Organism : Pseudomonas aeruginosa | Module List :
PA5399

probable ferredoxin (NCBI)

CircVis
Functional Annotations (4)
Function System
Fe-S oxidoreductase cog/ cog
electron transport go/ biological_process
electron carrier activity go/ molecular_function
iron-sulfur cluster binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA5399
(Mouseover regulator name to see its description)

PA5399 is regulated by 36 influences and regulates 0 modules.
Regulators for PA5399 (36)
Regulator Module Operator
PA0816 466 tf
PA1520 466 tf
PA1653 466 tf
PA1945 466 tf
PA1978 466 tf
PA2510 466 tf
PA2704 466 tf
PA3225 466 tf
PA3249 466 tf
PA3391 466 tf
PA3420 466 tf
PA3596 466 tf
PA3815 466 tf
PA4057 466 tf
PA4914 466 tf
PA5380 466 tf
PA5389 466 tf
PA0393 470 tf
PA0436 470 tf
PA0707 470 tf
PA0816 470 tf
PA1309 470 tf
PA1653 470 tf
PA1978 470 tf
PA2320 470 tf
PA2692 470 tf
PA2704 470 tf
PA3225 470 tf
PA3249 470 tf
PA3420 470 tf
PA3815 470 tf
PA3921 470 tf
PA4769 470 tf
PA4914 470 tf
PA5380 470 tf
PA5389 470 tf

Warning: PA5399 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
3748 1.20e+04 ttGTCGtT.TcG
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3749 3.00e+04 CTTTCA
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3756 2.70e+01 aCccAcAAcaACAAagagGA
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3757 7.30e+03 CcgTttCAG
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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 PA5399

PA5399 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Fe-S oxidoreductase cog/ cog
electron transport go/ biological_process
electron carrier activity go/ molecular_function
iron-sulfur cluster binding go/ molecular_function
Module neighborhood information for PA5399

PA5399 has total of 28 gene neighbors in modules 466, 470
Gene neighbors (28)
Gene Common Name Description Module membership
PA1978 PA1978 probable transcriptional regulator (NCBI) 335, 470
PA2762 PA2762 hypothetical protein (NCBI) 466, 470
PA3079 PA3079 hypothetical protein (NCBI) 470, 491
PA3080 PA3080 hypothetical protein (NCBI) 470, 491
PA3232 PA3232 DNA polymerase III subunit epsilon (NCBI) 470, 491
PA3233 PA3233 hypothetical protein (NCBI) 470, 491
PA3236 PA3236 probable glycine betaine-binding protein precursor (NCBI) 466, 470
PA4909 PA4909 probable ATP-binding component of ABC transporter (NCBI) 466, 470
PA4910 PA4910 probable ATP-binding component of ABC transporter (NCBI) 74, 470
PA4911 PA4911 probable permease of ABC branched-chain amino acid transporter (NCBI) 74, 470
PA4912 PA4912 probable permease of ABC branched chain amino acid transporter (NCBI) 466, 470
PA5168 PA5168 probable dicarboxylate transporter (NCBI) 470, 491
PA5169 PA5169 probable C4-dicarboxylate transporter (NCBI) 470, 491
PA5379 sdaB L-serine dehydratase (NCBI) 180, 470
PA5396 PA5396 hypothetical protein (NCBI) 466, 470
PA5397 PA5397 hypothetical protein (NCBI) 466, 470
PA5398 PA5398 probable FMN oxidoreductase (NCBI) 466, 470
PA5399 PA5399 probable ferredoxin (NCBI) 466, 470
PA5400 PA5400 probable electron transfer flavoprotein alpha subunit (NCBI) 466, 470
PA5401 PA5401 hypothetical protein (NCBI) 466, 470
PA5410 PA5410 probable ring hydroxylating dioxygenase, alpha-subunit (NCBI) 466, 470
PA5411 PA5411 probable ferredoxin (NCBI) 466, 470
PA5416 soxB sarcosine oxidase beta subunit (NCBI) 466, 470
PA5417 soxD sarcosine oxidase delta subunit (NCBI) 466, 470
PA5418 soxA sarcosine oxidase alpha subunit (NCBI) 466, 470
PA5419 soxG sarcosine oxidase gamma subunit (NCBI) 466, 470
PA5420 purU2 formyltetrahydrofolate deformylase (NCBI) 466, 470
PA5421 fdhA glutathione-independent formaldehyde dehydrogenase (NCBI) 466, 470
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 PA5399
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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