Organism : Pseudomonas aeruginosa | Module List :
PA1422 gbuR

GbuR (NCBI)

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

Cytoscape Web
Regulation information for PA1422
(Mouseover regulator name to see its description)

PA1422 is regulated by 30 influences and regulates 22 modules.
Regulators for PA1422 gbuR (30)
Regulator Module Operator
PA0123 517 tf
PA0393 517 tf
PA0455 517 tf
PA0961 517 tf
PA1422 517 tf
PA1484 517 tf
PA1490 517 tf
PA2047 517 tf
PA3002 517 tf
PA3604 517 tf
PA3622 517 tf
PA3804 517 tf
PA4853 517 tf
PA4890 517 tf
PA5344 517 tf
PA5562 517 tf
PA1128 151 tf
PA1422 151 tf
PA1504 151 tf
PA1653 151 tf
PA2028 151 tf
PA2921 151 tf
PA3322 151 tf
PA3583 151 tf
PA3864 151 tf
PA4196 151 tf
PA4745 151 tf
PA4890 151 tf
PA5261 151 tf
PA5403 151 tf

Warning: PA1422 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
3132 1.40e-09 atgcgtCAaA..gcTtgaccgAaa
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3133 1.90e-05 AG.gTa.a.At..CtGA.CTGA.a
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3848 4.70e+02 atTTTtcGcCa
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3849 2.30e+04 ATaTCTAAA
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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 PA1422

PA1422 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for PA1422

PA1422 has total of 45 gene neighbors in modules 151, 517
Gene neighbors (45)
Gene Common Name Description Module membership
PA0267 PA0267 hypothetical protein (NCBI) 170, 517
PA0285 PA0285 hypothetical protein (NCBI) 517, 528
PA0455 dbpA RNA helicase DbpA (NCBI) 306, 517
PA0772 recO DNA repair protein RecO (NCBI) 151, 387
PA0834 PA0834 hypothetical protein (NCBI) 261, 517
PA0925 PA0925 hypothetical protein (NCBI) 493, 517
PA1304 PA1304 probable oligopeptidase (NCBI) 499, 517
PA1416 PA1416 hypothetical protein (NCBI) 151, 240
PA1417 PA1417 probable decarboxylase (NCBI) 151, 240
PA1418 PA1418 probable sodium:solute symport protein (NCBI) 151, 240
PA1419 PA1419 probable transporter (NCBI) 151, 240
PA1420 PA1420 hypothetical protein (NCBI) 151, 240
PA1421 gbuA guanidinobutyrase (NCBI) 151, 240
PA1422 gbuR GbuR (NCBI) 151, 517
PA1490 PA1490 probable transcriptional regulator (NCBI) 384, 517
PA1653 PA1653 probable transcriptional regulator (NCBI) 151, 550
PA1654 PA1654 probable aminotransferase (NCBI) 151, 462
PA1655 PA1655 probable glutathione S-transferase (NCBI) 151, 462
PA1758 pabB para-aminobenzoate synthase component I (NCBI) 1, 517
PA2560 PA2560 hypothetical protein (NCBI) 151, 248
PA2561 PA2561 probable chemotaxis transducer (NCBI) 48, 151
PA2843 PA2843 probable aldolase (NCBI) 151, 374
PA2977 murB UDP-N-acetylenolpyruvoylglucosamine reductase (NCBI) 1, 517
PA3297 PA3297 probable ATP-dependent helicase (NCBI) 442, 517
PA3539 PA3539 hypothetical protein (NCBI) 517, 528
PA3862 PA3862 hypothetical protein (NCBI) 151, 517
PA3863 PA3863 hypothetical protein (NCBI) 49, 517
PA3984 lnt apolipoprotein N-acyltransferase (NCBI) 517, 528
PA4045 PA4045 hypothetical protein (NCBI) 126, 151
PA4455 PA4455 probable permease of ABC transporter (NCBI) 474, 517
PA4498 PA4498 probable metallopeptidase (NCBI) 131, 517
PA4618 PA4618 hypothetical protein (NCBI) 3, 517
PA4619 PA4619 probable c-type cytochrome (NCBI) 1, 517
PA4620 PA4620 hypothetical protein (NCBI) 1, 517
PA4621 PA4621 probable oxidoreductase (NCBI) 401, 517
PA4731 panD aspartate 1-decarboxylase precursor (NCBI) 384, 517
PA4845 dipZ thiol:disulfide interchange protein precursor (NCBI) 249, 517
PA4923 PA4923 hypothetical protein (NCBI) 255, 517
PA5074 PA5074 probable ATP-binding component of ABC transporter (NCBI) 43, 151
PA5075 PA5075 probable permease of ABC transporter (NCBI) 151, 234
PA5250 PA5250 hypothetical protein (NCBI) 151, 480
PA5251 PA5251 hypothetical protein (NCBI) 82, 151
PA5252 PA5252 probable ATP-binding component of ABC transporter (NCBI) 151, 490
PA5302 dadX catabolic alanine racemase (NCBI) 3, 517
PA5516 pdxY pyridoxine kinase (NCBI) 151, 387
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 PA1422
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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