Organism : Pseudomonas aeruginosa | Module List :
PA4806

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (5)
Function System
DNA-binding HTH domain-containing proteins cog/ cog
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 PA4806
(Mouseover regulator name to see its description)

PA4806 is regulated by 38 influences and regulates 24 modules.
Regulators for PA4806 (38)
Regulator Module Operator
PA0207 445 tf
PA0393 445 tf
PA0491 445 tf
PA0701 445 tf
PA0828 445 tf
PA1067 445 tf
PA1347 445 tf
PA1980 445 tf
PA2050 445 tf
PA2227 445 tf
PA2547 445 tf
PA2704 445 tf
PA2737 445 tf
PA3045 445 tf
PA3133 445 tf
PA3381 445 tf
PA3420 445 tf
PA3594 445 tf
PA4806 445 tf
PA0828 546 tf
PA1290 546 tf
PA1347 546 tf
PA1484 546 tf
PA1603 546 tf
PA1850 546 tf
PA1864 546 tf
PA2220 546 tf
PA2423 546 tf
PA2846 546 tf
PA2879 546 tf
PA3027 546 tf
PA3995 546 tf
PA4021 546 tf
PA4196 546 tf
PA4659 546 tf
PA4806 546 tf
PA4890 546 tf
PA4906 546 tf
Regulated by PA4806 (24)
Module Residual Genes
25 0.40 13
80 0.43 20
148 0.42 19
156 0.44 25
180 0.41 14
183 0.38 14
211 0.44 19
214 0.50 19
226 0.64 16
254 0.44 24
303 0.46 18
312 0.48 15
324 0.51 27
333 0.50 27
369 0.37 15
372 0.52 24
379 0.36 14
389 0.60 24
394 0.44 24
445 0.52 21
472 0.45 27
486 0.47 21
487 0.49 23
546 0.54 31
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
3710 4.00e+01 TATcgGTGaAtAATcTGA
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3711 3.70e+02 cTGGTtGAgcGCcTgGaacatCtC
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3904 7.70e-11 tTattTaTaTaaaaatattaa
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3905 7.30e-01 act.ttcaT.ca..cA.atA
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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 PA4806

PA4806 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
DNA-binding HTH domain-containing proteins cog/ cog
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 PA4806

PA4806 has total of 51 gene neighbors in modules 445, 546
Gene neighbors (51)
Gene Common Name Description Module membership
PA0251 PA0251 hypothetical protein (NCBI) 324, 445
PA0435 PA0435 hypothetical protein (NCBI) 156, 445
PA0452 PA0452 probable stomatin-like protein (NCBI) 74, 546
PA0561 PA0561 hypothetical protein (NCBI) 157, 445
PA0977 PA0977 hypothetical protein (NCBI) 324, 445
PA1210 PA1210 hypothetical protein (NCBI) 288, 546
PA1290 PA1290 probable transcriptional regulator (NCBI) 469, 546
PA1347 PA1347 probable transcriptional regulator (NCBI) 394, 546
PA1368 PA1368 hypothetical protein (NCBI) 320, 445
PA1402 PA1402 hypothetical protein (NCBI) 283, 546
PA1542 PA1542 hypothetical protein (NCBI) 92, 546
PA1600 PA1600 probable cytochrome c (NCBI) 240, 546
PA1601 PA1601 probable aldehyde dehydrogenase (NCBI) 240, 546
PA1602 PA1602 probable oxidoreductase (NCBI) 240, 546
PA1621 PA1621 probable hydrolase (NCBI) 294, 546
PA1864 PA1864 probable transcriptional regulator (NCBI) 74, 546
PA1865 PA1865 hypothetical protein (NCBI) 366, 546
PA1866 PA1866 hypothetical protein (NCBI) 366, 546
PA1935 PA1935 hypothetical protein (NCBI) 324, 445
PA1936 PA1936 hypothetical protein (NCBI) 295, 445
PA2017 PA2017 hypothetical protein (NCBI) 288, 546
PA2036 PA2036 hypothetical protein (NCBI) 231, 445
PA2075 PA2075 hypothetical protein (NCBI) 288, 546
PA2610 PA2610 hypothetical protein (NCBI) 140, 546
PA2704 PA2704 probable transcriptional regulator (NCBI) 445, 497
PA2763 PA2763 hypothetical protein (NCBI) 335, 445
PA2773 PA2773 hypothetical protein (NCBI) 229, 445
PA2846 PA2846 probable transcriptional regulator (NCBI) 373, 546
PA2879 PA2879 probable transcriptional regulator (NCBI) 321, 546
PA3305 PA3305 hypothetical protein (NCBI) 321, 546
PA3323 PA3323 hypothetical protein (NCBI) 292, 546
PA3324 PA3324 short chain dehydrogenase (NCBI) 197, 546
PA3501 PA3501 hypothetical protein (NCBI) 254, 445
PA3868 PA3868 hypothetical protein (NCBI) 197, 445
PA3885 PA3885 hypothetical protein (NCBI) 197, 445
PA3933 PA3933 probable choline transporter (NCBI) 291, 445
PA3943 PA3943 hypothetical protein (NCBI) 443, 546
PA3971 PA3971 hypothetical protein (NCBI) 163, 546
PA3972 PA3972 probable acyl-CoA dehydrogenase (NCBI) 163, 546
PA3995 PA3995 probable transcriptional regulator (NCBI) 295, 546
PA4074 PA4074 probable transcriptional regulator (NCBI) 171, 445
PA4179 PA4179 probable porin (NCBI) 206, 445
PA4281 sbcD exonuclease SbcD (NCBI) 53, 546
PA4658 PA4658 hypothetical protein (NCBI) 450, 546
PA4659 PA4659 probable transcriptional regulator (NCBI) 450, 546
PA4660 phr deoxyribodipyrimidine photolyase (NCBI) 109, 546
PA4802 PA4802 hypothetical protein (NCBI) 337, 445
PA4806 PA4806 probable transcriptional regulator (NCBI) 445, 546
PA5309 PA5309 probable oxidoreductase (NCBI) 335, 445
PA5372 betA choline dehydrogenase (NCBI) 524, 546
PA5532 PA5532 hypothetical protein (NCBI) 23, 445
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 PA4806
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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