Organism : Pseudomonas aeruginosa | Module List :
PA5163 rmlA

glucose-1-phosphate thymidylyltransferase (NCBI)

CircVis
Functional Annotations (8)
Function System
dTDP-glucose pyrophosphorylase cog/ cog
glucose-1-phosphate thymidylyltransferase activity go/ molecular_function
extracellular polysaccharide biosynthetic process go/ biological_process
Streptomycin biosynthesis kegg/ kegg pathway
Polyketide sugar unit biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
rmlA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA5163
(Mouseover regulator name to see its description)

PA5163 is regulated by 42 influences and regulates 0 modules.
Regulators for PA5163 rmlA (42)
Regulator Module Operator
PA0279 464 tf
PA0393 464 tf
PA0436 464 tf
PA0707 464 tf
PA0893 464 tf
PA0905 464 tf
PA1484 464 tf
PA1754 464 tf
PA2586 464 tf
PA3002 464 tf
PA3563 464 tf
PA3721 464 tf
PA3879 464 tf
PA4270 464 tf
PA4547 464 tf
PA5125 464 tf
PA5166 464 tf
PA5324 464 tf
PA0279 179 tf
PA0393 179 tf
PA0576 179 tf
PA0652 179 tf
PA0873 179 tf
PA0893 179 tf
PA1241 179 tf
PA2020 179 tf
PA2054 179 tf
PA2447 179 tf
PA2758 179 tf
PA3002 179 tf
PA3266 179 tf
PA3477 179 tf
PA3565 179 tf
PA3965 179 tf
PA4185 179 tf
PA4269 179 tf
PA4270 179 tf
PA4493 179 tf
PA4547 179 tf
PA5116 179 tf
PA5125 179 tf
PA5324 179 tf

Warning: PA5163 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
3186 4.70e-01 TtTcgaatTTTGT
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3187 2.30e+03 ACAcGTCC
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3744 2.00e+01 TtTtcgTt..aA
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3745 1.20e+02 TaGGtA.AgCT
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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 PA5163

PA5163 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
dTDP-glucose pyrophosphorylase cog/ cog
glucose-1-phosphate thymidylyltransferase activity go/ molecular_function
extracellular polysaccharide biosynthetic process go/ biological_process
Streptomycin biosynthesis kegg/ kegg pathway
Polyketide sugar unit biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
rmlA tigr/ tigrfam
Module neighborhood information for PA5163

PA5163 has total of 28 gene neighbors in modules 179, 464
Gene neighbors (28)
Gene Common Name Description Module membership
PA0387 PA0387 putative deoxyribonucleotide triphosphate pyrophosphatase (NCBI) 129, 464
PA0388 PA0388 hypothetical protein (NCBI) 129, 464
PA0589 glpE thiosulfate sulfurtransferase (NCBI) 202, 464
PA0590 apaH diadenosinetetraphosphatase (NCBI) 18, 464
PA0591 PA0591 hypothetical protein (NCBI) 202, 464
PA1155 nrdB ribonucleotide-diphosphate reductase beta subunit (NCBI) 179, 213
PA1156 nrdA ribonucleotide-diphosphate reductase alpha subunit (NCBI) 179, 213
PA1787 acnB aconitate hydratase (NCBI) 179, 329
PA1802 clpX ATP-dependent protease ATP-binding subunit (NCBI) 57, 464
PA1803 lon Lon protease (NCBI) 393, 464
PA2080 kynU kynureninase (NCBI) 179, 464
PA2631 PA2631 probable acetyl transferase (NCBI) 129, 464
PA2632 PA2632 hypothetical protein (NCBI) 390, 464
PA2633 PA2633 hypothetical protein (NCBI) 390, 464
PA3172 PA3172 probable hydrolase (NCBI) 179, 390
PA3173 PA3173 short chain dehydrogenase (NCBI) 179, 389
PA3528 rnt ribonuclease T (NCBI) 113, 179
PA3977 hemL glutamate-1-semialdehyde aminotransferase (NCBI) 179, 244
PA4367 PA4367 hypothetical protein (NCBI) 378, 464
PA4370 icmP Insulin-cleaving metalloproteinase outer membrane protein precursor (NCBI) 98, 179
PA4947 amiB N-acetylmuramoyl-L-alanine amidase (NCBI) 81, 464
PA5125 ntrC two-component response regulator NtrC (NCBI) 203, 464
PA5162 rmlD dTDP-4-dehydrorhamnose reductase (NCBI) 179, 464
PA5163 rmlA glucose-1-phosphate thymidylyltransferase (NCBI) 179, 464
PA5164 rmlC dTDP-4-dehydrorhamnose 3,5-epimerase (NCBI) 179, 464
PA5429 aspA aspartate ammonia-lyase (NCBI) 179, 202
PA5435 PA5435 oxaloacetate decarboxylase (NCBI) 47, 179
PA5436 PA5436 acetyl-CoA carboxylase (NCBI) 47, 179
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 PA5163
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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