Organism : Pseudomonas aeruginosa | Module List :
PA2337 mtlR

transcriptional regulator MtlR (NCBI)

CircVis
Functional Annotations (6)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2337
(Mouseover regulator name to see its description)

PA2337 is regulated by 31 influences and regulates 18 modules.
Regulators for PA2337 mtlR (31)
Regulator Module Operator
PA0815 34 tf
PA0828 34 tf
PA0942 34 tf
PA1484 34 tf
PA1603 34 tf
PA2259 34 tf
PA2267 34 tf
PA2484 34 tf
PA2622 34 tf
PA2758 34 tf
PA3363 34 tf
PA3815 34 tf
PA3864 34 tf
PA4070 34 tf
PA4238 34 tf
PA5562 34 tf
PA2259 494 tf
PA2270 494 tf
PA2276 494 tf
PA2281 494 tf
PA2320 494 tf
PA2332 494 tf
PA2337 494 tf
PA2383 494 tf
PA2387 494 tf
PA2417 494 tf
PA2423 494 tf
PA2467 494 tf
PA2468 494 tf
PA2484 494 tf
PA2492 494 tf

Warning: PA2337 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
2900 3.00e+01 aAatCaAtATGcAta
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2901 1.60e+00 TtCataTTtaTCtaCTAaCaGacA
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3802 1.40e-10 AAaAa.aC.CgTCat..tttAaaa
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3803 4.40e-06 AActT.ATgatTt...ActGc
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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 PA2337

PA2337 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for PA2337

PA2337 has total of 55 gene neighbors in modules 34, 494
Gene neighbors (55)
Gene Common Name Description Module membership
PA0101 PA0101 hypothetical protein (NCBI) 11, 34
PA0275 PA0275 probable transcriptional regulator (NCBI) 34, 70
PA0276 PA0276 hypothetical protein (NCBI) 30, 34
PA0338 PA0338 hypothetical protein (NCBI) 34, 39
PA0529 PA0529 hypothetical protein (NCBI) 34, 536
PA0739 PA0739 probable transcriptional regulator (NCBI) 34, 61
PA0861 PA0861 hypothetical protein (NCBI) 34, 87
PA0908 PA0908 hypothetical protein (NCBI) 11, 34
PA0909 PA0909 hypothetical protein (NCBI) 11, 34
PA1036 PA1036 hypothetical protein (NCBI) 34, 457
PA1168 PA1168 hypothetical protein (NCBI) 34, 473
PA1209 PA1209 hypothetical protein (NCBI) 34, 70
PA1604 PA1604 hypothetical protein (NCBI) 34, 432
PA2229 PA2229 hypothetical protein (NCBI) 34, 189
PA2271 PA2271 probable acetyltransferase (NCBI) 196, 494
PA2272 pbpC penicillin-binding protein 3A (NCBI) 257, 494
PA2281 PA2281 probable transcriptional regulator (NCBI) 135, 494
PA2301 PA2301 hypothetical protein (NCBI) 34, 257
PA2326 PA2326 hypothetical protein (NCBI) 34, 290
PA2332 PA2332 probable transcriptional regulator (NCBI) 257, 494
PA2337 mtlR transcriptional regulator MtlR (NCBI) 34, 494
PA2358 PA2358 hypothetical protein (NCBI) 291, 494
PA2380 PA2380 hypothetical protein (NCBI) 257, 494
PA2383 PA2383 probable transcriptional regulator (NCBI) 257, 494
PA2387 PA2387 probable sigma-70 factor, ECF subfamily (NCBI) 257, 494
PA2388 PA2388 probable transmembrane sensor (NCBI) 257, 494
PA2417 PA2417 probable transcriptional regulator (NCBI) 257, 494
PA2422 PA2422 hypothetical protein (NCBI) 34, 289
PA2423 PA2423 hypothetical protein (NCBI) 257, 494
PA2427 PA2427 hypothetical protein (NCBI) 34, 414
PA2434 PA2434 hypothetical protein (NCBI) 34, 334
PA2436 PA2436 hypothetical protein (NCBI) 34, 257
PA2440 PA2440 hypothetical protein (NCBI) 33, 34
PA2447 PA2447 probable transcriptional regulator (NCBI) 34, 196
PA2456 PA2456 hypothetical protein (NCBI) 34, 476
PA2464 PA2464 hypothetical protein (NCBI) 257, 494
PA2467 PA2467 probable transmembrane sensor (NCBI) 325, 494
PA2468 PA2468 probable sigma-70 factor, ECF subfamily (NCBI) 325, 494
PA2484 PA2484 hypothetical protein (NCBI) 139, 494
PA2486 PA2486 hypothetical protein (NCBI) 441, 494
PA2491 PA2491 probable oxidoreductase (NCBI) 257, 494
PA2492 mexT transcriptional regulator MexT (NCBI) 257, 494
PA2493 mexE Resistance-Nodulation-Cell Division (RND) multidrug efflux membrane fusion protein MexE precursor (NCBI) 108, 494
PA2494 mexF Resistance-Nodulation-Cell Division (RND) multidrug efflux transporter MexF (NCBI) 108, 494
PA2495 oprN Multidrug efflux outer membrane protein OprN precursor (NCBI) 108, 494
PA3056 PA3056 hypothetical protein (NCBI) 34, 361
PA3057 PA3057 hypothetical protein (NCBI) 34, 361
PA3362 PA3362 hypothetical protein (NCBI) 30, 34
PA3363 amiR aliphatic amidase regulator (NCBI) 34, 294
PA3364 amiC aliphatic amidase expression-regulating protein (NCBI) 34, 294
PA3365 PA3365 probable chaperone (NCBI) 34, 171
PA3366 amiE aliphatic amidase (NCBI) 34, 294
PA4327 PA4327 hypothetical protein (NCBI) 34, 87
PA4507 PA4507 hypothetical protein (NCBI) 34, 44
PA4630 PA4630 hypothetical protein (NCBI) 34, 70
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 PA2337
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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