Organism : Pseudomonas aeruginosa | Module List :
PA2579 kynA

hypothetical protein (NCBI)

CircVis
Functional Annotations (6)
Function System
Tryptophan 2,3-dioxygenase (vermilion) cog/ cog
tryptophan 2,3-dioxygenase activity go/ molecular_function
tryptophan metabolic process go/ biological_process
Tryptophan metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
trp_2_3_diox tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2579
(Mouseover regulator name to see its description)

PA2579 is regulated by 33 influences and regulates 0 modules.
Regulators for PA2579 kynA (33)
Regulator Module Operator
PA0167 4 tf
PA1504 4 tf
PA1776 4 tf
PA1945 4 tf
PA3285 4 tf
PA3965 4 tf
PA4238 4 tf
PA4451 4 tf
PA4462 4 tf
PA4600 4 tf
PA4755 4 tf
PA4853 4 tf
PA5337 4 tf
PA5344 4 tf
PA0652 281 tf
PA0764 281 tf
PA1159 281 tf
PA1504 281 tf
PA3002 281 tf
PA3604 281 tf
PA3921 281 tf
PA4057 281 tf
PA4238 281 tf
PA4270 281 tf
PA4275 281 tf
PA4279 281 tf
PA4451 281 tf
PA4745 281 tf
PA4755 281 tf
PA4853 281 tf
PA4890 281 tf
PA5337 281 tf
PA5344 281 tf

Warning: PA2579 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
2844 2.10e+00 AAgcgaTaCTtTGCgCcAaaa
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2845 1.50e+02 aTCG...cCtTg.CgGccaTC
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3390 1.80e+02 ttTgCGagg.Ggcg
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3391 1.30e+04 C.GcGATcGtA
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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 PA2579

PA2579 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Tryptophan 2,3-dioxygenase (vermilion) cog/ cog
tryptophan 2,3-dioxygenase activity go/ molecular_function
tryptophan metabolic process go/ biological_process
Tryptophan metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
trp_2_3_diox tigr/ tigrfam
Module neighborhood information for PA2579

PA2579 has total of 30 gene neighbors in modules 4, 281
Gene neighbors (30)
Gene Common Name Description Module membership
PA0782 putA proline dehydrogenase PutA (NCBI) 4, 315
PA0937 PA0937 hypothetical protein (NCBI) 281, 286
PA1160 PA1160 hypothetical protein (NCBI) 41, 281
PA1161 rrmA rRNA methyltransferase (NCBI) 281, 442
PA1162 dapE succinyl-diaminopimelate desuccinylase (NCBI) 59, 281
PA1206 PA1206 hypothetical protein (NCBI) 4, 100
PA1816 dnaQ DNA polymerase III subunit epsilon (NCBI) 4, 78
PA2029 PA2029 hypothetical protein (NCBI) 4, 20
PA2453 PA2453 hypothetical protein (NCBI) 1, 281
PA2454 PA2454 hypothetical protein (NCBI) 281, 363
PA2579 kynA hypothetical protein (NCBI) 4, 281
PA3117 asd aspartate-semialdehyde dehydrogenase (NCBI) 123, 281
PA3295 PA3295 probable HIT family protein (NCBI) 4, 368
PA3468 PA3468 hypothetical protein (NCBI) 4, 78
PA3469 PA3469 hypothetical protein (NCBI) 4, 9
PA3470 PA3470 hypothetical protein (NCBI) 4, 9
PA3525 argG argininosuccinate synthase (NCBI) 260, 281
PA3538 PA3538 probable ATP-binding component of ABC transporter (NCBI) 4, 499
PA3965 PA3965 probable transcriptional regulator (NCBI) 4, 477
PA4069 PA4069 hypothetical protein (NCBI) 281, 398
PA4454 PA4454 hypothetical protein (NCBI) 4, 341
PA4569 ispB octaprenyl-diphosphate synthase (NCBI) 281, 360
PA5237 PA5237 hypothetical protein (NCBI) 123, 281
PA5268 corA magnesium/cobalt transport protein (NCBI) 4, 368
PA5269 PA5269 hypothetical protein (NCBI) 4, 368
PA5270 PA5270 hypothetical protein (NCBI) 4, 368
PA5300 cycB cytochrome c5 (NCBI) 281, 327
PA5317 PA5317 probable binding protein component of ABC dipeptide transporter (NCBI) 4, 380
PA5362 PA5362 hypothetical protein (NCBI) 4, 398
PA5414 PA5414 hypothetical protein (NCBI) 281, 286
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 PA2579
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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