Organism : Pseudomonas aeruginosa | Module List :
PA3804

hypothetical protein (NCBI)

CircVis
Functional Annotations (6)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3804
(Mouseover regulator name to see its description)

PA3804 is regulated by 32 influences and regulates 79 modules.
Regulators for PA3804 (32)
Regulator Module Operator
PA1003 329 tf
PA2047 329 tf
PA3604 329 tf
PA3804 329 tf
PA4070 329 tf
PA4238 329 tf
PA4269 329 tf
PA4275 329 tf
PA4451 329 tf
PA4600 329 tf
PA4755 329 tf
PA5239 329 tf
PA5525 329 tf
PA5562 329 tf
PA0275 270 tf
PA0762 270 tf
PA0890 270 tf
PA0961 270 tf
PA1335 270 tf
PA1898 270 tf
PA2511 270 tf
PA2556 270 tf
PA2622 270 tf
PA3002 270 tf
PA3804 270 tf
PA4052 270 tf
PA4238 270 tf
PA4269 270 tf
PA4547 270 tf
PA5239 270 tf
PA5550 270 tf
PA5562 270 tf

Warning: PA3804 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
3368 5.60e-01 AaaCgAaA
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3369 3.20e+03 tGaaaAAgctG
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3484 9.20e-01 GTAaaAcTttGaaAaaA
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3485 1.40e+03 GaCtATaAgTGGc.gTtT
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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 PA3804

PA3804 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for PA3804

PA3804 has total of 34 gene neighbors in modules 270, 329
Gene neighbors (34)
Gene Common Name Description Module membership
PA1688 PA1688 hypothetical protein (NCBI) 78, 329
PA1689 PA1689 hypothetical protein (NCBI) 78, 329
PA1787 acnB aconitate hydratase (NCBI) 179, 329
PA2630 PA2630 hypothetical protein (NCBI) 225, 270
PA3167 serC phosphoserine aminotransferase (NCBI) 329, 403
PA3632 PA3632 hypothetical protein (NCBI) 174, 270
PA3640 dnaE DNA polymerase III subunit alpha (NCBI) 270, 552
PA3643 lpxB lipid-A-disaccharide synthase (NCBI) 270, 277
PA3650 dxr 1-deoxy-D-xylulose 5-phosphate reductoisomerase (NCBI) 131, 270
PA3652 uppS undecaprenyl pyrophosphate synthetase (NCBI) 270, 353
PA3799 engA GTP-binding protein EngA (NCBI) 270, 353
PA3800 PA3800 hypothetical protein (NCBI) 270, 329
PA3801 PA3801 hypothetical protein (NCBI) 329, 543
PA3804 PA3804 hypothetical protein (NCBI) 270, 329
PA3805 pilF type 4 fimbrial biogenesis protein PilF (NCBI) 94, 329
PA3820 secF protein export protein SecF (NCBI) 270, 277
PA4237 rplQ 50S ribosomal protein L17 (NCBI) 277, 329
PA4238 rpoA DNA-directed RNA polymerase alpha subunit (NCBI) 329, 484
PA4239 rpsD 30S ribosomal protein S4 (NCBI) 329, 484
PA4250 rpsN 30S ribosomal protein S14 (NCBI) 131, 329
PA4252 rplX 50S ribosomal protein L24 (NCBI) 329, 484
PA4255 rpmC 50S ribosomal protein L29 (NCBI) 329, 484
PA4449 hisG ATP phosphoribosyltransferase (NCBI) 270, 510
PA4727 pcnB poly(A) polymerase (NCBI) 214, 270
PA4729 panB 3-methyl-2-oxobutanoate hydroxymethyltransferase (NCBI) 329, 433
PA4730 panC pantoate--beta-alanine ligase (NCBI) 329, 433
PA4757 PA4757 hypothetical protein (NCBI) 270, 453
PA5001 PA5001 hypothetical protein (NCBI) 270, 353
PA5002 PA5002 hypothetical protein (NCBI) 270, 353
PA5003 PA5003 hypothetical protein (NCBI) 174, 270
PA5046 PA5046 malic enzyme (NCBI) 329, 453
PA5052 PA5052 hypothetical protein (NCBI) 225, 270
PA5549 glmS D-fructose-6-phosphate amidotransferase (NCBI) 270, 353
PA5552 glmU glucosamine-1-phosphate acetyltransferase/N-acetylglucosamine-1-phosphate uridyltransferase (NCBI) 270, 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 PA3804
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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