Organism : Pseudomonas aeruginosa | Module List :
PA4429

probable cytochrome c1 precursor (NCBI)

CircVis
Functional Annotations (9)
Function System
Cytochrome c1 cog/ cog
electron transporter activity go/ molecular_function
iron ion binding go/ molecular_function
electron transport go/ biological_process
ubiquinol-cytochrome-c reductase activity go/ molecular_function
electron carrier activity go/ molecular_function
heme binding go/ molecular_function
Oxidative phosphorylation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4429
(Mouseover regulator name to see its description)

PA4429 is regulated by 64 influences and regulates 0 modules.
Regulators for PA4429 (64)
Regulator Module Operator
PA0393 155 tf
PA0533 155 tf
PA0652 155 tf
PA0707 155 tf
PA0815 155 tf
PA0839 155 tf
PA0873 155 tf
PA1003 155 tf
PA1097 155 tf
PA1347 155 tf
PA1422 155 tf
PA2082 155 tf
PA2123 155 tf
PA2312 155 tf
PA2359 155 tf
PA2484 155 tf
PA2692 155 tf
PA2879 155 tf
PA2896 155 tf
PA2917 155 tf
PA3067 155 tf
PA3197 155 tf
PA3364 155 tf
PA3458 155 tf
PA3815 155 tf
PA4132 155 tf
PA4238 155 tf
PA4269 155 tf
PA4275 155 tf
PA4341 155 tf
PA4547 155 tf
PA4755 155 tf
PA5125 155 tf
PA5288 155 tf
PA5506 155 tf
PA5562 155 tf
PA0393 29 tf
PA0533 29 tf
PA0652 29 tf
PA0707 29 tf
PA0815 29 tf
PA0839 29 tf
PA1097 29 tf
PA1544 29 tf
PA2082 29 tf
PA2123 29 tf
PA2312 29 tf
PA2484 29 tf
PA2879 29 tf
PA2896 29 tf
PA2921 29 tf
PA3364 29 tf
PA4132 29 tf
PA4238 29 tf
PA4269 29 tf
PA4275 29 tf
PA4341 29 tf
PA4984 29 tf
PA5116 29 tf
PA5125 29 tf
PA5255 29 tf
PA5308 29 tf
PA5506 29 tf
PA5562 29 tf

Warning: PA4429 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 PA4429

PA4429 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Cytochrome c1 cog/ cog
electron transporter activity go/ molecular_function
iron ion binding go/ molecular_function
electron transport go/ biological_process
ubiquinol-cytochrome-c reductase activity go/ molecular_function
electron carrier activity go/ molecular_function
heme binding go/ molecular_function
Oxidative phosphorylation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Module neighborhood information for PA4429

PA4429 has total of 11 gene neighbors in modules 29, 155
Gene neighbors (11)
Gene Common Name Description Module membership
PA4429 PA4429 probable cytochrome c1 precursor (NCBI) 29, 155
PA4430 PA4430 probable cytochrome b (NCBI) 29, 198
PA4431 PA4431 probable iron-sulfur protein (NCBI) 29, 198
PA5553 atpC ATP synthase subunit epsilon (NCBI) 155, 427
PA5554 atpD ATP synthase subunit B (NCBI) 29, 155
PA5555 atpG ATP synthase subunit C (NCBI) 29, 155
PA5556 atpA ATP synthase subunit A (NCBI) 29, 155
PA5557 atpH ATP synthase subunit D (NCBI) 29, 155
PA5558 atpF ATP synthase subunit B (NCBI) 29, 155
PA5559 atpE ATP synthase subunit C (NCBI) 29, 155
PA5560 atpB ATP synthase subunit A (NCBI) 29, 155
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 PA4429
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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