Organism : Pseudomonas aeruginosa | Module List :
PA3465

hypothetical protein (NCBI)

CircVis
Functional Annotations (4)
Function System
Arabinose efflux permease cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
integral to membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3465
(Mouseover regulator name to see its description)

PA3465 is regulated by 33 influences and regulates 0 modules.
Regulators for PA3465 (33)
Regulator Module Operator
PA0034 388 tf
PA0159 388 tf
PA0179 388 tf
PA0893 388 tf
PA1097 388 tf
PA1430 388 tf
PA1760 388 tf
PA1998 388 tf
PA2047 388 tf
PA2359 388 tf
PA2586 388 tf
PA2588 388 tf
PA4296 388 tf
PA4547 388 tf
PA4778 388 tf
PA5059 388 tf
PA5105 388 tf
PA0133 38 tf
PA0515 38 tf
PA0527 38 tf
PA0831 38 tf
PA1998 38 tf
PA2126 38 tf
PA2622 38 tf
PA2802 38 tf
PA3458 38 tf
PA3622 38 tf
PA3879 38 tf
PA4269 38 tf
PA4493 38 tf
PA4853 38 tf
PA5105 38 tf
PA5356 38 tf

Warning: PA3465 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
2908 6.80e-14 TTGATgc.gaTCAg
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2909 3.80e-01 aGccCTaTAcGaAggTTCCg
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3600 1.60e+00 agTcttgGaaAAagA
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3601 1.00e+04 TTtgccGgcaTTcTa
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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 PA3465

PA3465 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Arabinose efflux permease cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
integral to membrane go/ cellular_component
Module neighborhood information for PA3465

PA3465 has total of 42 gene neighbors in modules 38, 388
Gene neighbors (42)
Gene Common Name Description Module membership
PA0156 PA0156 probable Resistance-Nodulation-Cell Division (RND) efflux membrane fusion protein precursor (NCBI) 127, 388
PA0157 PA0157 probable Resistance-Nodulation-Cell Division (RND) efflux membrane fusion protein precursor (NCBI) 127, 388
PA0158 PA0158 probable Resistance-Nodulation-Cell Division (RND) efflux transporter (NCBI) 127, 388
PA0395 pilT twitching motility protein PilT (NCBI) 127, 388
PA0704 PA0704 amidase (NCBI) 388, 443
PA0835 pta phosphate acetyltransferase (NCBI) 38, 167
PA0928 gacS sensor/response regulator hybrid (NCBI) 81, 388
PA1119 PA1119 probable outer membrane protein precursor (NCBI) 388, 390
PA1120 PA1120 hypothetical protein (NCBI) 20, 388
PA1121 PA1121 hypothetical protein (NCBI) 159, 388
PA1789 PA1789 hypothetical protein (NCBI) 38, 416
PA1967 PA1967 hypothetical protein (NCBI) 166, 388
PA2618 PA2618 arginyl-tRNA-protein transferase (NCBI) 388, 390
PA3091 PA3091 hypothetical protein (NCBI) 127, 388
PA3340 PA3340 hypothetical protein (NCBI) 388, 437
PA3458 PA3458 probable transcriptional regulator (NCBI) 38, 162
PA3465 PA3465 hypothetical protein (NCBI) 38, 388
PA3613 PA3613 hypothetical protein (NCBI) 38, 416
PA3614 PA3614 hypothetical protein (NCBI) 38, 416
PA3615 PA3615 hypothetical protein (NCBI) 38, 141
PA3702 wspR probable two-component response regulator (NCBI) 81, 388
PA3703 wspF probable methylesterase (NCBI) 53, 388
PA3704 wspE probable chemotaxis sensor/effector fusion protein (NCBI) 81, 388
PA3705 wspD hypothetical protein (NCBI) 81, 388
PA3706 wspC probable protein methyltransferase (NCBI) 60, 388
PA3707 wspB hypothetical protein (NCBI) 3, 388
PA3708 wspA probable chemotaxis transducer (NCBI) 81, 388
PA3879 narL two-component response regulator NarL (NCBI) 38, 162
PA4117 PA4117 probable bacteriophytochrome (NCBI) 35, 388
PA4312 PA4312 hypothetical protein (NCBI) 388, 492
PA4313 PA4313 hypothetical protein (NCBI) 31, 388
PA4328 PA4328 hypothetical protein (NCBI) 38, 416
PA4571 PA4571 probable cytochrome c (NCBI) 38, 225
PA4610 PA4610 hypothetical protein (NCBI) 38, 162
PA4677 PA4677 hypothetical protein (NCBI) 127, 388
PA5112 estA esterase EstA (NCBI) 193, 388
PA5171 arcA arginine deiminase (NCBI) 38, 514
PA5172 arcB ornithine carbamoyltransferase, catabolic (NCBI) 38, 514
PA5173 arcC carbamate kinase (NCBI) 38, 514
PA5230 PA5230 probable permease of ABC transporter (NCBI) 38, 225
PA5231 PA5231 probable ATP-binding/permease fusion ABC transporter (NCBI) 38, 225
PA5232 PA5232 hypothetical protein (NCBI) 21, 38
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 PA3465
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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