Organism : Pseudomonas aeruginosa | Module List :
PA4596

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (4)
Function System
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
transcription regulator activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4596
(Mouseover regulator name to see its description)

PA4596 is regulated by 31 influences and regulates 14 modules.
Regulators for PA4596 (31)
Regulator Module Operator
PA0218 550 tf
PA0780 550 tf
PA0839 550 tf
PA1097 550 tf
PA1363 550 tf
PA1653 550 tf
PA2100 550 tf
PA2601 550 tf
PA3002 550 tf
PA3587 550 tf
PA3678 550 tf
PA4203 550 tf
PA4596 550 tf
PA4878 550 tf
PA5431 550 tf
PA0424 212 tf
PA0535 212 tf
PA1754 212 tf
PA2047 212 tf
PA3006 212 tf
PA3948 212 tf
PA3965 212 tf
PA4185 212 tf
PA4275 212 tf
PA4451 212 tf
PA4600 212 tf
PA4906 212 tf
PA5239 212 tf
PA5308 212 tf
PA5337 212 tf
PA5438 212 tf
Regulated by PA4596 (14)
Module Residual Genes
33 0.54 23
55 0.48 19
81 0.51 21
115 0.41 15
117 0.58 31
265 0.49 21
300 0.44 18
363 0.48 19
414 0.48 21
420 0.56 21
431 0.44 19
462 0.56 25
487 0.49 23
550 0.57 28
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
3252 6.30e+00 ACaTAAAA
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3253 7.00e-02 TGtaaaTaTaTT
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3912 2.40e-01 AaGcAgttTGcggaaggTtTC
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3913 4.80e-02 gTtcttaTgcTtGGcGGaagAgtA
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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 PA4596

PA4596 is enriched for 4 functions in 2 categories.
Enrichment Table (4)
Function System
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
transcription regulator activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for PA4596

PA4596 has total of 57 gene neighbors in modules 212, 550
Gene neighbors (57)
Gene Common Name Description Module membership
PA0320 PA0320 hypothetical protein (NCBI) 9, 212
PA0328 PA0328 hypothetical protein (NCBI) 313, 550
PA0377 PA0377 hypothetical protein (NCBI) 212, 341
PA0457 PA0457 hypothetical protein (NCBI) 3, 550
PA0530 PA0530 probable class III pyridoxal phosphate-dependent aminotransferase (NCBI) 536, 550
PA0534 PA0534 hypothetical protein (NCBI) 152, 212
PA0535 PA0535 probable transcriptional regulator (NCBI) 152, 212
PA0653 PA0653 hypothetical protein (NCBI) 212, 499
PA0730 PA0730 probable transferase (NCBI) 212, 371
PA0777 PA0777 hypothetical protein (NCBI) 157, 550
PA0780 pruR proline utilization regulator (NCBI) 245, 550
PA0839 PA0839 probable transcriptional regulator (NCBI) 26, 550
PA0840 PA0840 probable oxidoreductase (NCBI) 523, 550
PA0848 PA0848 probable alkyl hydroperoxide reductase (NCBI) 152, 550
PA0936 lpxO2 lipopolysaccharide biosynthetic protein LpxO2 (NCBI) 86, 212
PA1035 PA1035 hypothetical protein (NCBI) 212, 271
PA1183 dctA C4-dicarboxylate transport protein (NCBI) 166, 212
PA1363 PA1363 probable sigma-70 factor, ECF subfamily (NCBI) 99, 550
PA1364 PA1364 probable transmembrane sensor (NCBI) 99, 550
PA1536 PA1536 hypothetical protein (NCBI) 313, 550
PA1608 PA1608 probable chemotaxis transducer (NCBI) 212, 268
PA1653 PA1653 probable transcriptional regulator (NCBI) 151, 550
PA1755 PA1755 hypothetical protein (NCBI) 23, 550
PA2020 PA2020 probable transcriptional regulator (NCBI) 212, 309
PA2026 PA2026 hypothetical protein (NCBI) 26, 550
PA2687 pfeS two-component sensor PfeS (NCBI) 339, 550
PA2769 PA2769 hypothetical protein (NCBI) 126, 212
PA2839 PA2839 hypothetical protein (NCBI) 140, 550
PA3240 PA3240 hypothetical protein (NCBI) 39, 212
PA3387 rhlG beta-ketoacyl reductase (NCBI) 192, 550
PA3587 metR transcriptional regulator MetR (NCBI) 243, 550
PA3676 PA3676 probable Resistance-Nodulation-Cell Division (RND) efflux transporter (NCBI) 39, 550
PA3677 PA3677 probable Resistance-Nodulation-Cell Division (RND) efflux membrane fusion protein precursor (NCBI) 528, 550
PA3678 PA3678 probable transcriptional regulator (NCBI) 452, 550
PA3721 PA3721 probable transcriptional regulator (NCBI) 189, 212
PA3730 PA3730 hypothetical protein (NCBI) 212, 468
PA3866 PA3866 pyocin protein (NCBI) 11, 212
PA3916 moaE molybdopterin converting factor, large subunit (NCBI) 212, 376
PA3917 moaD molybdopterin converting factor, small subunit (NCBI) 212, 376
PA3918 moaC molybdenum cofactor biosynthesis protein C (NCBI) 212, 376
PA3941 PA3941 hypothetical protein (NCBI) 100, 550
PA3948 PA3948 probable two-component response regulator (NCBI) 212, 477
PA3951 PA3951 hypothetical protein (NCBI) 212, 306
PA3959 PA3959 hypothetical protein (NCBI) 425, 550
PA4185 PA4185 probable transcriptional regulator (NCBI) 125, 212
PA4405 PA4405 hypothetical protein (NCBI) 212, 511
PA4427 sspB stringent starvation protein B (NCBI) 131, 212
PA4499 PA4499 probable transcriptional regulator (NCBI) 131, 212
PA4596 PA4596 probable transcriptional regulator (NCBI) 212, 550
PA4878 PA4878 probable transcriptional regulator (NCBI) 407, 550
PA5157 PA5157 probable transcriptional regulator (NCBI) 212, 473
PA5249 PA5249 hypothetical protein (NCBI) 507, 550
PA5330 PA5330 hypothetical protein (NCBI) 212, 352
PA5350 rubA2 rubredoxin 2 (NCBI) 212, 338
PA5375 betT1 choline transporter BetT (NCBI) 545, 550
PA5512 PA5512 probable two-component sensor (NCBI) 374, 550
PA5527 PA5527 hypothetical protein (NCBI) 212, 224
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 PA4596
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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