Organism : Pseudomonas aeruginosa | Module List :
PA2639 nuoD

NADH dehydrogenase I chain C,D (NCBI)

CircVis
Functional Annotations (6)
Function System
NADH:ubiquinone oxidoreductase 49 kD subunit 7 cog/ cog
mitochondrial electron transport, NADH to ubiquinone go/ biological_process
NADH dehydrogenase (ubiquinone) activity go/ molecular_function
NAD binding go/ molecular_function
Oxidative phosphorylation kegg/ kegg pathway
NuoC_fam tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2639
(Mouseover regulator name to see its description)

PA2639 is regulated by 99 influences and regulates 0 modules.
Regulators for PA2639 nuoD (99)
Regulator Module Operator
PA0155 32 tf
PA0367 32 tf
PA0393 32 tf
PA0455 32 tf
PA0491 32 tf
PA0533 32 tf
PA0707 32 tf
PA0748 32 tf
PA0815 32 tf
PA0831 32 tf
PA0876 32 tf
PA0890 32 tf
PA1003 32 tf
PA1015 32 tf
PA1138 32 tf
PA1223 32 tf
PA1335 32 tf
PA1380 32 tf
PA1504 32 tf
PA1544 32 tf
PA1633 32 tf
PA1776 32 tf
PA2010 32 tf
PA2056 32 tf
PA2220 32 tf
PA2376 32 tf
PA2484 32 tf
PA2551 32 tf
PA2586 32 tf
PA2601 32 tf
PA2758 32 tf
PA2877 32 tf
PA2899 32 tf
PA3002 32 tf
PA3006 32 tf
PA3266 32 tf
PA3410 32 tf
PA3587 32 tf
PA3804 32 tf
PA3815 32 tf
PA4269 32 tf
PA4270 32 tf
PA4581 32 tf
PA4896 32 tf
PA5116 32 tf
PA5157 32 tf
PA5166 32 tf
PA5562 32 tf
PA0155 531 tf
PA0279 531 tf
PA0456 531 tf
PA0610 531 tf
PA0707 531 tf
PA0815 531 tf
PA0831 531 tf
PA0876 531 tf
PA0890 531 tf
PA1003 531 tf
PA1138 531 tf
PA1223 531 tf
PA1309 531 tf
PA1335 531 tf
PA1403 531 tf
PA1504 531 tf
PA1544 531 tf
PA1619 531 tf
PA1633 531 tf
PA1759 531 tf
PA1776 531 tf
PA1998 531 tf
PA2010 531 tf
PA2056 531 tf
PA2220 531 tf
PA2246 531 tf
PA2312 531 tf
PA2376 531 tf
PA2484 531 tf
PA2551 531 tf
PA2586 531 tf
PA2877 531 tf
PA2899 531 tf
PA2930 531 tf
PA3002 531 tf
PA3006 531 tf
PA3133 531 tf
PA3249 531 tf
PA3341 531 tf
PA3410 531 tf
PA3587 531 tf
PA3711 531 tf
PA3804 531 tf
PA4269 531 tf
PA4270 531 tf
PA4581 531 tf
PA4984 531 tf
PA5116 531 tf
PA5157 531 tf
PA5166 531 tf
PA5562 531 tf

Warning: PA2639 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

Warning: No Motifs were found!

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 PA2639

PA2639 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
NADH:ubiquinone oxidoreductase 49 kD subunit 7 cog/ cog
mitochondrial electron transport, NADH to ubiquinone go/ biological_process
NADH dehydrogenase (ubiquinone) activity go/ molecular_function
NAD binding go/ molecular_function
Oxidative phosphorylation kegg/ kegg pathway
NuoC_fam tigr/ tigrfam
Module neighborhood information for PA2639

PA2639 has total of 12 gene neighbors in modules 32, 531
Gene neighbors (12)
Gene Common Name Description Module membership
PA2638 nuoB NADH dehydrogenase beta subunit (NCBI) 32, 82
PA2639 nuoD NADH dehydrogenase I chain C,D (NCBI) 32, 531
PA2640 nuoE ATP synthase subunit E (NCBI) 32, 531
PA2641 nuoF NADH dehydrogenase I chain F (NCBI) 32, 531
PA2642 nuoG NADH dehydrogenase gamma subunit (NCBI) 32, 531
PA2643 nuoH NADH dehydrogenase subunit H (NCBI) 32, 531
PA2644 nuoI NADH dehydrogenase subunit I (NCBI) 32, 531
PA2645 nuoJ NADH dehydrogenase subunit J (NCBI) 32, 531
PA2646 nuoK NADH dehydrogenase kappa subunit (NCBI) 32, 531
PA2647 nuoL NADH dehydrogenase subunit L (NCBI) 32, 531
PA2648 nuoM NADH dehydrogenase subunit M (NCBI) 32, 531
PA2649 nuoN NADH dehydrogenase subunit N (NCBI) 32, 531
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 PA2639
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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