Organism : Pseudomonas aeruginosa | Module List :
PA2737

hypothetical protein (NCBI)

CircVis
Functional Annotations (5)
Function System
Predicted transcriptional regulators cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2737
(Mouseover regulator name to see its description)

PA2737 is regulated by 30 influences and regulates 30 modules.
Regulators for PA2737 (30)
Regulator Module Operator
PA0167 513 tf
PA0436 513 tf
PA1159 513 tf
PA2577 513 tf
PA2586 513 tf
PA2737 513 tf
PA2899 513 tf
PA3563 513 tf
PA4057 513 tf
PA4493 513 tf
PA5253 513 tf
PA5344 513 tf
PA0133 51 tf
PA0167 51 tf
PA0289 51 tf
PA0376 51 tf
PA0393 51 tf
PA0436 51 tf
PA0780 51 tf
PA0815 51 tf
PA2551 51 tf
PA2577 51 tf
PA2713 51 tf
PA2718 51 tf
PA2737 51 tf
PA2859 51 tf
PA2897 51 tf
PA5253 51 tf
PA5255 51 tf
PA5344 51 tf

Warning: PA2737 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
2934 1.40e+01 TTCCccttGtGcCGGaGcCgttc
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2935 3.20e+01 CgaCAATcCGTCcCgGagC
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3840 1.10e+01 AaaCaaCGaAtcggCGccAgC
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3841 1.00e+01 GgTCAtccgaGggcTgtCTG
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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 PA2737

PA2737 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Predicted transcriptional regulators cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for PA2737

PA2737 has total of 42 gene neighbors in modules 51, 513
Gene neighbors (42)
Gene Common Name Description Module membership
PA0055 PA0055 hypothetical protein (NCBI) 237, 513
PA0318 PA0318 hypothetical protein (NCBI) 51, 513
PA0336 ygdP dinucleoside polyphosphate hydrolase (NCBI) 51, 70
PA0376 rpoH sigma factor RpoH (NCBI) 51, 455
PA0867 PA0867 hypothetical protein (NCBI) 51, 316
PA0900 PA0900 hypothetical protein (NCBI) 95, 513
PA1307 PA1307 hypothetical protein (NCBI) 378, 513
PA1376 aceK bifunctional isocitrate dehydrogenase kinase/phosphatase protein (NCBI) 513, 551
PA1377 PA1377 hypothetical protein (NCBI) 248, 513
PA1505 moaA2 molybdopterin biosynthetic protein A2 (NCBI) 51, 63
PA1640 PA1640 hypothetical protein (NCBI) 51, 384
PA1813 PA1813 probable hydroxyacylglutathione hydrolase (NCBI) 51, 513
PA1815 rnhA ribonuclease H (NCBI) 51, 208
PA1832 PA1832 probable protease (NCBI) 51, 268
PA2586 gacA response regulator GacA (NCBI) 57, 513
PA2737 PA2737 hypothetical protein (NCBI) 51, 513
PA2738 ihfA integration host factor subunit alpha (NCBI) 88, 513
PA3202 PA3202 hypothetical protein (NCBI) 18, 513
PA3260 PA3260 probable transcriptional regulator (NCBI) 51, 248
PA3472 PA3472 hypothetical protein (NCBI) 368, 513
PA4026 PA4026 probable acetyltransferase (NCBI) 51, 523
PA4090 PA4090 hypothetical protein (NCBI) 316, 513
PA4316 sbcB exodeoxyribonuclease I (NCBI) 51, 117
PA4493 PA4493 probable two-component response regulator (NCBI) 75, 513
PA4532 PA4532 hypothetical protein (NCBI) 51, 405
PA4533 PA4533 hypothetical protein (NCBI) 51, 405
PA4534 PA4534 hypothetical protein (NCBI) 51, 405
PA4535 PA4535 hypothetical protein (NCBI) 63, 513
PA4536 PA4536 hypothetical protein (NCBI) 51, 405
PA4537 PA4537 hypothetical protein (NCBI) 51, 70
PA4538 ndh NADH dehydrogenase (NCBI) 51, 405
PA4578 PA4578 hypothetical protein (NCBI) 95, 513
PA4639 PA4639 hypothetical protein (NCBI) 6, 51
PA4698 PA4698 hypothetical protein (NCBI) 316, 513
PA4699 PA4699 hypothetical protein (NCBI) 316, 513
PA4714 PA4714 hypothetical protein (NCBI) 51, 208
PA4726 cbrB two-component response regulator CbrB (NCBI) 51, 88
PA4793 PA4793 hypothetical protein (NCBI) 513, 551
PA4872 PA4872 hypothetical protein (NCBI) 51, 540
PA4951 orn oligoribonuclease (NCBI) 51, 202
PA5255 algQ Alginate regulatory protein AlgQ (NCBI) 51, 248
PA5364 PA5364 probable two-component response regulator (NCBI) 316, 513
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 PA2737
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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