Organism : Pseudomonas aeruginosa | Module List :
PA2520 czcA

Resistance-Nodulation-Cell Division (RND) divalent metal cation efflux transporter CzcA (NCBI)

CircVis
Functional Annotations (5)
Function System
Putative silver efflux pump cog/ cog
cation transport go/ biological_process
cation transmembrane transporter activity go/ molecular_function
integral to membrane go/ cellular_component
2A0601 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2520
(Mouseover regulator name to see its description)

PA2520 is regulated by 36 influences and regulates 0 modules.
Regulators for PA2520 czcA (36)
Regulator Module Operator
PA0163 24 tf
PA0191 24 tf
PA0477 24 tf
PA1526 24 tf
PA1980 24 tf
PA2050 24 tf
PA2056 24 tf
PA2276 24 tf
PA2519 24 tf
PA3002 24 tf
PA3045 24 tf
PA3420 24 tf
PA3630 24 tf
PA3757 24 tf
PA4341 24 tf
PA5293 24 tf
PA5431 24 tf
PA0701 446 tf
PA1347 446 tf
PA2050 446 tf
PA2258 446 tf
PA2276 446 tf
PA2354 446 tf
PA2376 446 tf
PA2447 446 tf
PA2519 446 tf
PA2547 446 tf
PA2785 446 tf
PA2838 446 tf
PA3420 446 tf
PA3594 446 tf
PA3596 446 tf
PA4169 446 tf
PA4341 446 tf
PA5032 446 tf
PA5293 446 tf

Warning: PA2520 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
2884 1.70e-06 atatCttAttcgaaAatc.taAaa
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2885 5.20e-05 aCtgataaaaATAAa.Acg.tTGA
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3712 3.30e+02 tGTTTCC
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3713 1.70e+03 TaATCgAACcGAAcC
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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 PA2520

PA2520 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Putative silver efflux pump cog/ cog
cation transport go/ biological_process
cation transmembrane transporter activity go/ molecular_function
integral to membrane go/ cellular_component
2A0601 tigr/ tigrfam
Module neighborhood information for PA2520

PA2520 has total of 47 gene neighbors in modules 24, 446
Gene neighbors (47)
Gene Common Name Description Module membership
PA0208 mdcA malonate decarboxylase alpha subunit (NCBI) 24, 206
PA0209 PA0209 triphosphoribosyl-dephosphocoenzyme-A synthase (NCBI) 24, 394
PA0210 mdcC malonate decarboxylase subunit delta (NCBI) 24, 394
PA0211 mdcD acetyl-CoA carboxylase beta subunit (NCBI) 24, 507
PA0212 mdcE malonate decarboxylase gamma subunit (NCBI) 24, 330
PA0213 PA0213 phosphoribosyl-dephospho-CoA transferase (NCBI) 24, 394
PA0214 PA0214 probable acyl transferase (NCBI) 24, 330
PA0216 PA0216 probable transporter (NCBI) 24, 507
PA0240 PA0240 probable porin (NCBI) 394, 446
PA0557 PA0557 hypothetical protein (NCBI) 24, 408
PA0878 PA0878 hypothetical protein (NCBI) 24, 526
PA1251 PA1251 probable chemotaxis transducer (NCBI) 394, 446
PA1254 PA1254 probable dihydrodipicolinate synthetase (NCBI) 24, 408
PA1256 PA1256 probable ATP-binding component of ABC transporter (NCBI) 24, 33
PA1259 PA1259 hypothetical protein (NCBI) 24, 408
PA1260 PA1260 probable binding protein component of ABC transporter (NCBI) 24, 148
PA1268 PA1268 hypothetical protein (NCBI) 16, 24
PA1428 PA1428 hypothetical protein (NCBI) 24, 323
PA1507 PA1507 probable transporter (NCBI) 24, 236
PA1743 PA1743 hypothetical protein (NCBI) 108, 446
PA2055 PA2055 probable major facilitator superfamily (MFS) transporter (NCBI) 24, 235
PA2056 PA2056 probable transcriptional regulator (NCBI) 24, 33
PA2243 pslM hypothetical protein (NCBI) 24, 344
PA2244 pslN hypothetical protein (NCBI) 24, 280
PA2245 pslO hypothetical protein (NCBI) 24, 346
PA2257 pvcD pyoverdine biosynthesis protein PvcD (NCBI) 199, 446
PA2286 PA2286 hypothetical protein (NCBI) 199, 446
PA2346 PA2346 hypothetical protein (NCBI) 304, 446
PA2347 PA2347 hypothetical protein (NCBI) 289, 446
PA2350 PA2350 probable ATP-binding component of ABC transporter (NCBI) 235, 446
PA2351 PA2351 probable permease of ABC transporter (NCBI) 235, 446
PA2357 msuE NADH-dependent FMN reductase MsuE (NCBI) 156, 446
PA2437 PA2437 hypothetical protein (NCBI) 320, 446
PA2438 PA2438 hypothetical protein (NCBI) 446, 519
PA2439 PA2439 hypothetical protein (NCBI) 199, 446
PA2519 xylS transcriptional regulator XylS (NCBI) 172, 446
PA2520 czcA Resistance-Nodulation-Cell Division (RND) divalent metal cation efflux transporter CzcA (NCBI) 24, 446
PA2521 czcB Resistance-Nodulation-Cell Division (RND) divalent metal cation efflux membrane fusion protein CzcB precursor (NCBI) 175, 446
PA2522 czcC outer membrane protein precursor CzcC (NCBI) 418, 446
PA2935 PA2935 hypothetical protein (NCBI) 24, 71
PA2936 PA2936 hypothetical protein (NCBI) 24, 119
PA3428 PA3428 hypothetical protein (NCBI) 74, 446
PA3761 PA3761 probable phosphotransferase system protein (NCBI) 24, 523
PA3946 PA3946 probable two-component sensor (NCBI) 201, 446
PA3964 PA3964 hypothetical protein (NCBI) 24, 340
PA4096 PA4096 probable major facilitator superfamily (MFS) transporter (NCBI) 446, 545
PA4097 PA4097 probable alcohol dehydrogenase (Zn-dependent) (NCBI) 446, 545
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 PA2520
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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