Organism : Pseudomonas aeruginosa | Module List :
PA5457

hypothetical protein (NCBI)

CircVis
Functional Annotations (3)
Function System
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase cog/ cog
metabolic process go/ biological_process
methyltransferase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA5457
(Mouseover regulator name to see its description)

PA5457 is regulated by 27 influences and regulates 0 modules.
Regulators for PA5457 (27)
Regulator Module Operator
PA0037 375 tf
PA0294 375 tf
PA0306 375 tf
PA0455 375 tf
PA1884 375 tf
PA1998 375 tf
PA2115 375 tf
PA2121 375 tf
PA2547 375 tf
PA3477 375 tf
PA3778 375 tf
PA3898 375 tf
PA5253 375 tf
PA0167 20 tf
PA0233 20 tf
PA0294 20 tf
PA0564 20 tf
PA1099 20 tf
PA1182 20 tf
PA1261 20 tf
PA1627 20 tf
PA1859 20 tf
PA2547 20 tf
PA3027 20 tf
PA3220 20 tf
PA5032 20 tf
PA5218 20 tf

Warning: PA5457 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
2876 2.30e+03 aaAaaaGAAcAA
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2877 3.50e+05 CGAaTCCTACaAAcaccTTTcCTT
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3574 3.10e-02 CatGAAGTcaatGGaCAATcaaGA
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3575 6.60e-02 tc.TttctGTgCgGagaAacctgc
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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 PA5457

PA5457 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase cog/ cog
metabolic process go/ biological_process
methyltransferase activity go/ molecular_function
Module neighborhood information for PA5457

PA5457 has total of 74 gene neighbors in modules 20, 375
Gene neighbors (74)
Gene Common Name Description Module membership
PA0010 tag DNA-3-methyladenine glycosidase I (NCBI) 65, 375
PA0013 PA0013 hypothetical protein (NCBI) 335, 375
PA0030 PA0030 hypothetical protein (NCBI) 20, 340
PA0037 trpI transcriptional regulator TrpI (NCBI) 375, 377
PA0043 PA0043 hypothetical protein (NCBI) 20, 425
PA0054 PA0054 RNA 2'-phosphotransferase (NCBI) 20, 337
PA0233 PA0233 probable transcriptional regulator (NCBI) 20, 313
PA0294 aguR transcriptional regulator AguR (NCBI) 20, 375
PA0305 PA0305 hypothetical protein (NCBI) 375, 380
PA0306 PA0306 probable transcriptional regulator (NCBI) 295, 375
PA0343 PA0343 hypothetical protein (NCBI) 20, 450
PA0383 PA0383 hypothetical protein (NCBI) 375, 377
PA0508 PA0508 probable acyl-CoA dehydrogenase (NCBI) 20, 373
PA0544 PA0544 hypothetical protein (NCBI) 313, 375
PA0545 PA0545 hypothetical protein (NCBI) 162, 375
PA0560 PA0560 hypothetical protein (NCBI) 229, 375
PA0605 PA0605 probable permease of ABC transporter (NCBI) 20, 234
PA0703 PA0703 probable major facilitator superfamily (MFS) transporter (NCBI) 283, 375
PA0735 PA0735 hypothetical protein (NCBI) 20, 384
PA0799 PA0799 probable helicase (NCBI) 20, 60
PA0827 PA0827 hypothetical protein (NCBI) 20, 384
PA1044 PA1044 hypothetical protein (NCBI) 101, 375
PA1046 PA1046 hypothetical protein (NCBI) 241, 375
PA1110 PA1110 hypothetical protein (NCBI) 101, 375
PA1120 PA1120 hypothetical protein (NCBI) 20, 388
PA1170 PA1170 hypothetical protein (NCBI) 20, 195
PA1182 PA1182 probable transcriptional regulator (NCBI) 9, 20
PA1189 PA1189 hypothetical protein (NCBI) 20, 181
PA1234 PA1234 hypothetical protein (NCBI) 20, 241
PA1261 PA1261 probable transcriptional regulator (NCBI) 20, 408
PA1303 PA1303 probable signal peptidase (NCBI) 20, 499
PA1488 PA1488 hypothetical protein (NCBI) 295, 375
PA1489 PA1489 hypothetical protein (NCBI) 295, 375
PA1496 PA1496 probable potassium channel (NCBI) 20, 295
PA1748 PA1748 enoyl-CoA hydratase (NCBI) 20, 384
PA1831 PA1831 hypothetical protein (NCBI) 283, 375
PA1844 PA1844 hypothetical protein (NCBI) 235, 375
PA1884 PA1884 probable transcriptional regulator (NCBI) 335, 375
PA1898 qscR quorum-sensing control repressor (NCBI) 9, 20
PA2029 PA2029 hypothetical protein (NCBI) 4, 20
PA2117 PA2117 hypothetical protein (NCBI) 20, 165
PA2628 PA2628 hypothetical protein (NCBI) 20, 375
PA2661 PA2661 hypothetical protein (NCBI) 375, 478
PA2954 PA2954 hypothetical protein (NCBI) 20, 371
PA3016 PA3016 hypothetical protein (NCBI) 48, 375
PA3077 PA3077 probable two-component response regulator (NCBI) 20, 493
PA3078 PA3078 probable two-component sensor (NCBI) 20, 337
PA3191 PA3191 probable two-component sensor (NCBI) 20, 374
PA3220 PA3220 probable transcriptional regulator (NCBI) 20, 170
PA3265 PA3265 probable transporter (NCBI) 20, 507
PA3403 PA3403 hypothetical protein (NCBI) 372, 375
PA3532 PA3532 hypothetical protein (NCBI) 375, 377
PA3660 PA3660 probable sodium/hydrogen antiporter (NCBI) 20, 337
PA3826 PA3826 hypothetical protein (NCBI) 266, 375
PA3884 PA3884 hypothetical protein (NCBI) 20, 337
PA3963 PA3963 probable transporter (NCBI) 20, 253
PA4036 PA4036 probable two-component sensor (NCBI) 20, 313
PA4086 cupB1 probable fimbrial subunit CupB1 (NCBI) 20, 373
PA4339 PA4339 probable phospholipase (NCBI) 20, 220
PA4375 PA4375 probable RND efflux transporter (NCBI) 20, 380
PA4393 PA4393 probable permease (NCBI) 20, 62
PA4593 PA4593 probable permease of ABC transporter (NCBI) 20, 313
PA4999 waaL O-antigen ligase, WaaL (NCBI) 231, 375
PA5121 PA5121 hypothetical protein (NCBI) 40, 375
PA5149 PA5149 hypothetical protein (NCBI) 20, 353
PA5159 PA5159 multidrug resistance protein (NCBI) 20, 473
PA5218 PA5218 probable transcriptional regulator (NCBI) 20, 192
PA5273 PA5273 hypothetical protein (NCBI) 20, 268
PA5349 PA5349 probable rubredoxin reductase (NCBI) 20, 338
PA5457 PA5457 hypothetical protein (NCBI) 20, 375
PA5458 PA5458 hypothetical protein (NCBI) 20, 215
PA5468 PA5468 probable citrate transporter (NCBI) 344, 375
PA5469 PA5469 hypothetical protein (NCBI) 344, 375
PA5518 PA5518 probable potassium efflux transporter (NCBI) 40, 375
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 PA5457
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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