Organism : Pseudomonas aeruginosa | Module List :
PA2957

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2957
(Mouseover regulator name to see its description)

PA2957 is regulated by 28 influences and regulates 54 modules.
Regulators for PA2957 (28)
Regulator Module Operator
PA0167 178 tf
PA0564 178 tf
PA0961 178 tf
PA1015 178 tf
PA1526 178 tf
PA2115 178 tf
PA2246 178 tf
PA2957 178 tf
PA3027 178 tf
PA3322 178 tf
PA3604 178 tf
PA3804 178 tf
PA4275 178 tf
PA4451 178 tf
PA4764 178 tf
PA5105 178 tf
PA5274 178 tf
PA5344 178 tf
PA0125 354 tf
PA0456 354 tf
PA2020 354 tf
PA2957 354 tf
PA3266 354 tf
PA4275 354 tf
PA4451 354 tf
PA4745 354 tf
PA4853 354 tf
PA5403 354 tf

Warning: PA2957 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
3184 6.80e+00 gtccgccaccgt.GCAatGgc
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3185 3.70e+02 gGtcATGGCaTGgaGCGAga
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3532 2.10e+00 tAaaAtagccggC.t
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3533 9.30e+03 TAATTAA
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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 PA2957

PA2957 is enriched for 5 functions in 3 categories.
Module neighborhood information for PA2957

PA2957 has total of 33 gene neighbors in modules 178, 354
Gene neighbors (33)
Gene Common Name Description Module membership
PA0115 PA0115 hypothetical protein (NCBI) 170, 178
PA0362 fdx1 ferredoxin (4Fe-4S) (NCBI) 139, 354
PA0363 coaD phosphopantetheine adenylyltransferase (NCBI) 72, 178
PA1192 PA1192 hypothetical protein (NCBI) 354, 474
PA1532 dnaX DNA polymerase III subunits gamma and tau (NCBI) 94, 178
PA1674 folE2 GTP cyclohydrolase I precursor (NCBI) 122, 178
PA1734 PA1734 hypothetical protein (NCBI) 178, 266
PA1735 PA1735 hypothetical protein (NCBI) 178, 266
PA2019 PA2019 RND multidrug efflux membrane fusion protein precursor (NCBI) 309, 354
PA2957 PA2957 probable transcriptional regulator (NCBI) 178, 354
PA3131 PA3131 probable aldolase (NCBI) 178, 229
PA3243 minC septum formation inhibitor (NCBI) 178, 271
PA3245 minE cell division topological specificity factor MinE (NCBI) 178, 271
PA3621 fdxA ferredoxin I (NCBI) 354, 424
PA3639 accA acetyl-CoA carboxylase alpha subunit (NCBI) 77, 178
PA3817 PA3817 probable methyltransferase (NCBI) 354, 424
PA3822 yajC preprotein translocase subunit YajC (NCBI) 178, 271
PA3828 PA3828 hypothetical protein (NCBI) 111, 354
PA3966 PA3966 hypothetical protein (NCBI) 354, 424
PA4035 PA4035 hypothetical protein (NCBI) 178, 315
PA4042 xseB exodeoxyribonuclease VII small subunit (NCBI) 123, 178
PA4043 ispA geranyltranstransferase (NCBI) 123, 178
PA4381 PA4381 probable two-component response regulator (NCBI) 178, 315
PA4451 PA4451 hypothetical protein (NCBI) 354, 424
PA4456 PA4456 probable ATP-binding component of ABC transporter (NCBI) 178, 474
PA4642 PA4642 hypothetical protein (NCBI) 354, 384
PA4746 PA4746 hypothetical protein (NCBI) 354, 424
PA4753 PA4753 hypothetical protein (NCBI) 232, 354
PA5049 rpmE 50S ribosomal protein L31 (NCBI) 354, 454
PA5184 PA5184 chorismate mutase (NCBI) 178, 251
PA5274 rnk nucleoside diphosphate kinase regulator (NCBI) 77, 178
PA5286 PA5286 hypothetical protein (NCBI) 354, 424
PA5561 atpI ATP synthase subunit I (NCBI) 131, 354
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 PA2957
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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