Organism : Pseudomonas aeruginosa | Module List :
PA1397

probable two-component response regulator (NCBI)

CircVis
Functional Annotations (7)
Function System
Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA1397
(Mouseover regulator name to see its description)

PA1397 is regulated by 41 influences and regulates 16 modules.
Regulators for PA1397 (41)
Regulator Module Operator
PA0893 387 tf
PA1099 387 tf
PA1397 387 tf
PA1526 387 tf
PA1754 387 tf
PA2100 387 tf
PA2383 387 tf
PA2802 387 tf
PA2859 387 tf
PA2921 387 tf
PA3197 387 tf
PA3322 387 tf
PA3458 387 tf
PA3583 387 tf
PA3778 387 tf
PA3965 387 tf
PA3973 387 tf
PA4279 387 tf
PA5342 387 tf
PA5356 387 tf
PA5403 387 tf
PA5483 387 tf
PA0765 117 tf
PA1159 117 tf
PA1397 117 tf
PA1853 117 tf
PA2056 117 tf
PA2489 117 tf
PA2859 117 tf
PA2877 117 tf
PA2921 117 tf
PA3266 117 tf
PA3285 117 tf
PA3322 117 tf
PA4057 117 tf
PA4275 117 tf
PA4530 117 tf
PA4596 117 tf
PA4769 117 tf
PA4787 117 tf
PA5344 117 tf

Warning: PA1397 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
3064 1.20e-04 CgaAAaaGcgA
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3065 7.30e+03 tgcGgcAGccTgCtc
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3598 1.60e-04 tgcgcgCatttccgGcGgAAA
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3599 6.00e+01 CTGtTTCGccCCCTtcGTCACGaA
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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 PA1397

PA1397 is enriched for 7 functions in 3 categories.
Module neighborhood information for PA1397

PA1397 has total of 59 gene neighbors in modules 117, 387
Gene neighbors (59)
Gene Common Name Description Module membership
PA0379 PA0379 hypothetical protein (NCBI) 387, 438
PA0668 tyrZ tyrosyl-tRNA synthetase (NCBI) 117, 541
PA0772 recO DNA repair protein RecO (NCBI) 151, 387
PA0773 pdxJ pyridoxal phosphate biosynthetic protein (NCBI) 202, 387
PA0800 PA0800 hypothetical protein (NCBI) 99, 117
PA0802 PA0802 hypothetical protein (NCBI) 99, 117
PA0846 PA0846 putative sulfate transport protein CysZ (NCBI) 117, 220
PA0859 PA0859 hypothetical protein (NCBI) 117, 130
PA1396 PA1396 probable two-component sensor (NCBI) 372, 387
PA1397 PA1397 probable two-component response regulator (NCBI) 117, 387
PA1622 PA1622 probable hydrolase (NCBI) 320, 387
PA1710 exsC ExsC, exoenzyme S synthesis protein C precursor. (NCBI) 117, 218
PA1711 exsE ExsE (NCBI) 117, 218
PA1852 PA1852 hypothetical protein (NCBI) 117, 224
PA1853 PA1853 probable transcriptional regulator (NCBI) 117, 490
PA2043 PA2043 hypothetical protein (NCBI) 372, 387
PA2063 PA2063 hypothetical protein (NCBI) 65, 387
PA2533 PA2533 probable sodium:alanine symporter (NCBI) 117, 315
PA2584 pgsA CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (NCBI) 117, 261
PA2651 PA2651 hypothetical protein (NCBI) 30, 117
PA2856 tesA acyl-CoA thioesterase I precursor (NCBI) 70, 117
PA2857 PA2857 probable ATP-binding component of ABC transporter (NCBI) 31, 117
PA2858 PA2858 hypothetical protein (NCBI) 60, 117
PA2859 greB transcription elongation factor GreB (NCBI) 117, 268
PA2871 PA2871 hypothetical protein (NCBI) 117, 387
PA2872 PA2872 hypothetical protein (NCBI) 117, 387
PA2873 PA2873 hypothetical protein (NCBI) 49, 387
PA2874 PA2874 hypothetical protein (NCBI) 117, 387
PA2875 PA2875 hypothetical protein (NCBI) 117, 387
PA2901 PA2901 hypothetical protein (NCBI) 8, 117
PA2902 PA2902 hypothetical protein (NCBI) 8, 117
PA2982 PA2982 hypothetical protein (NCBI) 387, 490
PA3012 PA3012 hypothetical protein (NCBI) 117, 195
PA3033 PA3033 hypothetical protein (NCBI) 117, 220
PA3072 PA3072 hypothetical protein (NCBI) 320, 387
PA3073 PA3073 hypothetical protein (NCBI) 60, 387
PA3086 PA3086 hypothetical protein (NCBI) 62, 387
PA3106 PA3106 short chain dehydrogenase (NCBI) 387, 442
PA3315 PA3315 probable permease of ABC transporter (NCBI) 92, 387
PA3316 PA3316 probable permease of ABC transporter (NCBI) 171, 387
PA3322 PA3322 hypothetical protein (NCBI) 58, 387
PA3345 PA3345 hypothetical protein (NCBI) 139, 387
PA3401 PA3401 hypothetical protein (NCBI) 374, 387
PA3402 PA3402 hypothetical protein (NCBI) 337, 387
PA3764 PA3764 hypothetical protein (NCBI) 374, 387
PA3854 PA3854 hypothetical protein (NCBI) 72, 117
PA4048 PA4048 hypothetical protein (NCBI) 99, 387
PA4051 thiL thiamine monophosphate kinase (NCBI) 99, 387
PA4060 PA4060 hypothetical protein (NCBI) 228, 387
PA4286 PA4286 hypothetical protein (NCBI) 8, 117
PA4316 sbcB exodeoxyribonuclease I (NCBI) 51, 117
PA4580 PA4580 hypothetical protein (NCBI) 326, 387
PA4678 rimI peptide n-acetyltransferase RimI (NCBI) 103, 387
PA4769 PA4769 probable transcriptional regulator (NCBI) 59, 117
PA5065 ubiB ubiquinone biosynthetic protein UbiB (NCBI) 43, 387
PA5071 PA5071 hypothetical protein (NCBI) 65, 387
PA5351 rubA1 Rubredoxin 1 (NCBI) 117, 490
PA5443 uvrD DNA helicase II (NCBI) 117, 261
PA5516 pdxY pyridoxine kinase (NCBI) 151, 387
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 PA1397
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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