Organism : Pseudomonas aeruginosa | Module List :
PA4500

probable binding protein component of ABC transporter (NCBI)

CircVis
Functional Annotations (4)
Function System
ABC-type dipeptide transport system, periplasmic component cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
ABC transporters kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4500
(Mouseover regulator name to see its description)

PA4500 is regulated by 58 influences and regulates 0 modules.
Regulators for PA4500 (58)
Regulator Module Operator
PA0149 491 tf
PA0533 491 tf
PA0797 491 tf
PA1159 491 tf
PA1759 491 tf
PA1760 491 tf
PA1853 491 tf
PA1949 491 tf
PA1978 491 tf
PA2020 491 tf
PA2056 491 tf
PA2121 491 tf
PA2376 491 tf
PA2551 491 tf
PA2917 491 tf
PA3895 491 tf
PA4196 491 tf
PA4354 491 tf
PA4436 491 tf
PA4769 491 tf
PA4853 491 tf
PA5189 491 tf
PA5380 491 tf
PA5428 491 tf
PA0149 142 tf
PA0533 142 tf
PA0797 142 tf
PA0828 142 tf
PA0942 142 tf
PA1351 142 tf
PA1653 142 tf
PA1759 142 tf
PA1760 142 tf
PA1859 142 tf
PA1949 142 tf
PA2020 142 tf
PA2115 142 tf
PA2277 142 tf
PA2312 142 tf
PA2376 142 tf
PA2692 142 tf
PA2848 142 tf
PA2917 142 tf
PA3133 142 tf
PA3341 142 tf
PA3420 142 tf
PA3921 142 tf
PA4052 142 tf
PA4436 142 tf
PA4451 142 tf
PA4769 142 tf
PA4914 142 tf
PA5105 142 tf
PA5324 142 tf
PA5356 142 tf
PA5380 142 tf
PA5428 142 tf
PA5562 142 tf

Warning: PA4500 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
3114 6.00e-02 CaAtcacAagAAaggcagc
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3115 1.80e+01 tT.GAAaA
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3796 2.30e-09 acaacAA.aAcAA.aagag
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3797 2.00e+02 attccCtt.caaaaaGaaAAcat
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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 PA4500

PA4500 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
ABC-type dipeptide transport system, periplasmic component cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
ABC transporters kegg/ kegg pathway
Module neighborhood information for PA4500

PA4500 has total of 38 gene neighbors in modules 142, 491
Gene neighbors (38)
Gene Common Name Description Module membership
PA0887 acsA acetyl-coenzyme A synthetase (NCBI) 239, 491
PA1818 PA1818 probable Orn/Arg/Lys decarboxylase (NCBI) 193, 491
PA1991 PA1991 probable iron-containing alcohol dehydrogenase (NCBI) 239, 491
PA1992 PA1992 probable two-component sensor (NCBI) 425, 491
PA2862 lipA lactonizing lipase precursor (NCBI) 491, 515
PA3038 PA3038 probable porin (NCBI) 239, 491
PA3079 PA3079 hypothetical protein (NCBI) 470, 491
PA3080 PA3080 hypothetical protein (NCBI) 470, 491
PA3232 PA3232 DNA polymerase III subunit epsilon (NCBI) 470, 491
PA3233 PA3233 hypothetical protein (NCBI) 470, 491
PA3234 actP acetate permease (NCBI) 239, 491
PA3235 PA3235 hypothetical protein (NCBI) 239, 491
PA3710 PA3710 probable GMC-type oxidoreductase (NCBI) 142, 239
PA4496 PA4496 probable binding protein component of ABC transporter (NCBI) 142, 491
PA4497 PA4497 probable binding protein component of ABC transporter (NCBI) 142, 491
PA4500 PA4500 probable binding protein component of ABC transporter (NCBI) 142, 491
PA4501 PA4501 probable porin (NCBI) 142, 491
PA4502 PA4502 probable binding protein component of ABC transporter (NCBI) 142, 491
PA4503 PA4503 probable permease of ABC transporter (NCBI) 142, 491
PA4504 PA4504 probable permease of ABC transporter (NCBI) 142, 491
PA4505 PA4505 probable ATP-binding component of ABC transporter (NCBI) 142, 491
PA4506 PA4506 probable ATP-binding component of ABC dipeptide transporter (NCBI) 142, 491
PA5091 hutG N-formylglutamate amidohydrolase (NCBI) 84, 142
PA5092 hutI imidazolonepropionase (NCBI) 84, 142
PA5093 PA5093 probable histidine/phenylalanine ammonia-lyase (NCBI) 142, 345
PA5094 PA5094 probable ATP-binding component of ABC transporter (NCBI) 142, 345
PA5095 PA5095 probable permease of ABC transporter (NCBI) 84, 142
PA5096 PA5096 probable binding protein component of ABC transporter (NCBI) 84, 142
PA5097 PA5097 probable amino acid permease (NCBI) 142, 345
PA5098 hutH histidine ammonia-lyase (NCBI) 142, 345
PA5099 PA5099 probable transporter (NCBI) 142, 425
PA5167 PA5167 probable c4-dicarboxylate-binding protein (NCBI) 193, 491
PA5168 PA5168 probable dicarboxylate transporter (NCBI) 470, 491
PA5169 PA5169 probable C4-dicarboxylate transporter (NCBI) 470, 491
PA5380 PA5380 probable transcriptional regulator (NCBI) 239, 491
PA5542 PA5542 hypothetical protein (NCBI) 483, 491
PA5543 PA5543 hypothetical protein (NCBI) 491, 515
PA5545 PA5545 hypothetical protein (NCBI) 491, 515
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 PA4500
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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