Organism : Pseudomonas aeruginosa | Module List :
PA4398

probable two-component sensor (NCBI)

CircVis
Functional Annotations (8)
Function System
Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation 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
membrane go/ cellular_component
peptidyl-histidine phosphorylation go/ biological_process
sensory_box tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4398
(Mouseover regulator name to see its description)

PA4398 is regulated by 29 influences and regulates 0 modules.
Regulators for PA4398 (29)
Regulator Module Operator
PA0533 196 tf
PA1738 196 tf
PA1945 196 tf
PA2432 196 tf
PA2447 196 tf
PA2469 196 tf
PA2489 196 tf
PA3094 196 tf
PA3124 196 tf
PA3776 196 tf
PA3778 196 tf
PA4581 196 tf
PA5029 196 tf
PA5431 196 tf
PA0116 253 tf
PA0191 253 tf
PA0393 253 tf
PA0873 253 tf
PA0893 253 tf
PA1050 253 tf
PA2423 253 tf
PA3094 253 tf
PA3126 253 tf
PA3477 253 tf
PA3804 253 tf
PA4547 253 tf
PA4906 253 tf
PA5342 253 tf
PA5562 253 tf

Warning: PA4398 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
3220 1.30e-15 TgaaTatatcgaaaAtCatgtAga
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3221 8.00e-07 tTt.AGGttAattGgCata.gctg
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3334 3.70e-02 GgTAtaaTgcggcGc..ttcc
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3335 1.10e+01 aGccTT..CcCCg.CC.gCCGc
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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 PA4398

PA4398 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation 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
membrane go/ cellular_component
peptidyl-histidine phosphorylation go/ biological_process
sensory_box tigr/ tigrfam
Module neighborhood information for PA4398

PA4398 has total of 64 gene neighbors in modules 196, 253
Gene neighbors (64)
Gene Common Name Description Module membership
PA0116 PA0116 hypothetical protein (NCBI) 253, 268
PA0154 pcaG protocatechuate 3,4-dioxygenase, alpha subunit (NCBI) 196, 536
PA0181 PA0181 probable transcriptional regulator (NCBI) 196, 373
PA0182 PA0182 probable short-chain dehydrogenase (NCBI) 196, 313
PA0501 bioF 8-amino-7-oxononanoate synthase (NCBI) 91, 253
PA0502 PA0502 probable biotin biosynthesis protein bioH (NCBI) 91, 253
PA0504 bioD dithiobiotin synthetase (NCBI) 62, 253
PA0556 PA0556 hypothetical protein (NCBI) 14, 253
PA0575 PA0575 hypothetical protein (NCBI) 196, 483
PA0658 PA0658 probable short-chain dehydrogenase (NCBI) 189, 253
PA0935 PA0935 hypothetical protein (NCBI) 253, 341
PA0951 PA0951 probable ribonuclease (NCBI) 229, 253
PA1050 PA1050 hypothetical protein (NCBI) 162, 253
PA1531 PA1531 hypothetical protein (NCBI) 196, 432
PA1679 PA1679 hypothetical protein (NCBI) 253, 496
PA1682 PA1682 probable MFS metabolite transporter (NCBI) 214, 253
PA1685 masA enolase-phosphatase E-1 (NCBI) 253, 384
PA1738 PA1738 probable transcriptional regulator (NCBI) 138, 196
PA1973 pqqF pyrroloquinoline quinone biosynthesis protein F (NCBI) 253, 483
PA1993 PA1993 hypothetical protein (NCBI) 196, 236
PA2269 PA2269 hypothetical protein (NCBI) 196, 326
PA2271 PA2271 probable acetyltransferase (NCBI) 196, 494
PA2344 mtlZ fructokinase (NCBI) 196, 307
PA2390 PA2390 probable ATP-binding/permease fusion ABC transporter (NCBI) 196, 414
PA2391 opmQ probable outer membrane protein precursor (NCBI) 196, 414
PA2432 PA2432 probable transcriptional regulator (NCBI) 196, 346
PA2447 PA2447 probable transcriptional regulator (NCBI) 34, 196
PA2496 PA2496 hypothetical protein (NCBI) 196, 519
PA2523 PA2523 probable two-component response regulator (NCBI) 196, 418
PA2525 PA2525 probable outer membrane protein precursor (NCBI) 104, 196
PA2526 PA2526 probable Resistance-Nodulation-Cell Division (RND) efflux transporter (NCBI) 196, 418
PA2527 PA2527 probable Resistance-Nodulation-Cell Division (RND) efflux transporter (NCBI) 196, 418
PA3071 PA3071 hypothetical protein (NCBI) 253, 511
PA3075 PA3075 hypothetical protein (NCBI) 253, 511
PA3087 PA3087 hypothetical protein (NCBI) 3, 253
PA3124 PA3124 probable transcriptional regulator (NCBI) 196, 320
PA3125 PA3125 hypothetical protein (NCBI) 196, 497
PA3241 PA3241 hypothetical protein (NCBI) 253, 483
PA3304 PA3304 hypothetical protein (NCBI) 196, 321
PA3312 PA3312 probable 3-hydroxyisobutyrate dehydrogenase (NCBI) 196, 438
PA3683 PA3683 hypothetical protein (NCBI) 253, 493
PA3750 PA3750 hypothetical protein (NCBI) 3, 253
PA3853 PA3853 probable transferase (NCBI) 14, 253
PA3963 PA3963 probable transporter (NCBI) 20, 253
PA4186 PA4186 hypothetical protein (NCBI) 125, 196
PA4347 PA4347 hypothetical protein (NCBI) 241, 253
PA4398 PA4398 probable two-component sensor (NCBI) 196, 253
PA4716 PA4716 hypothetical protein (NCBI) 196, 245
PA4906 PA4906 probable transcriptional regulator (NCBI) 39, 253
PA4992 PA4992 hypothetical protein (NCBI) 253, 266
PA5022 PA5022 hypothetical protein (NCBI) 60, 253
PA5029 PA5029 probable transcriptional regulator (NCBI) 58, 196
PA5030 PA5030 probable major facilitator superfamily (MFS) transporter (NCBI) 101, 196
PA5103 PA5103 hypothetical protein (NCBI) 171, 196
PA5126 PA5126 hypothetical protein (NCBI) 196, 321
PA5179 PA5179 probable transcriptional regulator (NCBI) 253, 313
PA5198 PA5198 LD-carboxypeptidase (NCBI) 3, 253
PA5199 envZ two-component sensor EnvZ (NCBI) 220, 253
PA5200 ompR two-component response regulator OmpR (NCBI) 245, 253
PA5202 PA5202 hypothetical protein (NCBI) 253, 451
PA5281 PA5281 probable hydrolase (NCBI) 42, 253
PA5318 PA5318 hypothetical protein (NCBI) 253, 450
PA5342 PA5342 probable transcriptional regulator (NCBI) 170, 253
PA5343 PA5343 hypothetical protein (NCBI) 170, 253
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 PA4398
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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