Organism : Pseudomonas aeruginosa | Module List :
PA4117

probable bacteriophytochrome (NCBI)

CircVis
Functional Annotations (10)
Function System
Bacteriophytochrome (light-regulated signal transduction histidine kinase) cog/ cog
two-component sensor activity go/ molecular_function
ATP binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
signal transduction go/ biological_process
sensory perception go/ biological_process
G-protein coupled photoreceptor activity go/ molecular_function
membrane go/ cellular_component
peptidyl-histidine phosphorylation go/ biological_process
protein-chromophore linkage go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4117
(Mouseover regulator name to see its description)

PA4117 is regulated by 39 influences and regulates 0 modules.
Regulators for PA4117 (39)
Regulator Module Operator
PA0125 35 tf
PA0527 35 tf
PA0828 35 tf
PA1003 35 tf
PA1128 35 tf
PA1335 35 tf
PA1607 35 tf
PA1663 35 tf
PA1760 35 tf
PA2376 35 tf
PA2588 35 tf
PA2848 35 tf
PA3477 35 tf
PA3622 35 tf
PA3921 35 tf
PA4070 35 tf
PA4354 35 tf
PA4547 35 tf
PA4778 35 tf
PA5293 35 tf
PA5356 35 tf
PA5525 35 tf
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

Warning: PA4117 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
2902 5.60e-01 AAacgACtaacAgcaaACAAtAC
Loader icon
2903 1.20e+00 cgTAaGATAtcGGC.CgCccG
Loader icon
3600 1.60e+00 agTcttgGaaAAagA
Loader icon
3601 1.00e+04 TTtgccGgcaTTcTa
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 PA4117

PA4117 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Bacteriophytochrome (light-regulated signal transduction histidine kinase) cog/ cog
two-component sensor activity go/ molecular_function
ATP binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
signal transduction go/ biological_process
sensory perception go/ biological_process
G-protein coupled photoreceptor activity go/ molecular_function
membrane go/ cellular_component
peptidyl-histidine phosphorylation go/ biological_process
protein-chromophore linkage go/ biological_process
Module neighborhood information for PA4117

PA4117 has total of 44 gene neighbors in modules 35, 388
Gene neighbors (44)
Gene Common Name Description Module membership
PA0143 nuh nonspecific ribonucleoside hydrolase (NCBI) 35, 127
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
PA0399 PA0399 cystathionine beta-synthase (NCBI) 35, 191
PA0400 PA0400 probable cystathionine gamma-lyase (NCBI) 35, 191
PA0704 PA0704 amidase (NCBI) 388, 443
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
PA1967 PA1967 hypothetical protein (NCBI) 166, 388
PA2618 PA2618 arginyl-tRNA-protein transferase (NCBI) 388, 390
PA3091 PA3091 hypothetical protein (NCBI) 127, 388
PA3095 xcpZ general secretion pathway protein M (NCBI) 35, 402
PA3096 xcpY general secretion pathway protein L (NCBI) 35, 402
PA3097 xcpX general secretion pathway protein K (NCBI) 35, 402
PA3098 xcpW general secretion pathway protein J (NCBI) 35, 402
PA3099 xcpV general secretion pathway protein I (NCBI) 35, 402
PA3100 xcpU General secretion pathway outer membrane protein H precursor (NCBI) 35, 402
PA3101 xcpT general secretion pathway protein G (NCBI) 35, 402
PA3102 xcpS general secretion pathway protein F (NCBI) 35, 402
PA3103 xcpR general secretion pathway protein E (NCBI) 35, 402
PA3104 xcpP secretion protein XcpP (NCBI) 35, 402
PA3105 xcpQ general secretion pathway protein D (NCBI) 35, 402
PA3340 PA3340 hypothetical protein (NCBI) 388, 437
PA3465 PA3465 hypothetical protein (NCBI) 38, 388
PA3535 PA3535 probable serine protease (NCBI) 35, 365
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
PA4117 PA4117 probable bacteriophytochrome (NCBI) 35, 388
PA4190 pqsL probable FAD-dependent monooxygenase (NCBI) 35, 164
PA4312 PA4312 hypothetical protein (NCBI) 388, 492
PA4313 PA4313 hypothetical protein (NCBI) 31, 388
PA4590 pra protein activator (NCBI) 35, 127
PA4677 PA4677 hypothetical protein (NCBI) 127, 388
PA4778 PA4778 probable transcriptional regulator (NCBI) 2, 35
PA5112 estA esterase EstA (NCBI) 193, 388
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 PA4117
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