Organism : Pseudomonas aeruginosa | Module List :
PA3963

probable transporter (NCBI)

CircVis
Functional Annotations (8)
Function System
Predicted Co/Zn/Cd cation transporters cog/ cog
cation transport go/ biological_process
cation transmembrane transporter activity go/ molecular_function
coenzyme A metabolic process go/ biological_process
membrane go/ cellular_component
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor go/ molecular_function
coenzyme binding go/ molecular_function
CDF tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3963
(Mouseover regulator name to see its description)

PA3963 is regulated by 29 influences and regulates 0 modules.
Regulators for PA3963 (29)
Regulator Module Operator
PA0116 253 tf
PA0191 253 tf
PA0393 253 tf
PA0873 253 tf
PA0893 253 tf
PA1050 253 tf
PA2423 253 tf
PA3094 253 tf
PA3126 253 tf
PA3477 253 tf
PA3804 253 tf
PA4547 253 tf
PA4906 253 tf
PA5342 253 tf
PA5562 253 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: PA3963 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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3334 3.70e-02 GgTAtaaTgcggcGc..ttcc
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3335 1.10e+01 aGccTT..CcCCg.CC.gCCGc
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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 PA3963

PA3963 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Predicted Co/Zn/Cd cation transporters cog/ cog
cation transport go/ biological_process
cation transmembrane transporter activity go/ molecular_function
coenzyme A metabolic process go/ biological_process
membrane go/ cellular_component
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor go/ molecular_function
coenzyme binding go/ molecular_function
CDF tigr/ tigrfam
Module neighborhood information for PA3963

PA3963 has total of 80 gene neighbors in modules 20, 253
Gene neighbors (80)
Gene Common Name Description Module membership
PA0030 PA0030 hypothetical protein (NCBI) 20, 340
PA0043 PA0043 hypothetical protein (NCBI) 20, 425
PA0054 PA0054 RNA 2'-phosphotransferase (NCBI) 20, 337
PA0116 PA0116 hypothetical protein (NCBI) 253, 268
PA0233 PA0233 probable transcriptional regulator (NCBI) 20, 313
PA0294 aguR transcriptional regulator AguR (NCBI) 20, 375
PA0343 PA0343 hypothetical protein (NCBI) 20, 450
PA0501 bioF 8-amino-7-oxononanoate synthase (NCBI) 91, 253
PA0502 PA0502 probable biotin biosynthesis protein bioH (NCBI) 91, 253
PA0504 bioD dithiobiotin synthetase (NCBI) 62, 253
PA0508 PA0508 probable acyl-CoA dehydrogenase (NCBI) 20, 373
PA0556 PA0556 hypothetical protein (NCBI) 14, 253
PA0605 PA0605 probable permease of ABC transporter (NCBI) 20, 234
PA0658 PA0658 probable short-chain dehydrogenase (NCBI) 189, 253
PA0735 PA0735 hypothetical protein (NCBI) 20, 384
PA0799 PA0799 probable helicase (NCBI) 20, 60
PA0827 PA0827 hypothetical protein (NCBI) 20, 384
PA0935 PA0935 hypothetical protein (NCBI) 253, 341
PA0951 PA0951 probable ribonuclease (NCBI) 229, 253
PA1050 PA1050 hypothetical protein (NCBI) 162, 253
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
PA1496 PA1496 probable potassium channel (NCBI) 20, 295
PA1679 PA1679 hypothetical protein (NCBI) 253, 496
PA1682 PA1682 probable MFS metabolite transporter (NCBI) 214, 253
PA1685 masA enolase-phosphatase E-1 (NCBI) 253, 384
PA1748 PA1748 enoyl-CoA hydratase (NCBI) 20, 384
PA1898 qscR quorum-sensing control repressor (NCBI) 9, 20
PA1973 pqqF pyrroloquinoline quinone biosynthesis protein F (NCBI) 253, 483
PA2029 PA2029 hypothetical protein (NCBI) 4, 20
PA2117 PA2117 hypothetical protein (NCBI) 20, 165
PA2628 PA2628 hypothetical protein (NCBI) 20, 375
PA2954 PA2954 hypothetical protein (NCBI) 20, 371
PA3071 PA3071 hypothetical protein (NCBI) 253, 511
PA3075 PA3075 hypothetical protein (NCBI) 253, 511
PA3077 PA3077 probable two-component response regulator (NCBI) 20, 493
PA3078 PA3078 probable two-component sensor (NCBI) 20, 337
PA3087 PA3087 hypothetical protein (NCBI) 3, 253
PA3191 PA3191 probable two-component sensor (NCBI) 20, 374
PA3220 PA3220 probable transcriptional regulator (NCBI) 20, 170
PA3241 PA3241 hypothetical protein (NCBI) 253, 483
PA3265 PA3265 probable transporter (NCBI) 20, 507
PA3660 PA3660 probable sodium/hydrogen antiporter (NCBI) 20, 337
PA3683 PA3683 hypothetical protein (NCBI) 253, 493
PA3750 PA3750 hypothetical protein (NCBI) 3, 253
PA3853 PA3853 probable transferase (NCBI) 14, 253
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
PA4347 PA4347 hypothetical protein (NCBI) 241, 253
PA4375 PA4375 probable RND efflux transporter (NCBI) 20, 380
PA4393 PA4393 probable permease (NCBI) 20, 62
PA4398 PA4398 probable two-component sensor (NCBI) 196, 253
PA4593 PA4593 probable permease of ABC transporter (NCBI) 20, 313
PA4906 PA4906 probable transcriptional regulator (NCBI) 39, 253
PA4992 PA4992 hypothetical protein (NCBI) 253, 266
PA5022 PA5022 hypothetical protein (NCBI) 60, 253
PA5149 PA5149 hypothetical protein (NCBI) 20, 353
PA5159 PA5159 multidrug resistance protein (NCBI) 20, 473
PA5179 PA5179 probable transcriptional regulator (NCBI) 253, 313
PA5198 PA5198 LD-carboxypeptidase (NCBI) 3, 253
PA5199 envZ two-component sensor EnvZ (NCBI) 220, 253
PA5200 ompR two-component response regulator OmpR (NCBI) 245, 253
PA5202 PA5202 hypothetical protein (NCBI) 253, 451
PA5218 PA5218 probable transcriptional regulator (NCBI) 20, 192
PA5273 PA5273 hypothetical protein (NCBI) 20, 268
PA5281 PA5281 probable hydrolase (NCBI) 42, 253
PA5318 PA5318 hypothetical protein (NCBI) 253, 450
PA5342 PA5342 probable transcriptional regulator (NCBI) 170, 253
PA5343 PA5343 hypothetical protein (NCBI) 170, 253
PA5349 PA5349 probable rubredoxin reductase (NCBI) 20, 338
PA5457 PA5457 hypothetical protein (NCBI) 20, 375
PA5458 PA5458 hypothetical protein (NCBI) 20, 215
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 PA3963
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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