Organism : Pseudomonas aeruginosa | Module List :
PA1619

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 PA1619
(Mouseover regulator name to see its description)

PA1619 is regulated by 11 influences and regulates 9 modules.
Regulators for PA1619 (11)
Regulator Module Operator
PA0163 362 tf
PA0191 362 tf
PA0272 362 tf
PA1413 362 tf
PA2050 362 tf
PA2093 362 tf
PA3133 362 tf
PA3391 362 tf
PA3594 362 tf
PA3932 362 tf
PA4174 362 tf

Warning: PA1619 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
3468 5.60e+02 AaacccCgtCTTTT
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3469 2.10e+01 tAaCcgggcGgcTtCGccctG.a
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3548 1.80e-07 TttTtgTTATg.a
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3549 2.70e+00 tAt.c.aTatgGttATAagaA
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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 PA1619

PA1619 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 PA1619

PA1619 has total of 58 gene neighbors in modules 321, 362
Gene neighbors (58)
Gene Common Name Description Module membership
PA0183 atsA arylsulfatase (NCBI) 201, 362
PA0184 PA0184 probable ATP-binding component of ABC transporter (NCBI) 50, 362
PA0185 PA0185 probable permease of ABC transporter (NCBI) 359, 362
PA0186 PA0186 probable binding protein component of ABC transporter (NCBI) 362, 497
PA0191 PA0191 probable transcriptional regulator (NCBI) 362, 406
PA0197 PA0197 hypothetical protein (NCBI) 93, 362
PA0198 exbB1 transport protein ExbB (NCBI) 93, 362
PA0199 exbD1 transport protein ExbD (NCBI) 93, 362
PA0202 PA0202 probable amidase (NCBI) 197, 362
PA0203 PA0203 probable binding protein component of ABC transporter (NCBI) 197, 362
PA0206 PA0206 probable ATP-binding component of ABC transporter (NCBI) 355, 362
PA0416 chpD probable transcriptional regulator (NCBI) 3, 321
PA0698 PA0698 hypothetical protein (NCBI) 321, 400
PA0988 PA0988 hypothetical protein (NCBI) 209, 321
PA1060 PA1060 hypothetical protein (NCBI) 321, 511
PA1407 PA1407 hypothetical protein (NCBI) 321, 451
PA1506 PA1506 hypothetical protein (NCBI) 320, 321
PA1619 PA1619 probable transcriptional regulator (NCBI) 321, 362
PA1620 PA1620 hypothetical protein (NCBI) 92, 362
PA1651 PA1651 probable transporter (NCBI) 320, 321
PA1834 PA1834 hypothetical protein (NCBI) 189, 321
PA1886 polB DNA polymerase II (NCBI) 321, 483
PA2050 PA2050 probable sigma-70 factor, ECF subfamily (NCBI) 362, 545
PA2126 PA2126 hypothetical protein (NCBI) 162, 321
PA2202 PA2202 probable amino acid permease (NCBI) 362, 406
PA2203 PA2203 probable amino acid permease (NCBI) 362, 406
PA2583 PA2583 probable sensor/response regulator hybrid (NCBI) 296, 321
PA2790 PA2790 hypothetical protein (NCBI) 321, 457
PA2879 PA2879 probable transcriptional regulator (NCBI) 321, 546
PA2884 PA2884 hypothetical protein (NCBI) 321, 450
PA3140 PA3140 hypothetical protein (NCBI) 321, 401
PA3197 PA3197 hypothetical protein (NCBI) 321, 374
PA3304 PA3304 hypothetical protein (NCBI) 196, 321
PA3305 PA3305 hypothetical protein (NCBI) 321, 546
PA3355 PA3355 hypothetical protein (NCBI) 321, 330
PA3386 PA3386 hypothetical protein (NCBI) 362, 412
PA3447 PA3447 probable ATP-binding component of ABC transporter (NCBI) 93, 362
PA3448 PA3448 probable permease of ABC transporter (NCBI) 93, 362
PA3578 PA3578 hypothetical protein (NCBI) 224, 321
PA3623 PA3623 hypothetical protein (NCBI) 321, 341
PA3881 PA3881 hypothetical protein (NCBI) 8, 321
PA3939 PA3939 hypothetical protein (NCBI) 326, 362
PA4016 PA4016 hypothetical protein (NCBI) 3, 321
PA4034 aqpZ aquaporin Z (NCBI) 30, 321
PA4094 PA4094 probable transcriptional regulator (NCBI) 61, 321
PA4191 PA4191 probable iron/ascorbate oxidoreductase (NCBI) 301, 362
PA4192 PA4192 probable ATP-binding component of ABC transporter (NCBI) 301, 362
PA4195 PA4195 probable binding protein component of ABC transporter (NCBI) 301, 362
PA4295 PA4295 hypothetical protein (NCBI) 159, 321
PA4510 PA4510 hypothetical protein (NCBI) 321, 537
PA4531 PA4531 hypothetical protein (NCBI) 245, 321
PA4683 PA4683 hypothetical protein (NCBI) 321, 371
PA5086 PA5086 hypothetical protein (NCBI) 231, 321
PA5126 PA5126 hypothetical protein (NCBI) 196, 321
PA5175 cysQ CysQ protein (NCBI) 220, 321
PA5177 PA5177 probable hydrolase (NCBI) 232, 321
PA5474 PA5474 probable metalloprotease (NCBI) 321, 405
PA5477 PA5477 hypothetical protein (NCBI) 321, 355
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 PA1619
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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