Organism : Pseudomonas aeruginosa | Module List :
PA1015

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA1015
(Mouseover regulator name to see its description)

PA1015 is regulated by 40 influences and regulates 23 modules.
Regulators for PA1015 (40)
Regulator Module Operator
PA0121 319 tf
PA0123 319 tf
PA0159 319 tf
PA0527 319 tf
PA0873 319 tf
PA1003 319 tf
PA1015 319 tf
PA1269 319 tf
PA1290 319 tf
PA1351 319 tf
PA1430 319 tf
PA1633 319 tf
PA1653 319 tf
PA1859 319 tf
PA2588 319 tf
PA2692 319 tf
PA2758 319 tf
PA4070 319 tf
PA4279 319 tf
PA4462 319 tf
PA4890 319 tf
PA0120 52 tf
PA0121 52 tf
PA0123 52 tf
PA0236 52 tf
PA0527 52 tf
PA0547 52 tf
PA1003 52 tf
PA1015 52 tf
PA1269 52 tf
PA1290 52 tf
PA1430 52 tf
PA1633 52 tf
PA1653 52 tf
PA1859 52 tf
PA2588 52 tf
PA2758 52 tf
PA4070 52 tf
PA4462 52 tf
PA4890 52 tf

Warning: PA1015 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
2936 7.20e+02 a.TGTcgAtcA
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2937 5.30e+03 aAtaCTGctTGcaAg.Acaa.AA
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3464 1.10e+03 TccccgggCggttc.Tct.gCaGg
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3465 3.50e+03 aTGtCgATcA
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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 PA1015

PA1015 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for PA1015

PA1015 has total of 21 gene neighbors in modules 52, 319
Gene neighbors (21)
Gene Common Name Description Module membership
PA1015 PA1015 probable transcriptional regulator (NCBI) 52, 319
PA1016 PA1016 thiolase (NCBI) 52, 319
PA1017 pauA pimeloyl-CoA synthetase (NCBI) 52, 319
PA1018 PA1018 hypothetical protein (NCBI) 52, 319
PA1019 mucK cis,cis-muconate transporter MucK (NCBI) 52, 61
PA1020 PA1020 probable acyl-CoA dehydrogenase (NCBI) 52, 319
PA1021 PA1021 probable enoyl-CoA hydratase/isomerase (NCBI) 52, 319
PA1022 PA1022 probable acyl-CoA dehydrogenase (NCBI) 52, 319
PA1023 PA1023 probable short-chain dehydrogenase (NCBI) 52, 319
PA1024 PA1024 hypothetical protein (NCBI) 52, 319
PA1632 kdpF KdpF protein (NCBI) 267, 319
PA1633 kdpA potassium-transporting ATPase subunit A (NCBI) 291, 319
PA1634 kdpB potassium-transporting ATPase, B chain (NCBI) 267, 319
PA4101 PA4101 probable two-component response regulator (NCBI) 52, 319
PA4102 PA4102 probable two-component sensor (NCBI) 52, 319
PA4103 PA4103 hypothetical protein (NCBI) 52, 319
PA4104 PA4104 hypothetical protein (NCBI) 52, 319
PA4105 PA4105 hypothetical protein (NCBI) 52, 319
PA4106 PA4106 hypothetical protein (NCBI) 52, 319
PA4107 PA4107 hypothetical protein (NCBI) 52, 319
PA4110 ampC beta-lactamase precursor (NCBI) 52, 319
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 PA1015
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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