Organism : Pseudomonas aeruginosa | Module List :
PA3587 metR

transcriptional regulator MetR (NCBI)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3587
(Mouseover regulator name to see its description)

PA3587 is regulated by 33 influences and regulates 13 modules.
Regulators for PA3587 metR (33)
Regulator Module Operator
PA0218 550 tf
PA0780 550 tf
PA0839 550 tf
PA1097 550 tf
PA1363 550 tf
PA1653 550 tf
PA2100 550 tf
PA2601 550 tf
PA3002 550 tf
PA3587 550 tf
PA3678 550 tf
PA4203 550 tf
PA4596 550 tf
PA4878 550 tf
PA5431 550 tf
PA0456 243 tf
PA0762 243 tf
PA0815 243 tf
PA0877 243 tf
PA0939 243 tf
PA0942 243 tf
PA1607 243 tf
PA2591 243 tf
PA2713 243 tf
PA2849 243 tf
PA2896 243 tf
PA3007 243 tf
PA3587 243 tf
PA3689 243 tf
PA3804 243 tf
PA4147 243 tf
PA5116 243 tf
PA5525 243 tf
Regulated by PA3587 (13)
Module Residual Genes
32 0.32 12
186 0.42 13
243 0.57 28
250 0.40 18
301 0.41 18
376 0.54 22
409 0.45 14
447 0.28 10
450 0.57 23
472 0.45 27
514 0.31 8
531 0.31 11
550 0.57 28
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
3314 1.20e-11 agtc.aTaCagaaTTgGcAAgcAc
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3315 7.30e-09 AAAAcagacctGgaaAAcaGa
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3912 2.40e-01 AaGcAgttTGcggaaggTtTC
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3913 4.80e-02 gTtcttaTgcTtGGcGGaagAgtA
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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 PA3587

PA3587 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for PA3587

PA3587 has total of 55 gene neighbors in modules 243, 550
Gene neighbors (55)
Gene Common Name Description Module membership
PA0328 PA0328 hypothetical protein (NCBI) 313, 550
PA0457 PA0457 hypothetical protein (NCBI) 3, 550
PA0530 PA0530 probable class III pyridoxal phosphate-dependent aminotransferase (NCBI) 536, 550
PA0665 PA0665 hypothetical protein (NCBI) 243, 309
PA0777 PA0777 hypothetical protein (NCBI) 157, 550
PA0780 pruR proline utilization regulator (NCBI) 245, 550
PA0813 PA0813 hypothetical protein (NCBI) 243, 443
PA0814 PA0814 hypothetical protein (NCBI) 243, 334
PA0815 PA0815 probable transcriptional regulator (NCBI) 243, 443
PA0839 PA0839 probable transcriptional regulator (NCBI) 26, 550
PA0840 PA0840 probable oxidoreductase (NCBI) 523, 550
PA0848 PA0848 probable alkyl hydroperoxide reductase (NCBI) 152, 550
PA0877 PA0877 probable transcriptional regulator (NCBI) 243, 526
PA0907 PA0907 hypothetical protein (NCBI) 243, 468
PA0939 PA0939 hypothetical protein (NCBI) 243, 469
PA0940 PA0940 hypothetical protein (NCBI) 243, 469
PA0941 PA0941 hypothetical protein (NCBI) 243, 469
PA0942 PA0942 probable transcriptional regulator (NCBI) 243, 469
PA1363 PA1363 probable sigma-70 factor, ECF subfamily (NCBI) 99, 550
PA1364 PA1364 probable transmembrane sensor (NCBI) 99, 550
PA1517 PA1517 hypothetical protein (NCBI) 243, 376
PA1518 PA1518 hypothetical protein (NCBI) 243, 376
PA1536 PA1536 hypothetical protein (NCBI) 313, 550
PA1607 PA1607 hypothetical protein (NCBI) 243, 457
PA1653 PA1653 probable transcriptional regulator (NCBI) 151, 550
PA1755 PA1755 hypothetical protein (NCBI) 23, 550
PA1814 PA1814 hypothetical protein (NCBI) 208, 243
PA2026 PA2026 hypothetical protein (NCBI) 26, 550
PA2687 pfeS two-component sensor PfeS (NCBI) 339, 550
PA2713 PA2713 hypothetical protein (NCBI) 243, 475
PA2839 PA2839 hypothetical protein (NCBI) 140, 550
PA2849 PA2849 probable transcriptional regulator (NCBI) 79, 243
PA3387 rhlG beta-ketoacyl reductase (NCBI) 192, 550
PA3587 metR transcriptional regulator MetR (NCBI) 243, 550
PA3676 PA3676 probable Resistance-Nodulation-Cell Division (RND) efflux transporter (NCBI) 39, 550
PA3677 PA3677 probable Resistance-Nodulation-Cell Division (RND) efflux membrane fusion protein precursor (NCBI) 528, 550
PA3678 PA3678 probable transcriptional regulator (NCBI) 452, 550
PA3684 PA3684 hypothetical protein (NCBI) 243, 455
PA3689 PA3689 probable transcriptional regulator (NCBI) 243, 457
PA3941 PA3941 hypothetical protein (NCBI) 100, 550
PA3959 PA3959 hypothetical protein (NCBI) 425, 550
PA3974 ladS LadS (NCBI) 53, 243
PA4573 PA4573 hypothetical protein (NCBI) 209, 243
PA4596 PA4596 probable transcriptional regulator (NCBI) 212, 550
PA4656 PA4656 hypothetical protein (NCBI) 243, 245
PA4878 PA4878 probable transcriptional regulator (NCBI) 407, 550
PA5249 PA5249 hypothetical protein (NCBI) 507, 550
PA5275 cyaY frataxin-like protein (NCBI) 243, 245
PA5371 PA5371 hypothetical protein (NCBI) 243, 251
PA5375 betT1 choline transporter BetT (NCBI) 545, 550
PA5512 PA5512 probable two-component sensor (NCBI) 374, 550
PA5522 PA5522 probable glutamine synthetase (NCBI) 243, 468
PA5523 PA5523 probable aminotransferase (NCBI) 243, 468
PA5524 PA5524 probable short-chain dehydrogenase (NCBI) 243, 468
PA5525 PA5525 probable transcriptional regulator (NCBI) 243, 468
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 PA3587
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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