxin (NCBI) 280, 295
PA1932 PA1932 probable hydroxylase molybdopterin-containing subunit (NCBI) 280, 537
PA1933 PA1933 probable hydroxylase large subunit (NCBI) 280, 537
PA2046 PA2046 hypothetical protein (NCBI) 311, 521
PA2107 PA2107 hypothetical protein (NCBI) 516, 521
PA2108 PA2108 pyruvate decarboxylase (NCBI) 280, 521
PA2135 PA2135 probable transporter (NCBI) 161, 521
PA2136 PA2136 hypothetical protein (NCBI) 280, 283
PA2137 PA2137 hypothetical protein (NCBI) 161, 280
PA2138 PA2138 DNA ligase (NCBI) 161, 280
PA2140 PA2140 probable metallothionein (NCBI) 161, 280
PA2141 PA2141 hypothetical protein (NCBI) 161, 280
PA2146 PA2146 hypothetical protein (NCBI) 194, 521
PA2147 katE catalase HPII (NCBI) 318, 521
PA2150 PA2150 hypothetical protein (NCBI) 280, 521
PA2154 PA2154 hypothetical protein (NCBI) 161, 521
PA2155 PA2155 probable phospholipase (NCBI) 161, 521
PA2166 PA2166 hypothetical protein (NCBI) 27, 521
PA2167 PA2167 hypothetical protein (NCBI) 479, 521
PA2168 PA2168 hypothetical protein (NCBI) 194, 521
PA2170 PA2170 hypothetical protein (NCBI) 187, 521
PA2178 PA2178 hypothetical protein (NCBI) 161, 280
PA2179 PA2179 hypothetical protein (NCBI) 161, 280
PA2181 PA2181 hypothetical protein (NCBI) 161, 280
PA2182 PA2182 hypothetical protein (NCBI) 189, 521
PA2183 PA2183 hypothetical protein (NCBI) 324, 521
PA2184 PA2184 hypothetical protein (NCBI) 187, 521
PA2185 katN non-heme catalase KatN (NCBI) 254, 521
PA2186 PA2186 hypothetical protein (NCBI) 97, 521
PA2187 PA2187 hypothetical protein (NCBI) 280, 521
PA2189 PA2189 hypothetical protein (NCBI) 161, 280
PA2190 PA2190 hypothetical protein (NCBI) 166, 521
PA2192 PA2192 hypothetical protein (NCBI) 324, 521
PA2244 pslN hypothetical protein (NCBI) 24, 280
PA2416 treA periplasmic trehalase precursor (NCBI) 194, 280
PA2708 PA2708 hypothetical protein (NCBI) 479, 521
PA3231 PA3231 hypothetical protein (NCBI) 328, 521
PA3273 PA3273 hypothetical protein (NCBI) 280, 479
PA3274 PA3274 hypothetical protein (NCBI) 280, 479
PA4172 PA4172 probable nuclease (NCBI) 280, 521
PA4344 PA4344 probable hydrolase (NCBI) 280, 334
PA4691 PA4691 hypothetical protein (NCBI) 157, 521
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 PA4172
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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