Organism : Pseudomonas aeruginosa | Module List :
PA0791

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 PA0791
(Mouseover regulator name to see its description)

PA0791 is regulated by 30 influences and regulates 21 modules.
Regulators for PA0791 (30)
Regulator Module Operator
PA0791 136 tf
PA1290 136 tf
PA1945 136 tf
PA2016 136 tf
PA2076 136 tf
PA2093 136 tf
PA2281 136 tf
PA3094 136 tf
PA3420 136 tf
PA3565 136 tf
PA4269 136 tf
PA4703 136 tf
PA4745 136 tf
PA4769 136 tf
PA5189 136 tf
PA5344 136 tf
PA5389 136 tf
PA0533 432 tf
PA0791 432 tf
PA1136 432 tf
PA1264 432 tf
PA1399 432 tf
PA1539 432 tf
PA2206 432 tf
PA3973 432 tf
PA4269 432 tf
PA4703 432 tf
PA4914 432 tf
PA5059 432 tf
PA5105 432 tf

Warning: PA0791 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
3102 3.30e-05 TTtgtcTcGTgATagccGgAat
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3103 2.60e-05 GCAgAAcAAGa
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3684 2.00e-03 TtCccatcGAAaAcCgccgcaga
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3685 2.70e+02 TGCCAGGCTgGCCaGacCTACCC
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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 PA0791

PA0791 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 PA0791

PA0791 has total of 46 gene neighbors in modules 136, 432
Gene neighbors (46)
Gene Common Name Description Module membership
PA0187 PA0187 hypothetical protein (NCBI) 326, 432
PA0229 pcaT dicarboxylic acid transporter PcaT (NCBI) 104, 432
PA0256 PA0256 hypothetical protein (NCBI) 136, 450
PA0348 PA0348 hypothetical protein (NCBI) 136, 471
PA0585 PA0585 hypothetical protein (NCBI) 74, 136
PA0741 PA0741 hypothetical protein (NCBI) 432, 475
PA0791 PA0791 probable transcriptional regulator (NCBI) 136, 432
PA1028 PA1028 probable oxidoreductase (NCBI) 136, 516
PA1136 PA1136 probable transcriptional regulator (NCBI) 323, 432
PA1208 PA1208 hypothetical protein (NCBI) 3, 432
PA1283 PA1283 probable transcriptional regulator (NCBI) 79, 432
PA1362 PA1362 hypothetical protein (NCBI) 373, 432
PA1433 PA1433 hypothetical protein (NCBI) 432, 538
PA1434 PA1434 hypothetical protein (NCBI) 432, 538
PA1531 PA1531 hypothetical protein (NCBI) 196, 432
PA1604 PA1604 hypothetical protein (NCBI) 34, 432
PA1747 PA1747 hypothetical protein (NCBI) 373, 432
PA1945 PA1945 probable transcriptional regulator (NCBI) 68, 136
PA1968 PA1968 hypothetical protein (NCBI) 208, 432
PA2048 PA2048 hypothetical protein (NCBI) 136, 461
PA2814 PA2814 hypothetical protein (NCBI) 136, 469
PA2868 PA2868 hypothetical protein (NCBI) 39, 432
PA2949 PA2949 probable lipase (NCBI) 313, 432
PA2958 PA2958 hypothetical protein (NCBI) 136, 461
PA3032 snr1 cytochrome c Snr1 (NCBI) 74, 432
PA3216 PA3216 hypothetical protein (NCBI) 136, 294
PA3287 PA3287 hypothetical protein (NCBI) 152, 432
PA3342 PA3342 hypothetical protein (NCBI) 136, 292
PA3499 PA3499 hypothetical protein (NCBI) 373, 432
PA3681 PA3681 hypothetical protein (NCBI) 394, 432
PA3787 PA3787 hypothetical protein (NCBI) 432, 469
PA3973 PA3973 probable transcriptional regulator (NCBI) 163, 432
PA4653 PA4653 hypothetical protein (NCBI) 367, 432
PA4680 PA4680 hypothetical protein (NCBI) 136, 292
PA4681 PA4681 hypothetical protein (NCBI) 136, 292
PA4682 PA4682 hypothetical protein (NCBI) 136, 292
PA4975 PA4975 NAD(P)H quinone oxidoreductase (NCBI) 97, 432
PA5185 PA5185 hypothetical protein (NCBI) 136, 397
PA5186 PA5186 probable iron-containing alcohol dehydrogenase (NCBI) 136, 397
PA5187 PA5187 probable acyl-CoA dehydrogenase (NCBI) 136, 397
PA5188 PA5188 probable 3-hydroxyacyl-CoA dehydrogenase (NCBI) 136, 397
PA5189 PA5189 probable transcriptional regulator (NCBI) 136, 397
PA5389 PA5389 probable transcriptional regulator (NCBI) 136, 294
PA5394 cls cardiolipin synthetase (NCBI) 373, 432
PA5395 PA5395 hypothetical protein (NCBI) 84, 432
PA5520 PA5520 hypothetical protein (NCBI) 136, 432
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 PA0791
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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