Organism : Pseudomonas aeruginosa | Module List :
PA2257 pvcD

pyoverdine biosynthesis protein PvcD (NCBI)

CircVis
Functional Annotations (5)
Function System
Cytochrome c553 cog/ cog
iron ion binding go/ molecular_function
electron transport go/ biological_process
electron carrier activity go/ molecular_function
heme binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2257
(Mouseover regulator name to see its description)

PA2257 is regulated by 34 influences and regulates 0 modules.
Regulators for PA2257 pvcD (34)
Regulator Module Operator
PA0601 199 tf
PA2258 199 tf
PA2276 199 tf
PA2281 199 tf
PA2316 199 tf
PA2334 199 tf
PA2337 199 tf
PA2354 199 tf
PA2376 199 tf
PA2432 199 tf
PA2510 199 tf
PA2511 199 tf
PA2519 199 tf
PA2838 199 tf
PA5562 199 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: PA2257 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
3226 9.20e+03 TacGcCaacGC
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3227 1.60e+02 gTggTCgACtAcCcggAtaGccTg
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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 PA2257

PA2257 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Cytochrome c553 cog/ cog
iron ion binding go/ molecular_function
electron transport go/ biological_process
electron carrier activity go/ molecular_function
heme binding go/ molecular_function
Module neighborhood information for PA2257

PA2257 has total of 43 gene neighbors in modules 199, 446
Gene neighbors (43)
Gene Common Name Description Module membership
PA0240 PA0240 probable porin (NCBI) 394, 446
PA1251 PA1251 probable chemotaxis transducer (NCBI) 394, 446
PA1743 PA1743 hypothetical protein (NCBI) 108, 446
PA2254 pvcA pyoverdine biosynthesis protein PvcA (NCBI) 33, 199
PA2255 pvcB pyoverdine biosynthesis protein PvcB (NCBI) 33, 199
PA2256 pvcC pyoverdine biosynthesis protein PvcC (NCBI) 199, 289
PA2257 pvcD pyoverdine biosynthesis protein PvcD (NCBI) 199, 446
PA2283 PA2283 hypothetical protein (NCBI) 199, 304
PA2284 PA2284 hypothetical protein (NCBI) 199, 304
PA2285 PA2285 hypothetical protein (NCBI) 199, 304
PA2286 PA2286 hypothetical protein (NCBI) 199, 446
PA2287 PA2287 hypothetical protein (NCBI) 199, 304
PA2313 PA2313 hypothetical protein (NCBI) 199, 304
PA2333 PA2333 probable sulfatase (NCBI) 199, 519
PA2339 PA2339 probable binding-protein-dependent maltose/mannitol transport protein (NCBI) 199, 304
PA2340 PA2340 probable binding-protein-dependent maltose/mannitol transport protein (NCBI) 199, 304
PA2342 mtlD mannitol dehydrogenase (NCBI) 199, 304
PA2343 mtlY xylulose kinase (NCBI) 199, 304
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
PA2418 PA2418 hypothetical protein (NCBI) 199, 519
PA2419 PA2419 probable hydrolase (NCBI) 33, 199
PA2420 PA2420 probable porin (NCBI) 199, 304
PA2421 PA2421 hypothetical protein (NCBI) 118, 199
PA2437 PA2437 hypothetical protein (NCBI) 320, 446
PA2438 PA2438 hypothetical protein (NCBI) 446, 519
PA2439 PA2439 hypothetical protein (NCBI) 199, 446
PA2473 PA2473 probable glutathione S-transferase (NCBI) 199, 304
PA2511 PA2511 probable transcriptional regulator (NCBI) 199, 500
PA2512 antA anthranilate dioxygenase large subunit (NCBI) 199, 500
PA2513 antB anthranilate dioxygenase small subunit (NCBI) 199, 500
PA2514 antC anthranilate dioxygenase reductase (NCBI) 199, 500
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
PA3428 PA3428 hypothetical protein (NCBI) 74, 446
PA3946 PA3946 probable two-component sensor (NCBI) 201, 446
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 PA2257
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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