Organism : Pseudomonas aeruginosa | Module List :
PA4814 fadH2

2,4-dienoyl-CoA reductase FadH2 (NCBI)

CircVis
Functional Annotations (7)
Function System
NADH:flavin oxidoreductases, Old Yellow Enzyme family cog/ cog
electron transport go/ biological_process
metabolic process go/ biological_process
2,4-dienoyl-CoA reductase (NADPH) activity go/ molecular_function
thiamine biosynthetic process go/ biological_process
FMN binding go/ molecular_function
disulfide oxidoreductase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4814
(Mouseover regulator name to see its description)

PA4814 is regulated by 38 influences and regulates 0 modules.
Regulators for PA4814 fadH2 (38)
Regulator Module Operator
PA0032 180 tf
PA0218 180 tf
PA0306 180 tf
PA0828 180 tf
PA1145 180 tf
PA1197 180 tf
PA1264 180 tf
PA1399 180 tf
PA1467 180 tf
PA1980 180 tf
PA2838 180 tf
PA3381 180 tf
PA3420 180 tf
PA3594 180 tf
PA3714 180 tf
PA4755 180 tf
PA4806 180 tf
PA5344 180 tf
PA5562 180 tf
PA0306 439 tf
PA0701 439 tf
PA0828 439 tf
PA0893 439 tf
PA1347 439 tf
PA1374 439 tf
PA1399 439 tf
PA1980 439 tf
PA2510 439 tf
PA2681 439 tf
PA2696 439 tf
PA2838 439 tf
PA3381 439 tf
PA3420 439 tf
PA3594 439 tf
PA3714 439 tf
PA3778 439 tf
PA4057 439 tf
PA4174 439 tf

Warning: PA4814 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
3188 7.60e+01 TGgcGgtTtC.GCa
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3189 4.50e+03 ACAaGaAatt
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3698 2.30e+03 AAGAAGGAA
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3699 6.10e+03 GaTgatC.gaTtGgt
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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 PA4814

PA4814 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
NADH:flavin oxidoreductases, Old Yellow Enzyme family cog/ cog
electron transport go/ biological_process
metabolic process go/ biological_process
2,4-dienoyl-CoA reductase (NADPH) activity go/ molecular_function
thiamine biosynthetic process go/ biological_process
FMN binding go/ molecular_function
disulfide oxidoreductase activity go/ molecular_function
Module neighborhood information for PA4814

PA4814 has total of 32 gene neighbors in modules 180, 439
Gene neighbors (32)
Gene Common Name Description Module membership
PA0057 PA0057 hypothetical protein (NCBI) 333, 439
PA0237 PA0237 probable oxidoreductase (NCBI) 180, 471
PA0238 PA0238 hypothetical protein (NCBI) 180, 471
PA0453 PA0453 hypothetical protein (NCBI) 434, 439
PA1187 PA1187 probable acyl-CoA dehydrogenase (NCBI) 366, 439
PA1252 PA1252 probable L-malate dehydrogenase (NCBI) 180, 295
PA1253 PA1253 probable semialdehyde dehydrogenase (NCBI) 201, 439
PA1498 pykF pyruvate kinase (NCBI) 180, 532
PA1916 PA1916 probable amino acid permease (NCBI) 439, 534
PA1917 PA1917 hypothetical protein (NCBI) 394, 439
PA1918 PA1918 hypothetical protein (NCBI) 201, 439
PA1952 PA1952 hypothetical protein (NCBI) 105, 180
PA2129 cupA2 chaperone CupA2 (NCBI) 36, 439
PA2130 cupA3 usher CupA3 (NCBI) 439, 471
PA2131 cupA4 fimbrial subunit CupA4 (NCBI) 439, 471
PA2132 cupA5 chaperone CupA5 (NCBI) 439, 471
PA2216 PA2216 hypothetical protein (NCBI) 289, 439
PA2878 PA2878 hypothetical protein (NCBI) 180, 288
PA3279 oprP Phosphate-specific outer membrane porin OprP precursor (NCBI) 132, 439
PA3714 PA3714 probable two-component response regulator (NCBI) 180, 326
PA3774 PA3774 probable acetylpolyamine aminohydrolase (NCBI) 439, 486
PA4083 cupB4 chaperone CupB4 (NCBI) 36, 439
PA4166 PA4166 probable acetyltransferase (NCBI) 439, 459
PA4814 fadH2 2,4-dienoyl-CoA reductase FadH2 (NCBI) 180, 439
PA4818 PA4818 hypothetical protein (NCBI) 180, 463
PA4819 PA4819 probable glycosyl transferase (NCBI) 180, 463
PA4884 PA4884 hypothetical protein (NCBI) 418, 439
PA5031 PA5031 probable short chain dehydrogenase (NCBI) 180, 471
PA5090 PA5090 hypothetical protein (NCBI) 439, 473
PA5327 PA5327 probable oxidoreductase (NCBI) 180, 507
PA5379 sdaB L-serine dehydratase (NCBI) 180, 470
PA5387 PA5387 hypothetical protein (NCBI) 156, 180
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 PA4814
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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