Organism : Pseudomonas aeruginosa | Module List :
PA4821

probable transporter (NCBI)

CircVis
Functional Annotations (6)
Function System
Na+-driven multidrug efflux pump cog/ cog
drug transmembrane transport go/ biological_process
drug transmembrane transporter activity go/ molecular_function
antiporter activity go/ molecular_function
membrane go/ cellular_component
matE tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4821
(Mouseover regulator name to see its description)

PA4821 is regulated by 34 influences and regulates 0 modules.
Regulators for PA4821 (34)
Regulator Module Operator
PA0056 463 tf
PA0133 463 tf
PA0306 463 tf
PA0701 463 tf
PA0828 463 tf
PA1109 463 tf
PA1351 463 tf
PA1399 463 tf
PA1826 463 tf
PA2050 463 tf
PA2376 463 tf
PA3002 463 tf
PA3045 463 tf
PA3381 463 tf
PA3594 463 tf
PA3714 463 tf
PA3771 463 tf
PA5032 463 tf
PA0032 335 tf
PA0163 335 tf
PA0236 335 tf
PA2050 335 tf
PA2115 335 tf
PA2957 335 tf
PA3458 335 tf
PA3714 335 tf
PA3864 335 tf
PA3921 335 tf
PA4169 335 tf
PA4989 335 tf
PA5253 335 tf
PA5382 335 tf
PA5431 335 tf
PA5437 335 tf

Warning: PA4821 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
3496 1.70e+02 cgcaattTagcCctT
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3497 1.80e+00 ATGAaAAA
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3742 5.00e-09 atAAGaAAaACA
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3743 2.20e-08 CgcGGcGaatcCttCGAaAA.C
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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 PA4821

PA4821 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Na+-driven multidrug efflux pump cog/ cog
drug transmembrane transport go/ biological_process
drug transmembrane transporter activity go/ molecular_function
antiporter activity go/ molecular_function
membrane go/ cellular_component
matE tigr/ tigrfam
Module neighborhood information for PA4821

PA4821 has total of 50 gene neighbors in modules 335, 463
Gene neighbors (50)
Gene Common Name Description Module membership
PA0013 PA0013 hypothetical protein (NCBI) 335, 375
PA0104 PA0104 hypothetical protein (NCBI) 320, 335
PA0219 PA0219 probable aldehyde dehydrogenase (NCBI) 335, 425
PA0236 PA0236 probable transcriptional regulator (NCBI) 299, 335
PA0241 PA0241 probable major facilitator superfamily (MFS) transporter (NCBI) 25, 463
PA0246 PA0246 probable major facilitator superfamily (MFS) transporter (NCBI) 92, 335
PA0573 PA0573 hypothetical protein (NCBI) 92, 335
PA0914 PA0914 hypothetical protein (NCBI) 207, 335
PA0915 PA0915 hypothetical protein (NCBI) 207, 335
PA1006 PA1006 hypothetical protein (NCBI) 247, 335
PA1007 PA1007 hypothetical protein (NCBI) 247, 335
PA1146 PA1146 probable iron-containing alcohol dehydrogenase (NCBI) 359, 463
PA1321 cyoE cytochrome o ubiquinol oxidase protein CyoE (NCBI) 23, 335
PA1367 PA1367 hypothetical protein (NCBI) 101, 335
PA1424 PA1424 hypothetical protein (NCBI) 23, 335
PA1425 PA1425 probable ATP-binding component of ABC transporter (NCBI) 335, 438
PA1591 PA1591 hypothetical protein (NCBI) 40, 335
PA1595 PA1595 hypothetical protein (NCBI) 313, 335
PA1826 PA1826 probable transcriptional regulator (NCBI) 373, 463
PA1827 PA1827 probable short-chain dehydrogenase (NCBI) 366, 463
PA1849 PA1849 hypothetical protein (NCBI) 335, 408
PA1884 PA1884 probable transcriptional regulator (NCBI) 335, 375
PA1978 PA1978 probable transcriptional regulator (NCBI) 335, 470
PA2745 PA2745 probable hydrolase (NCBI) 335, 372
PA2763 PA2763 hypothetical protein (NCBI) 335, 445
PA2852 PA2852 hypothetical protein (NCBI) 101, 335
PA3219 PA3219 hypothetical protein (NCBI) 211, 463
PA3571 mmsR transcriptional regulator MmsR (NCBI) 236, 335
PA3589 PA3589 acetyl-CoA acetyltransferase (NCBI) 36, 463
PA3590 PA3590 probable hydroxyacyl-CoA dehydrogenase (NCBI) 333, 463
PA3591 PA3591 probable enoyl-CoA hydratase/isomerase (NCBI) 36, 463
PA3592 PA3592 hypothetical protein (NCBI) 394, 463
PA3593 PA3593 probable acyl-CoA dehydrogenase (NCBI) 359, 463
PA3594 PA3594 probable transcriptional regulator (NCBI) 355, 463
PA3663 PA3663 hypothetical protein (NCBI) 335, 344
PA3679 PA3679 hypothetical protein (NCBI) 335, 438
PA4364 PA4364 hypothetical protein (NCBI) 463, 534
PA4365 PA4365 probable transporter (NCBI) 109, 463
PA4818 PA4818 hypothetical protein (NCBI) 180, 463
PA4819 PA4819 probable glycosyl transferase (NCBI) 180, 463
PA4820 PA4820 hypothetical protein (NCBI) 311, 463
PA4821 PA4821 probable transporter (NCBI) 335, 463
PA4989 PA4989 probable transcriptional regulator (NCBI) 266, 335
PA5034 hemE uroporphyrinogen decarboxylase (NCBI) 335, 422
PA5246 PA5246 hypothetical protein (NCBI) 61, 335
PA5256 dsbH disulfide bond formation protein (NCBI) 181, 335
PA5309 PA5309 probable oxidoreductase (NCBI) 335, 445
PA5311 PA5311 probable major facilitator superfamily (MFS) transporter (NCBI) 266, 335
PA5385 PA5385 hypothetical protein (NCBI) 177, 463
PA5547 PA5547 hypothetical protein (NCBI) 335, 373
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 PA4821
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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