Organism : Pseudomonas aeruginosa | Module List :
PA4135

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (8)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
phenylacetate catabolic process go/ biological_process
transcription repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
HpaR tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4135
(Mouseover regulator name to see its description)

PA4135 is regulated by 26 influences and regulates 7 modules.
Regulators for PA4135 (26)
Regulator Module Operator
PA0456 315 tf
PA2047 315 tf
PA2957 315 tf
PA4057 315 tf
PA4135 315 tf
PA4238 315 tf
PA4275 315 tf
PA4451 315 tf
PA4600 315 tf
PA4703 315 tf
PA4745 315 tf
PA4755 315 tf
PA4853 315 tf
PA4890 315 tf
PA5342 315 tf
PA5344 315 tf
PA0116 268 tf
PA0155 268 tf
PA2489 268 tf
PA3864 268 tf
PA3895 268 tf
PA4135 268 tf
PA4182 268 tf
PA4784 268 tf
PA4890 268 tf
PA5166 268 tf
Regulated by PA4135 (7)
Module Residual Genes
5 0.34 16
122 0.45 14
268 0.57 39
315 0.59 21
342 0.54 26
502 0.36 15
505 0.56 25
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
3364 1.80e+03 TTTTTCccaTatTcatgcgcaatt
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3365 6.50e+03 aTcCATTcCcga
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3456 1.50e+03 ATaa.AAcAAG
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3457 1.50e+02 GgCGccCGAtC
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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 PA4135

PA4135 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
phenylacetate catabolic process go/ biological_process
transcription repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
HpaR tigr/ tigrfam
Module neighborhood information for PA4135

PA4135 has total of 59 gene neighbors in modules 268, 315
Gene neighbors (59)
Gene Common Name Description Module membership
PA0116 PA0116 hypothetical protein (NCBI) 253, 268
PA0159 PA0159 probable transcriptional regulator (NCBI) 49, 268
PA0162 PA0162 probable porin (NCBI) 315, 451
PA0313 PA0313 probable permease of ABC transporter (NCBI) 268, 306
PA0454 PA0454 hypothetical protein (NCBI) 60, 268
PA0778 icp inhibitor of cysteine peptidase (NCBI) 315, 499
PA0782 putA proline dehydrogenase PutA (NCBI) 4, 315
PA0783 putP sodium/proline symporter PutP (NCBI) 131, 315
PA0952 PA0952 hypothetical protein (NCBI) 261, 315
PA1014 PA1014 probable glycosyl transferase (NCBI) 8, 315
PA1171 PA1171 probable transglycolase (NCBI) 268, 420
PA1326 ilvA2 threonine dehydratase, biosynthetic (NCBI) 268, 291
PA1423 PA1423 probable chemotaxis transducer (NCBI) 268, 320
PA1608 PA1608 probable chemotaxis transducer (NCBI) 212, 268
PA1613 PA1613 hypothetical protein (NCBI) 123, 268
PA1832 PA1832 probable protease (NCBI) 51, 268
PA1845 PA1845 hypothetical protein (NCBI) 45, 268
PA2028 PA2028 probable transcriptional regulator (NCBI) 268, 507
PA2201 PA2201 hypothetical protein (NCBI) 33, 315
PA2533 PA2533 probable sodium:alanine symporter (NCBI) 117, 315
PA2567 PA2567 hypothetical protein (NCBI) 26, 268
PA2683 PA2683 serine/threonine dehydratase (NCBI) 49, 268
PA2698 PA2698 probable hydrolase (NCBI) 152, 268
PA2823 PA2823 hypothetical protein (NCBI) 220, 315
PA2859 greB transcription elongation factor GreB (NCBI) 117, 268
PA2907 cobL precorrin-6y-dependent methyltransferase CobL (NCBI) 268, 442
PA3061 pelD hypothetical protein (NCBI) 268, 434
PA3215 PA3215 probable transcriptional regulator (NCBI) 268, 528
PA3222 PA3222 hypothetical protein (NCBI) 189, 268
PA3310 PA3310 hypothetical protein (NCBI) 78, 315
PA3638 PA3638 hypothetical protein (NCBI) 315, 528
PA3747 PA3747 hypothetical protein (NCBI) 315, 493
PA3748 PA3748 hypothetical protein (NCBI) 315, 493
PA3855 PA3855 hypothetical protein (NCBI) 220, 268
PA3864 PA3864 hypothetical protein (NCBI) 60, 268
PA3895 PA3895 probable transcriptional regulator (NCBI) 220, 268
PA3934 PA3934 hypothetical protein (NCBI) 268, 380
PA3950 PA3950 probable ATP-dependent RNA helicase (NCBI) 143, 315
PA4010 PA4010 3-methyladenine DNA glycosylase (NCBI) 170, 315
PA4035 PA4035 hypothetical protein (NCBI) 178, 315
PA4073 PA4073 probable aldehyde dehydrogenase (NCBI) 125, 268
PA4109 ampR transcriptional regulator AmpR (NCBI) 49, 268
PA4118 PA4118 hypothetical protein (NCBI) 59, 268
PA4135 PA4135 probable transcriptional regulator (NCBI) 268, 315
PA4138 tyrS tyrosyl-tRNA synthetase (NCBI) 268, 326
PA4157 PA4157 probable transcriptional regulator (NCBI) 138, 268
PA4182 PA4182 hypothetical protein (NCBI) 42, 268
PA4307 pctC chemotactic transducer PctC (NCBI) 170, 315
PA4381 PA4381 probable two-component response regulator (NCBI) 178, 315
PA4440 PA4440 hypothetical protein (NCBI) 123, 315
PA4543 PA4543 hypothetical protein (NCBI) 268, 528
PA4624 PA4624 hypothetical protein (NCBI) 185, 268
PA4725 cbrA two-component sensor CbrA (NCBI) 268, 295
PA4784 PA4784 probable transcriptional regulator (NCBI) 9, 268
PA5197 rimK ribosomal protein S6 modification protein (NCBI) 53, 268
PA5204 argA N-acetylglutamate synthase (NCBI) 268, 383
PA5215 gcvT1 aminomethyltransferase (NCBI) 143, 315
PA5273 PA5273 hypothetical protein (NCBI) 20, 268
PA5430 PA5430 hypothetical protein (NCBI) 268, 497
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 PA4135
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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