Organism : Pseudomonas aeruginosa | Module List :
PA3596

probable methylated-DNA--protein-cysteine methyltransferase (NCBI)

CircVis
Functional Annotations (10)
Function System
Adenosine deaminase cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
methylated-DNA-[protein]-cysteine S-methyltransferase activity go/ molecular_function
intracellular go/ cellular_component
DNA repair go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
zinc ion binding go/ molecular_function
sequence-specific DNA binding go/ molecular_function
ogt tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3596
(Mouseover regulator name to see its description)

PA3596 is regulated by 33 influences and regulates 30 modules.
Regulators for PA3596 (33)
Regulator Module Operator
PA1347 345 tf
PA1351 345 tf
PA1826 345 tf
PA1898 345 tf
PA1945 345 tf
PA2123 345 tf
PA3266 345 tf
PA3363 345 tf
PA3571 345 tf
PA3596 345 tf
PA3921 345 tf
PA4451 345 tf
PA4703 345 tf
PA4745 345 tf
PA5059 345 tf
PA0179 382 tf
PA0225 382 tf
PA0268 382 tf
PA0784 382 tf
PA1504 382 tf
PA1945 382 tf
PA1949 382 tf
PA2047 382 tf
PA2825 382 tf
PA2897 382 tf
PA3363 382 tf
PA3596 382 tf
PA4074 382 tf
PA4703 382 tf
PA4755 382 tf
PA5059 382 tf
PA5261 382 tf
PA5550 382 tf

Warning: PA3596 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
3516 1.30e-01 CGGAaAtcctgGaa
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3517 2.00e+04 GCcG.CGGcg.TTc
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3588 4.20e+03 aGCAcGccG.cGAcCAgCAG
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3589 5.60e+04 AAaACTCCaTCGAA
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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 PA3596

PA3596 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Adenosine deaminase cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
methylated-DNA-[protein]-cysteine S-methyltransferase activity go/ molecular_function
intracellular go/ cellular_component
DNA repair go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
zinc ion binding go/ molecular_function
sequence-specific DNA binding go/ molecular_function
ogt tigr/ tigrfam
Module neighborhood information for PA3596

PA3596 has total of 40 gene neighbors in modules 345, 382
Gene neighbors (40)
Gene Common Name Description Module membership
PA0007 PA0007 hypothetical protein (NCBI) 153, 382
PA0109 PA0109 hypothetical protein (NCBI) 349, 382
PA0173 PA0173 probable methylesterase (NCBI) 345, 415
PA0174 PA0174 hypothetical protein (NCBI) 345, 415
PA0776 PA0776 hypothetical protein (NCBI) 163, 345
PA0798 pmtA phospholipid methyltransferase (NCBI) 382, 482
PA0803 PA0803 hypothetical protein (NCBI) 163, 382
PA1065 PA1065 hypothetical protein (NCBI) 27, 382
PA1188 PA1188 hypothetical protein (NCBI) 345, 461
PA1350 PA1350 hypothetical protein (NCBI) 84, 345
PA1358 PA1358 hypothetical protein (NCBI) 185, 382
PA1470 PA1470 probable short-chain dehydrogenase (NCBI) 345, 475
PA1522 PA1522 hypothetical protein (NCBI) 39, 382
PA1646 PA1646 probable chemotaxis transducer (NCBI) 175, 345
PA1990 PA1990 probable peptidase (NCBI) 382, 399
PA2070 PA2070 hypothetical protein (NCBI) 132, 345
PA2544 PA2544 hypothetical protein (NCBI) 163, 382
PA2571 PA2571 probable two-component sensor (NCBI) 349, 382
PA2699 PA2699 hypothetical protein (NCBI) 345, 367
PA2700 PA2700 probable porin (NCBI) 132, 345
PA2701 PA2701 probable major facilitator superfamily (MFS) transporter (NCBI) 345, 483
PA2787 cpg2 glutamate carboxypepticase (NCBI) 200, 382
PA2920 PA2920 probable chemotaxis transducer (NCBI) 153, 382
PA3289 PA3289 hypothetical protein (NCBI) 382, 475
PA3346 PA3346 probable two-component response regulator (NCBI) 258, 382
PA3462 PA3462 probable sensor/response regulator hybrid (NCBI) 171, 345
PA3596 PA3596 probable methylated-DNA--protein-cysteine methyltransferase (NCBI) 345, 382
PA3690 PA3690 probable metal-transporting P-type ATPase (NCBI) 2, 382
PA4041 PA4041 hypothetical protein (NCBI) 345, 382
PA4112 PA4112 probable sensor/response regulator hybrid (NCBI) 200, 382
PA4362 PA4362 hypothetical protein (NCBI) 382, 482
PA4641 PA4641 None 159, 382
PA4788 PA4788 hypothetical protein (NCBI) 185, 345
PA4899 PA4899 probable aldehyde dehydrogenase (NCBI) 345, 538
PA5093 PA5093 probable histidine/phenylalanine ammonia-lyase (NCBI) 142, 345
PA5094 PA5094 probable ATP-binding component of ABC transporter (NCBI) 142, 345
PA5097 PA5097 probable amino acid permease (NCBI) 142, 345
PA5098 hutH histidine ammonia-lyase (NCBI) 142, 345
PA5307 PA5307 hypothetical protein (NCBI) 88, 345
PA5381 PA5381 hypothetical protein (NCBI) 192, 345
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 PA3596
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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