Organism : Pseudomonas aeruginosa | Module List :
PA3449

hypothetical protein (NCBI)

CircVis
Functional Annotations (8)
Function System
ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components cog/ cog
transporter activity go/ molecular_function
sulfur compound metabolic process go/ biological_process
transport go/ biological_process
membrane go/ cellular_component
outer membrane-bounded periplasmic space go/ cellular_component
ABC transporters kegg/ kegg pathway
SsuA_fam tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3449
(Mouseover regulator name to see its description)

PA3449 is regulated by 19 influences and regulates 0 modules.
Regulators for PA3449 (19)
Regulator Module Operator
PA0191 538 tf
PA1399 538 tf
PA1826 538 tf
PA1945 538 tf
PA1980 538 tf
PA2050 538 tf
PA2093 538 tf
PA3133 538 tf
PA3381 538 tf
PA3596 538 tf
PA4270 538 tf
PA4341 538 tf
PA4902 538 tf
PA5293 538 tf
PA0191 93 tf
PA2050 93 tf
PA2093 93 tf
PA3932 93 tf
PA4203 93 tf

Warning: PA3449 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
3018 1.40e+00 TTT.TTaT
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3019 3.90e+02 AAaaATtA.TT
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3888 1.10e-07 GaTacgCTttctatAAAgAagAa
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3889 4.00e-02 CtGaCcC.cgat.gacAATC
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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 PA3449

PA3449 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components cog/ cog
transporter activity go/ molecular_function
sulfur compound metabolic process go/ biological_process
transport go/ biological_process
membrane go/ cellular_component
outer membrane-bounded periplasmic space go/ cellular_component
ABC transporters kegg/ kegg pathway
SsuA_fam tigr/ tigrfam
Module neighborhood information for PA3449

PA3449 has total of 39 gene neighbors in modules 93, 538
Gene neighbors (39)
Gene Common Name Description Module membership
PA0197 PA0197 hypothetical protein (NCBI) 93, 362
PA0198 exbB1 transport protein ExbB (NCBI) 93, 362
PA0199 exbD1 transport protein ExbD (NCBI) 93, 362
PA1433 PA1433 hypothetical protein (NCBI) 432, 538
PA1434 PA1434 hypothetical protein (NCBI) 432, 538
PA1435 PA1435 probable Resistance-Nodulation-Cell Division (RND) efflux membrane fusion protein precursor (NCBI) 418, 538
PA1436 PA1436 probable Resistance-Nodulation-Cell Division (RND) efflux transporter (NCBI) 418, 538
PA1437 PA1437 probable two-component response regulator (NCBI) 418, 538
PA1438 PA1438 probable two-component sensor (NCBI) 418, 538
PA2084 PA2084 probable asparagine synthetase (NCBI) 287, 538
PA2085 PA2085 probable ring-hydroxylating dioxygenase small subunit (NCBI) 287, 538
PA2086 PA2086 probable epoxide hydrolase (NCBI) 287, 538
PA2087 PA2087 hypothetical protein (NCBI) 287, 538
PA2090 PA2090 hypothetical protein (NCBI) 287, 538
PA2091 PA2091 hypothetical protein (NCBI) 287, 538
PA2092 PA2092 probable major facilitator superfamily (MFS) transporter (NCBI) 287, 538
PA2093 PA2093 probable sigma-70 factor, ECF subfamily (NCBI) 287, 538
PA2594 PA2594 hypothetical protein (NCBI) 93, 301
PA2600 PA2600 hypothetical protein (NCBI) 93, 109
PA3237 PA3237 hypothetical protein (NCBI) 152, 538
PA3441 PA3441 probable molybdopterin-binding protein (NCBI) 93, 301
PA3442 PA3442 probable ATP-binding component of ABC transporter (NCBI) 93, 301
PA3443 PA3443 probable permease of ABC transporter (NCBI) 93, 301
PA3444 PA3444 alkanesulfonate monooxygenase (NCBI) 93, 301
PA3445 PA3445 hypothetical protein (NCBI) 93, 301
PA3447 PA3447 probable ATP-binding component of ABC transporter (NCBI) 93, 362
PA3448 PA3448 probable permease of ABC transporter (NCBI) 93, 362
PA3449 PA3449 hypothetical protein (NCBI) 93, 538
PA3932 PA3932 probable transcriptional regulator (NCBI) 93, 406
PA3935 tauD taurine dioxygenase (NCBI) 93, 301
PA3936 PA3936 probable permease of ABC taurine transporter (NCBI) 93, 301
PA3937 PA3937 probable ATP-binding component of ABC taurine transporter (NCBI) 93, 301
PA3938 PA3938 probable periplasmic taurine-binding protein precursor (NCBI) 93, 301
PA4898 PA4898 probable porin (NCBI) 536, 538
PA4899 PA4899 probable aldehyde dehydrogenase (NCBI) 345, 538
PA4900 PA4900 probable major facilitator superfamily (MFS) transporter (NCBI) 538, 545
PA4901 mdlC benzoylformate decarboxylase (NCBI) 532, 538
PA4902 PA4902 probable transcriptional regulator (NCBI) 536, 538
PA5102 PA5102 hypothetical protein (NCBI) 337, 538
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 PA3449
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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