Organism : Pseudomonas aeruginosa | Module List :
PA4802

hypothetical protein (NCBI)

CircVis
Functional Annotations (4)
Function System
Predicted amidohydrolase cog/ cog
nitrogen compound metabolic process go/ biological_process
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds go/ molecular_function
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4802
(Mouseover regulator name to see its description)

PA4802 is regulated by 29 influences and regulates 0 modules.
Regulators for PA4802 (29)
Regulator Module Operator
PA0207 445 tf
PA0393 445 tf
PA0491 445 tf
PA0701 445 tf
PA0828 445 tf
PA1067 445 tf
PA1347 445 tf
PA1980 445 tf
PA2050 445 tf
PA2227 445 tf
PA2547 445 tf
PA2704 445 tf
PA2737 445 tf
PA3045 445 tf
PA3133 445 tf
PA3381 445 tf
PA3420 445 tf
PA3594 445 tf
PA4806 445 tf
PA0272 337 tf
PA0564 337 tf
PA0701 337 tf
PA2547 337 tf
PA4354 337 tf
PA4581 337 tf
PA5032 337 tf
PA5253 337 tf
PA5324 337 tf
PA5431 337 tf

Warning: PA4802 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
3500 2.00e+02 TccCgCACcgATaaaaaaaAgga
Loader icon
3501 5.00e-01 TaCtCaGCCAgAAaataatCGAA
Loader icon
3710 4.00e+01 TATcgGTGaAtAATcTGA
Loader icon
3711 3.70e+02 cTGGTtGAgcGCcTgGaacatCtC
Loader icon
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 PA4802

PA4802 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted amidohydrolase cog/ cog
nitrogen compound metabolic process go/ biological_process
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds go/ molecular_function
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
Module neighborhood information for PA4802

PA4802 has total of 49 gene neighbors in modules 337, 445
Gene neighbors (49)
Gene Common Name Description Module membership
PA0041 PA0041 probable hemagglutinin (NCBI) 62, 337
PA0054 PA0054 RNA 2'-phosphotransferase (NCBI) 20, 337
PA0193 PA0193 hypothetical protein (NCBI) 337, 425
PA0251 PA0251 hypothetical protein (NCBI) 324, 445
PA0272 PA0272 probable transcriptional regulator (NCBI) 337, 537
PA0322 PA0322 probable transporter (NCBI) 267, 337
PA0435 PA0435 hypothetical protein (NCBI) 156, 445
PA0561 PA0561 hypothetical protein (NCBI) 157, 445
PA0564 PA0564 probable transcriptional regulator (NCBI) 333, 337
PA0606 PA0606 probable permease of ABC transporter (NCBI) 234, 337
PA0977 PA0977 hypothetical protein (NCBI) 324, 445
PA1051 PA1051 probable transporter (NCBI) 240, 337
PA1052 PA1052 hypothetical protein (NCBI) 240, 337
PA1229 PA1229 probable transcriptional regulator (NCBI) 71, 337
PA1233 PA1233 hypothetical protein (NCBI) 71, 337
PA1368 PA1368 hypothetical protein (NCBI) 320, 445
PA1469 PA1469 hypothetical protein (NCBI) 245, 337
PA1935 PA1935 hypothetical protein (NCBI) 324, 445
PA1936 PA1936 hypothetical protein (NCBI) 295, 445
PA2036 PA2036 hypothetical protein (NCBI) 231, 445
PA2704 PA2704 probable transcriptional regulator (NCBI) 445, 497
PA2712 PA2712 hypothetical protein (NCBI) 245, 337
PA2720 PA2720 hypothetical protein (NCBI) 306, 337
PA2763 PA2763 hypothetical protein (NCBI) 335, 445
PA2773 PA2773 hypothetical protein (NCBI) 229, 445
PA3078 PA3078 probable two-component sensor (NCBI) 20, 337
PA3402 PA3402 hypothetical protein (NCBI) 337, 387
PA3501 PA3501 hypothetical protein (NCBI) 254, 445
PA3660 PA3660 probable sodium/hydrogen antiporter (NCBI) 20, 337
PA3661 PA3661 hypothetical protein (NCBI) 291, 337
PA3749 PA3749 probable major facilitator superfamily (MFS) transporter (NCBI) 175, 337
PA3868 PA3868 hypothetical protein (NCBI) 197, 445
PA3884 PA3884 hypothetical protein (NCBI) 20, 337
PA3885 PA3885 hypothetical protein (NCBI) 197, 445
PA3933 PA3933 probable choline transporter (NCBI) 291, 445
PA4074 PA4074 probable transcriptional regulator (NCBI) 171, 445
PA4092 hpaC 4-hydroxyphenylacetate 3-monooxygenase small chain (NCBI) 192, 337
PA4179 PA4179 probable porin (NCBI) 206, 445
PA4354 PA4354 hypothetical protein (NCBI) 108, 337
PA4376 pncB2 nicotinate phosphoribosyltransferase (NCBI) 337, 384
PA4779 PA4779 hypothetical protein (NCBI) 313, 337
PA4802 PA4802 hypothetical protein (NCBI) 337, 445
PA4806 PA4806 probable transcriptional regulator (NCBI) 445, 546
PA4893 ureG urease accessory protein UreG (NCBI) 337, 380
PA4894 PA4894 hypothetical protein (NCBI) 337, 380
PA5102 PA5102 hypothetical protein (NCBI) 337, 538
PA5309 PA5309 probable oxidoreductase (NCBI) 335, 445
PA5324 PA5324 probable transcriptional regulator (NCBI) 30, 337
PA5532 PA5532 hypothetical protein (NCBI) 23, 445
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 PA4802
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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