Organism : Pseudomonas aeruginosa | Module List :
PA5453 gmd

GDP-mannose 4,6-dehydratase (NCBI)

CircVis
Functional Annotations (9)
Function System
GDP-D-mannose dehydratase cog/ cog
intracellular go/ cellular_component
GDP-mannose 4,6-dehydratase activity go/ molecular_function
GDP-mannose metabolic process go/ biological_process
coenzyme binding go/ molecular_function
Fructose and mannose metabolism kegg/ kegg pathway
Amino sugar and nucleotide sugar metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
gmd tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA5453
(Mouseover regulator name to see its description)

PA5453 is regulated by 63 influences and regulates 0 modules.
Regulators for PA5453 gmd (63)
Regulator Module Operator
PA0610 336 tf
PA1015 336 tf
PA1159 336 tf
PA1285 336 tf
PA1335 336 tf
PA1359 336 tf
PA1403 336 tf
PA1467 336 tf
PA1653 336 tf
PA1759 336 tf
PA1760 336 tf
PA1850 336 tf
PA1853 336 tf
PA2016 336 tf
PA2020 336 tf
PA2484 336 tf
PA2591 336 tf
PA3921 336 tf
PA4021 336 tf
PA4070 336 tf
PA4354 336 tf
PA4755 336 tf
PA4787 336 tf
PA5380 336 tf
PA0125 215 tf
PA0167 215 tf
PA0218 215 tf
PA0393 215 tf
PA0864 215 tf
PA0893 215 tf
PA0942 215 tf
PA1099 215 tf
PA1159 215 tf
PA1290 215 tf
PA1335 215 tf
PA1422 215 tf
PA1467 215 tf
PA1484 215 tf
PA1607 215 tf
PA1633 215 tf
PA1759 215 tf
PA1760 215 tf
PA1850 215 tf
PA1853 215 tf
PA1945 215 tf
PA1949 215 tf
PA2376 215 tf
PA2838 215 tf
PA3898 215 tf
PA3921 215 tf
PA4070 215 tf
PA4094 215 tf
PA4270 215 tf
PA4354 215 tf
PA4436 215 tf
PA4787 215 tf
PA5105 215 tf
PA5288 215 tf
PA5324 215 tf
PA5344 215 tf
PA5380 215 tf
PA5438 215 tf
PA5483 215 tf

Warning: PA5453 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
3258 3.60e+01 agaaccaGaACAggA
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3259 6.90e+02 GATgaAA
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3498 1.20e+01 AtaACAAC
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3499 9.40e+03 GATAAA
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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 PA5453

PA5453 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
GDP-D-mannose dehydratase cog/ cog
intracellular go/ cellular_component
GDP-mannose 4,6-dehydratase activity go/ molecular_function
GDP-mannose metabolic process go/ biological_process
coenzyme binding go/ molecular_function
Fructose and mannose metabolism kegg/ kegg pathway
Amino sugar and nucleotide sugar metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
gmd tigr/ tigrfam
Module neighborhood information for PA5453

PA5453 has total of 31 gene neighbors in modules 215, 336
Gene neighbors (31)
Gene Common Name Description Module membership
PA0230 pcaB 3-carboxy-cis,cis-muconate cycloisomerase (NCBI) 163, 215
PA0232 pcaC gamma-carboxymuconolactone decarboxylase (NCBI) 215, 399
PA0301 spuE polyamine transport protein (NCBI) 215, 234
PA0302 spuF polyamine transport protein PotG (NCBI) 215, 234
PA0303 spuG polyamine transport protein PotH (NCBI) 215, 234
PA0304 spuH polyamine transport protein PotI (NCBI) 215, 234
PA1070 braG branched-chain amino acid transport protein BraG (NCBI) 193, 336
PA1071 braF branched-chain amino acid transport protein BraF (NCBI) 193, 336
PA1072 braE branched-chain amino acid transport protein BraE (NCBI) 193, 336
PA1335 PA1335 probable two-component response regulator (NCBI) 49, 215
PA1336 PA1336 probable two-component sensor (NCBI) 49, 215
PA1337 ansB glutaminase-asparaginase (NCBI) 15, 336
PA1338 ggt gamma-glutamyltranspeptidase precursor (NCBI) 193, 336
PA1339 PA1339 probable ATP-binding component of ABC transporter (NCBI) 15, 336
PA1340 PA1340 probable permease of ABC transporter (NCBI) 193, 336
PA1341 PA1341 probable permease of ABC transporter (NCBI) 193, 336
PA1984 PA1984 probable aldehyde dehydrogenase (NCBI) 239, 336
PA4023 PA4023 probable transport protein (NCBI) 239, 336
PA4024 eutB ethanolamine ammonia-lyase large subunit (NCBI) 239, 336
PA4025 PA4025 ethanolamine ammonia-lyase small subunit (NCBI) 239, 336
PA5448 wbpY glycosyltransferase WbpY (NCBI) 215, 336
PA5449 wbpX glycosyltransferase WbpX (NCBI) 215, 336
PA5450 wzt ABC subunit of A-band LPS efflux transporter (NCBI) 215, 336
PA5451 wzm membrane subunit of A-band LPS efflux transporter (NCBI) 215, 336
PA5452 wbpW phosphomannose isomerase/GDP-mannose WbpW (NCBI) 215, 336
PA5453 gmd GDP-mannose 4,6-dehydratase (NCBI) 215, 336
PA5454 rmd oxidoreductase Rmd (NCBI) 215, 336
PA5455 PA5455 hypothetical protein (NCBI) 215, 540
PA5456 PA5456 hypothetical protein (NCBI) 37, 215
PA5458 PA5458 hypothetical protein (NCBI) 20, 215
PA5459 PA5459 hypothetical protein (NCBI) 215, 540
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 PA5453
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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