Organism : Pseudomonas aeruginosa | Module List :
PA2376

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (7)
Function System
Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
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 PA2376
(Mouseover regulator name to see its description)

PA2376 is regulated by 25 influences and regulates 35 modules.
Regulators for PA2376 (25)
Regulator Module Operator
PA0816 334 tf
PA1097 334 tf
PA1197 334 tf
PA1347 334 tf
PA1351 334 tf
PA1467 334 tf
PA1826 334 tf
PA1980 334 tf
PA2258 334 tf
PA2259 334 tf
PA2376 334 tf
PA2488 334 tf
PA3133 334 tf
PA3599 334 tf
PA4270 334 tf
PA5324 334 tf
PA1399 307 tf
PA1467 307 tf
PA2376 307 tf
PA2488 307 tf
PA2489 307 tf
PA2510 307 tf
PA2838 307 tf
PA3714 307 tf
PA5032 307 tf

Warning: PA2376 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
3440 5.20e-06 tagaAc.GcggcttaTcCAtC
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3441 5.60e-02 AagaaG.CgATG.aTGgtTcg
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3494 2.50e+00 GAcTTccttgttgttgTCG
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3495 8.90e-01 gACaCctgcAtAaGaaCaGCgC
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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 PA2376

PA2376 is enriched for 7 functions in 3 categories.
Module neighborhood information for PA2376

PA2376 has total of 35 gene neighbors in modules 307, 334
Gene neighbors (35)
Gene Common Name Description Module membership
PA0489 PA0489 probable phosphoribosyl transferase (NCBI) 334, 450
PA0814 PA0814 hypothetical protein (NCBI) 243, 334
PA0816 PA0816 probable transcriptional regulator (NCBI) 334, 359
PA1185 PA1185 probable glutathione S-transferase (NCBI) 140, 334
PA1399 PA1399 probable transcriptional regulator (NCBI) 44, 307
PA1400 PA1400 probable pyruvate carboxylase (NCBI) 44, 307
PA1782 PA1782 probable serine/threonine-protein kinase (NCBI) 307, 334
PA1882 PA1882 probable transporter (NCBI) 283, 307
PA1883 PA1883 probable NADH-ubiquinone/plastoquinone oxidoreductase (NCBI) 109, 307
PA2259 ptxS transcriptional regulator PtxS (NCBI) 100, 334
PA2260 PA2260 hypothetical protein (NCBI) 100, 334
PA2261 PA2261 probable 2-ketogluconate kinase (NCBI) 100, 334
PA2262 PA2262 probable 2-ketogluconate transporter (NCBI) 100, 334
PA2263 PA2263 probable 2-hydroxyacid dehydrogenase (NCBI) 100, 334
PA2344 mtlZ fructokinase (NCBI) 196, 307
PA2349 PA2349 hypothetical protein (NCBI) 289, 307
PA2376 PA2376 probable transcriptional regulator (NCBI) 307, 334
PA2429 PA2429 hypothetical protein (NCBI) 334, 519
PA2431 PA2431 hypothetical protein (NCBI) 334, 519
PA2434 PA2434 hypothetical protein (NCBI) 34, 334
PA2435 PA2435 probable cation-transporting P-type ATPase (NCBI) 235, 334
PA2487 PA2487 hypothetical protein (NCBI) 290, 307
PA2488 PA2488 probable transcriptional regulator (NCBI) 290, 307
PA2489 PA2489 probable transcriptional regulator (NCBI) 290, 307
PA2490 PA2490 hypothetical protein (NCBI) 290, 307
PA2510 catR transcriptional regulator CatR (NCBI) 307, 351
PA2589 PA2589 hypothetical protein (NCBI) 307, 366
PA2716 PA2716 probable FMN oxidoreductase (NCBI) 334, 386
PA2786 PA2786 hypothetical protein (NCBI) 307, 326
PA3275 PA3275 hypothetical protein (NCBI) 326, 334
PA3339 PA3339 hypothetical protein (NCBI) 65, 307
PA3597 PA3597 probable amino acid permease (NCBI) 334, 428
PA3598 PA3598 hypothetical protein (NCBI) 236, 334
PA3599 PA3599 probable transcriptional regulator (NCBI) 236, 334
PA4344 PA4344 probable hydrolase (NCBI) 280, 334
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 PA2376
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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