Organism : Pseudomonas aeruginosa | Module List :
PA2556

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (6)
Function System
Adenosine deaminase 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 PA2556
(Mouseover regulator name to see its description)

PA2556 is regulated by 34 influences and regulates 16 modules.
Regulators for PA2556 (34)
Regulator Module Operator
PA0207 87 tf
PA0905 87 tf
PA1125 87 tf
PA1241 87 tf
PA1484 87 tf
PA1850 87 tf
PA2032 87 tf
PA2047 87 tf
PA2556 87 tf
PA2718 87 tf
PA2897 87 tf
PA3363 87 tf
PA3921 87 tf
PA3965 87 tf
PA4169 87 tf
PA4196 87 tf
PA4493 87 tf
PA5239 87 tf
PA5253 87 tf
PA5431 87 tf
PA5437 87 tf
PA0191 320 tf
PA0207 320 tf
PA0791 320 tf
PA1125 320 tf
PA1467 320 tf
PA1484 320 tf
PA1850 320 tf
PA1998 320 tf
PA2047 320 tf
PA2299 320 tf
PA2713 320 tf
PA3124 320 tf
PA3594 320 tf

Warning: PA2556 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
3006 4.40e+03 AtCtTGa.CG
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3007 4.00e+04 ATGCTcTCAGCTaTcTCT
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3466 1.10e+06 CGGTGAcTcTCCGT
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3467 5.80e+01 tctTgCaGAtca.Ga
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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 PA2556

PA2556 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Adenosine deaminase 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 PA2556

PA2556 has total of 60 gene neighbors in modules 87, 320
Gene neighbors (60)
Gene Common Name Description Module membership
PA0104 PA0104 hypothetical protein (NCBI) 320, 335
PA0147 PA0147 probable oxidoreductase (NCBI) 74, 87
PA0231 pcaD beta-ketoadipate enol-lactone hydrolase (NCBI) 87, 399
PA0259 PA0259 hypothetical protein (NCBI) 87, 320
PA0314 PA0314 probable binding protein component of ABC transporter (NCBI) 53, 87
PA0333 PA0333 hypothetical protein (NCBI) 61, 320
PA0368 PA0368 hypothetical protein (NCBI) 320, 355
PA0656 PA0656 probable HIT family protein (NCBI) 87, 233
PA0851 PA0851 hypothetical protein (NCBI) 320, 475
PA0861 PA0861 hypothetical protein (NCBI) 34, 87
PA0983 PA0983 hypothetical protein (NCBI) 168, 320
PA1124 dgt deoxyguanosinetriphosphate triphosphohydrolase (NCBI) 87, 127
PA1125 PA1125 probable cobalamin biosynthetic protein (NCBI) 87, 127
PA1127 PA1127 probable oxidoreductase (NCBI) 26, 320
PA1181 PA1181 hypothetical protein (NCBI) 202, 320
PA1308 PA1308 hypothetical protein (NCBI) 53, 87
PA1368 PA1368 hypothetical protein (NCBI) 320, 445
PA1415 PA1415 hypothetical protein (NCBI) 87, 295
PA1423 PA1423 probable chemotaxis transducer (NCBI) 268, 320
PA1487 PA1487 probable carbohydrate kinase (NCBI) 295, 320
PA1494 PA1494 hypothetical protein (NCBI) 87, 293
PA1495 PA1495 hypothetical protein (NCBI) 87, 295
PA1506 PA1506 hypothetical protein (NCBI) 320, 321
PA1622 PA1622 probable hydrolase (NCBI) 320, 387
PA1624 PA1624 hypothetical protein (NCBI) 10, 320
PA1651 PA1651 probable transporter (NCBI) 320, 321
PA1819 PA1819 probable amino acid permease (NCBI) 87, 338
PA1934 PA1934 hypothetical protein (NCBI) 9, 320
PA1943 PA1943 hypothetical protein (NCBI) 87, 475
PA2049 PA2049 hypothetical protein (NCBI) 60, 320
PA2199 PA2199 probable dehydrogenase (NCBI) 320, 389
PA2345 PA2345 hypothetical protein (NCBI) 87, 475
PA2437 PA2437 hypothetical protein (NCBI) 320, 446
PA2556 PA2556 probable transcriptional regulator (NCBI) 87, 320
PA2778 PA2778 hypothetical protein (NCBI) 87, 163
PA2822 PA2822 hypothetical protein (NCBI) 295, 320
PA2825 PA2825 probable transcriptional regulator (NCBI) 79, 320
PA3072 PA3072 hypothetical protein (NCBI) 320, 387
PA3093 PA3093 hypothetical protein (NCBI) 157, 320
PA3124 PA3124 probable transcriptional regulator (NCBI) 196, 320
PA3138 uvrB excinuclease ABC subunit B (NCBI) 3, 87
PA3254 PA3254 probable ATP-binding component of ABC transporter (NCBI) 84, 320
PA3255 PA3255 hypothetical protein (NCBI) 84, 320
PA3317 PA3317 hypothetical protein (NCBI) 31, 320
PA3697 PA3697 hypothetical protein (NCBI) 7, 87
PA3751 purT 5'-phosphoribosylglycinamide transformylase (NCBI) 53, 87
PA3969 PA3969 hypothetical protein (NCBI) 320, 475
PA4018 PA4018 hypothetical protein (NCBI) 320, 355
PA4108 PA4108 hypothetical protein (NCBI) 87, 475
PA4162 PA4162 short chain dehydrogenase (NCBI) 39, 320
PA4183 PA4183 hypothetical protein (NCBI) 187, 320
PA4327 PA4327 hypothetical protein (NCBI) 34, 87
PA4388 PA4388 hypothetical protein (NCBI) 3, 320
PA4392 PA4392 hypothetical protein (NCBI) 320, 450
PA4486 PA4486 hypothetical protein (NCBI) 30, 320
PA4958 PA4958 hypothetical protein (NCBI) 81, 87
PA5123 PA5123 hypothetical protein (NCBI) 187, 320
PA5305 PA5305 hypothetical protein (NCBI) 87, 88
PA5376 PA5376 probable ATP-binding component of ABC transporter (NCBI) 87, 399
PA5377 PA5377 probable permease of ABC transporter (NCBI) 87, 399
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 PA2556
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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