Organism : Pseudomonas aeruginosa | Module List :
PA0306

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (6)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA binding go/ molecular_function
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 PA0306
(Mouseover regulator name to see its description)

PA0306 is regulated by 28 influences and regulates 17 modules.
Regulators for PA0306 (28)
Regulator Module Operator
PA0037 375 tf
PA0294 375 tf
PA0306 375 tf
PA0455 375 tf
PA1884 375 tf
PA1998 375 tf
PA2115 375 tf
PA2121 375 tf
PA2547 375 tf
PA3477 375 tf
PA3778 375 tf
PA3898 375 tf
PA5253 375 tf
PA0207 295 tf
PA0306 295 tf
PA1351 295 tf
PA1399 295 tf
PA1467 295 tf
PA1484 295 tf
PA1850 295 tf
PA2047 295 tf
PA2432 295 tf
PA2681 295 tf
PA2834 295 tf
PA3007 295 tf
PA3995 295 tf
PA4196 295 tf
PA4238 295 tf

Warning: PA0306 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
3418 1.10e+00 tCgGtgc.tgCcGAagAaagC
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3419 2.30e+01 CcGATGAtcgATcCG
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3574 3.10e-02 CatGAAGTcaatGGaCAATcaaGA
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3575 6.60e-02 tc.TttctGTgCgGagaAacctgc
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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 PA0306

PA0306 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA binding go/ molecular_function
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
Module neighborhood information for PA0306

PA0306 has total of 64 gene neighbors in modules 295, 375
Gene neighbors (64)
Gene Common Name Description Module membership
PA0010 tag DNA-3-methyladenine glycosidase I (NCBI) 65, 375
PA0013 PA0013 hypothetical protein (NCBI) 335, 375
PA0037 trpI transcriptional regulator TrpI (NCBI) 375, 377
PA0254 PA0254 hypothetical protein (NCBI) 295, 323
PA0294 aguR transcriptional regulator AguR (NCBI) 20, 375
PA0305 PA0305 hypothetical protein (NCBI) 375, 380
PA0306 PA0306 probable transcriptional regulator (NCBI) 295, 375
PA0383 PA0383 hypothetical protein (NCBI) 375, 377
PA0481 PA0481 hypothetical protein (NCBI) 291, 295
PA0544 PA0544 hypothetical protein (NCBI) 313, 375
PA0545 PA0545 hypothetical protein (NCBI) 162, 375
PA0560 PA0560 hypothetical protein (NCBI) 229, 375
PA0571 PA0571 hypothetical protein (NCBI) 62, 295
PA0703 PA0703 probable major facilitator superfamily (MFS) transporter (NCBI) 283, 375
PA1044 PA1044 hypothetical protein (NCBI) 101, 375
PA1046 PA1046 hypothetical protein (NCBI) 241, 375
PA1110 PA1110 hypothetical protein (NCBI) 101, 375
PA1252 PA1252 probable L-malate dehydrogenase (NCBI) 180, 295
PA1311 phnX 2-phosphonoacetaldehyde hydrolase (NCBI) 295, 486
PA1401 PA1401 hypothetical protein (NCBI) 295, 507
PA1415 PA1415 hypothetical protein (NCBI) 87, 295
PA1484 PA1484 probable transcriptional regulator (NCBI) 294, 295
PA1487 PA1487 probable carbohydrate kinase (NCBI) 295, 320
PA1488 PA1488 hypothetical protein (NCBI) 295, 375
PA1489 PA1489 hypothetical protein (NCBI) 295, 375
PA1495 PA1495 hypothetical protein (NCBI) 87, 295
PA1496 PA1496 probable potassium channel (NCBI) 20, 295
PA1648 PA1648 probable oxidoreductase (NCBI) 84, 295
PA1831 PA1831 hypothetical protein (NCBI) 283, 375
PA1844 PA1844 hypothetical protein (NCBI) 235, 375
PA1858 str streptomycin 3''-phosphotransferase (NCBI) 246, 295
PA1859 PA1859 probable transcriptional regulator (NCBI) 9, 295
PA1878 PA1878 hypothetical protein (NCBI) 283, 295
PA1884 PA1884 probable transcriptional regulator (NCBI) 335, 375
PA1929 PA1929 hypothetical protein (NCBI) 189, 295
PA1931 PA1931 probable ferredoxin (NCBI) 280, 295
PA1936 PA1936 hypothetical protein (NCBI) 295, 445
PA2095 PA2095 hypothetical protein (NCBI) 287, 295
PA2628 PA2628 hypothetical protein (NCBI) 20, 375
PA2661 PA2661 hypothetical protein (NCBI) 375, 478
PA2822 PA2822 hypothetical protein (NCBI) 295, 320
PA2824 PA2824 probable sensor/response regulator hybrid (NCBI) 206, 295
PA2833 PA2833 hypothetical protein (NCBI) 295, 486
PA2834 PA2834 probable transcriptional regulator (NCBI) 295, 486
PA2836 PA2836 probable secretion protein (NCBI) 295, 486
PA3016 PA3016 hypothetical protein (NCBI) 48, 375
PA3076 PA3076 hypothetical protein (NCBI) 49, 295
PA3207 PA3207 hypothetical protein (NCBI) 295, 366
PA3318 PA3318 hypothetical protein (NCBI) 295, 366
PA3373 PA3373 hypothetical protein (NCBI) 109, 295
PA3403 PA3403 hypothetical protein (NCBI) 372, 375
PA3532 PA3532 hypothetical protein (NCBI) 375, 377
PA3759 PA3759 probable aminotransferase (NCBI) 295, 523
PA3826 PA3826 hypothetical protein (NCBI) 266, 375
PA3995 PA3995 probable transcriptional regulator (NCBI) 295, 546
PA4380 PA4380 probable two-component sensor (NCBI) 53, 295
PA4725 cbrA two-component sensor CbrA (NCBI) 268, 295
PA4999 waaL O-antigen ligase, WaaL (NCBI) 231, 375
PA5121 PA5121 hypothetical protein (NCBI) 40, 375
PA5310 PA5310 hypothetical protein (NCBI) 295, 461
PA5457 PA5457 hypothetical protein (NCBI) 20, 375
PA5468 PA5468 probable citrate transporter (NCBI) 344, 375
PA5469 PA5469 hypothetical protein (NCBI) 344, 375
PA5518 PA5518 probable potassium efflux transporter (NCBI) 40, 375
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 PA0306
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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