Organism : Pseudomonas aeruginosa | Module List :
PA0024 hemF

coproporphyrinogen III oxidase (NCBI)

CircVis
Functional Annotations (6)
Function System
Coproporphyrinogen III oxidase cog/ cog
coproporphyrinogen oxidase activity go/ molecular_function
porphyrin-containing compound biosynthetic process go/ biological_process
Porphyrin and chlorophyll metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0024
(Mouseover regulator name to see its description)

PA0024 is regulated by 34 influences and regulates 0 modules.
Regulators for PA0024 hemF (34)
Regulator Module Operator
PA0456 271 tf
PA0652 271 tf
PA0961 271 tf
PA1945 271 tf
PA2047 271 tf
PA2246 271 tf
PA2957 271 tf
PA3604 271 tf
PA4238 271 tf
PA4275 271 tf
PA4451 271 tf
PA4600 271 tf
PA4745 271 tf
PA4755 271 tf
PA4764 271 tf
PA4853 271 tf
PA5344 271 tf
PA0116 374 tf
PA0163 374 tf
PA0815 374 tf
PA0961 374 tf
PA1504 374 tf
PA3126 374 tf
PA3197 374 tf
PA3423 374 tf
PA3583 374 tf
PA3604 374 tf
PA4703 374 tf
PA4853 374 tf
PA4890 374 tf
PA5342 374 tf
PA5403 374 tf
PA5511 374 tf
PA5550 374 tf

Warning: PA0024 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
3370 4.80e-17 GcTAgAaTggcggcctTt
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3371 4.50e+02 C.GaAACA
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3572 4.00e-02 GTGcTAtcgTcGcCgcctc
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3573 6.30e+01 tGCCgCcGTttc.AT.ctccg
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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 PA0024

PA0024 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Coproporphyrinogen III oxidase cog/ cog
coproporphyrinogen oxidase activity go/ molecular_function
porphyrin-containing compound biosynthetic process go/ biological_process
Porphyrin and chlorophyll metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Module neighborhood information for PA0024

PA0024 has total of 47 gene neighbors in modules 271, 374
Gene neighbors (47)
Gene Common Name Description Module membership
PA0005 lptA lysophosphatidic acid acyltransferase, LptA (NCBI) 271, 341
PA0024 hemF coproporphyrinogen III oxidase (NCBI) 271, 374
PA0064 PA0064 hypothetical protein (NCBI) 293, 374
PA0319 PA0319 hypothetical protein (NCBI) 276, 374
PA0356 PA0356 hypothetical protein (NCBI) 170, 374
PA0418 PA0418 hypothetical protein (NCBI) 170, 374
PA0607 rpe ribulose-phosphate 3-epimerase (NCBI) 271, 332
PA1034 PA1034 hypothetical protein (NCBI) 271, 371
PA1035 PA1035 hypothetical protein (NCBI) 212, 271
PA1563 PA1563 hypothetical protein (NCBI) 135, 374
PA1801 clpP ATP-dependent Clp protease proteolytic subunit (NCBI) 223, 271
PA2252 PA2252 probable AGCS sodium/alanine/glycine symporter (NCBI) 181, 374
PA2253 ansA L-asparaginase I (NCBI) 181, 374
PA2801 PA2801 hypothetical protein (NCBI) 306, 374
PA2842 PA2842 hypothetical protein (NCBI) 245, 374
PA2843 PA2843 probable aldolase (NCBI) 151, 374
PA3191 PA3191 probable two-component sensor (NCBI) 20, 374
PA3197 PA3197 hypothetical protein (NCBI) 321, 374
PA3243 minC septum formation inhibitor (NCBI) 178, 271
PA3245 minE cell division topological specificity factor MinE (NCBI) 178, 271
PA3400 PA3400 hypothetical protein (NCBI) 306, 374
PA3401 PA3401 hypothetical protein (NCBI) 374, 387
PA3423 PA3423 probable transcriptional regulator (NCBI) 313, 374
PA3480 PA3480 deoxycytidine triphosphate deaminase (NCBI) 122, 271
PA3579 PA3579 probable carbohydrate kinase (NCBI) 358, 374
PA3580 PA3580 hypothetical protein (NCBI) 358, 374
PA3611 PA3611 hypothetical protein (NCBI) 6, 271
PA3738 xerD tyrosine recombinase (NCBI) 374, 499
PA3764 PA3764 hypothetical protein (NCBI) 374, 387
PA3822 yajC preprotein translocase subunit YajC (NCBI) 178, 271
PA3896 PA3896 probable 2-hydroxyacid dehydrogenase (NCBI) 220, 374
PA4005 PA4005 hypothetical protein (NCBI) 271, 440
PA4232 ssb single-strand DNA-binding protein (NCBI) 6, 271
PA4314 purU1 formyltetrahydrofolate deformylase (NCBI) 271, 440
PA4396 PA4396 probable two-component response regulator (NCBI) 58, 374
PA4439 trpS tryptophanyl-tRNA synthetase (NCBI) 271, 306
PA4482 gatC aspartyl/glutamyl-tRNA amidotransferase subunit C (NCBI) 14, 271
PA4545 comL competence protein ComL (NCBI) 122, 271
PA4679 PA4679 hypothetical protein (NCBI) 103, 374
PA5050 priA primosome assembly protein PriA (NCBI) 374, 396
PA5132 PA5132 hypothetical protein (NCBI) 374, 511
PA5295 PA5295 hypothetical protein (NCBI) 170, 374
PA5357 PA5357 hypothetical protein (NCBI) 332, 374
PA5511 PA5511 probable two-component response regulator (NCBI) 332, 374
PA5512 PA5512 probable two-component sensor (NCBI) 374, 550
PA5513 poxA hypothetical protein (NCBI) 332, 374
PA5551 PA5551 hypothetical protein (NCBI) 374, 389
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 PA0024
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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