Organism : Pseudomonas aeruginosa | Module List :
PA4119 aph

aminoglycoside 3'-phosphotransferase type IIb (NCBI)

CircVis
Functional Annotations (2)
Function System
Aminoglycoside phosphotransferase cog/ cog
kanamycin kinase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4119
(Mouseover regulator name to see its description)

PA4119 is regulated by 51 influences and regulates 0 modules.
Regulators for PA4119 aph (51)
Regulator Module Operator
PA0120 501 tf
PA0207 501 tf
PA0236 501 tf
PA0831 501 tf
PA0905 501 tf
PA1128 501 tf
PA1142 501 tf
PA1422 501 tf
PA1627 501 tf
PA2032 501 tf
PA2047 501 tf
PA2115 501 tf
PA2258 501 tf
PA2718 501 tf
PA3921 501 tf
PA4021 501 tf
PA4157 501 tf
PA4279 501 tf
PA4354 501 tf
PA4769 501 tf
PA4853 501 tf
PA4890 501 tf
PA5059 501 tf
PA5437 501 tf
PA5483 501 tf
PA0034 65 tf
PA0376 65 tf
PA0479 65 tf
PA0780 65 tf
PA0815 65 tf
PA1067 65 tf
PA1754 65 tf
PA2016 65 tf
PA2047 65 tf
PA2547 65 tf
PA2577 65 tf
PA2622 65 tf
PA2802 65 tf
PA2957 65 tf
PA3133 65 tf
PA3622 65 tf
PA3714 65 tf
PA3778 65 tf
PA4169 65 tf
PA4279 65 tf
PA4853 65 tf
PA4890 65 tf
PA5059 65 tf
PA5403 65 tf
PA5437 65 tf
PA5550 65 tf

Warning: PA4119 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
2962 2.10e-01 CCgTTTCC
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2963 3.80e+00 GcccAGgctcGcgcA
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3816 8.40e+01 TTTTTcaT
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3817 1.90e+02 GtatttccaggAA.G
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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 PA4119

PA4119 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Aminoglycoside phosphotransferase cog/ cog
kanamycin kinase activity go/ molecular_function
Module neighborhood information for PA4119

PA4119 has total of 42 gene neighbors in modules 65, 501
Gene neighbors (42)
Gene Common Name Description Module membership
PA0010 tag DNA-3-methyladenine glycosidase I (NCBI) 65, 375
PA0015 PA0015 hypothetical protein (NCBI) 65, 143
PA0040 PA0040 hypothetical protein (NCBI) 265, 501
PA0245 aroQ2 3-dehydroquinate dehydratase (NCBI) 65, 377
PA0340 PA0340 hypothetical protein (NCBI) 65, 247
PA0559 PA0559 hypothetical protein (NCBI) 65, 230
PA0706 cat chloramphenicol acetyltransferase (NCBI) 384, 501
PA0860 PA0860 probable ATP-binding/permease fusion ABC transporter (NCBI) 40, 65
PA1037 PA1037 hypothetical protein (NCBI) 65, 99
PA1157 PA1157 probable two-component response regulator (NCBI) 501, 528
PA1791 PA1791 hypothetical protein (NCBI) 265, 501
PA1824 PA1824 hypothetical protein (NCBI) 65, 247
PA1839 PA1839 hypothetical protein (NCBI) 299, 501
PA1971 braZ branched chain amino acid transporter BraZ (NCBI) 40, 65
PA2063 PA2063 hypothetical protein (NCBI) 65, 387
PA2653 PA2653 probable transporter (NCBI) 65, 230
PA2660 PA2660 hypothetical protein (NCBI) 478, 501
PA3339 PA3339 hypothetical protein (NCBI) 65, 307
PA3725 recJ single-stranded-DNA-specific exonuclease RecJ (NCBI) 65, 299
PA3741 PA3741 hypothetical protein (NCBI) 404, 501
PA3850 PA3850 hypothetical protein (NCBI) 265, 501
PA3892 PA3892 hypothetical protein (NCBI) 65, 156
PA3955 PA3955 hypothetical protein (NCBI) 65, 377
PA4119 aph aminoglycoside 3'-phosphotransferase type IIb (NCBI) 65, 501
PA4583 PA4583 hypothetical protein (NCBI) 61, 501
PA4585 rtcA RNA 3'-terminal-phosphate cyclase (NCBI) 61, 501
PA4629 PA4629 hypothetical protein (NCBI) 65, 299
PA4644 PA4644 hypothetical protein (NCBI) 65, 422
PA4724 PA4724 glutamyl-tRNA synthetase (NCBI) 286, 501
PA4800 PA4800 hypothetical protein (NCBI) 61, 501
PA4817 PA4817 hypothetical protein (NCBI) 65, 377
PA4849 PA4849 hypothetical protein (NCBI) 65, 236
PA4928 PA4928 hypothetical protein (NCBI) 207, 501
PA4952 PA4952 ribosome-associated GTPase (NCBI) 306, 501
PA5048 PA5048 probable nuclease (NCBI) 135, 501
PA5071 PA5071 hypothetical protein (NCBI) 65, 387
PA5120 PA5120 hypothetical protein (NCBI) 48, 501
PA5156 PA5156 hypothetical protein (NCBI) 40, 65
PA5404 PA5404 hypothetical protein (NCBI) 40, 65
PA5405 PA5405 hypothetical protein (NCBI) 65, 377
PA5406 PA5406 hypothetical protein (NCBI) 65, 230
PA5407 PA5407 hypothetical protein (NCBI) 65, 230
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 PA4119
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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