Organism : Geobacter sulfurreducens | Module List :
GSU0803 ppsA

phosphoenolpyruvate synthase (NCBI)

CircVis
Functional Annotations (11)
Function System
Phosphoenolpyruvate synthase/pyruvate phosphate dikinase cog/ cog
ATP binding go/ molecular_function
gluconeogenesis go/ biological_process
pyruvate, water dikinase activity go/ molecular_function
phosphorylation go/ biological_process
Pyruvate metabolism kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Carbon fixation pathways in prokaryotes kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
PEP_synth tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0803
(Mouseover regulator name to see its description)

GSU0803 is regulated by 19 influences and regulates 0 modules.
Regulators for GSU0803 ppsA (19)
Regulator Module Operator
GSU0031 320 tf
GSU0625 320 tf
GSU1218 320 tf
GSU1525 320 tf
GSU1692 320 tf
GSU2185 320 tf
GSU2520 320 tf
GSU2964 320 tf
GSU3045 320 tf
GSU0031 182 tf
GSU0581 182 tf
GSU0732 182 tf
GSU1013 182 tf
GSU1218 182 tf
GSU1525 182 tf
GSU1626 182 tf
GSU1727 182 tf
GSU2581 182 tf
GSU2964 182 tf

Warning: GSU0803 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
2524 3.80e+01 GaGGGtCA
Loader icon
2525 2.40e+01 cGgtgcaAcGAtGCggA
Loader icon
2796 5.60e-02 TTtTtcCTgcA
Loader icon
2797 1.70e+04 AATTCTAT
Loader icon
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 GSU0803

GSU0803 is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
Phosphoenolpyruvate synthase/pyruvate phosphate dikinase cog/ cog
ATP binding go/ molecular_function
gluconeogenesis go/ biological_process
pyruvate, water dikinase activity go/ molecular_function
phosphorylation go/ biological_process
Pyruvate metabolism kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Carbon fixation pathways in prokaryotes kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
PEP_synth tigr/ tigrfam
Module neighborhood information for GSU0803

GSU0803 has total of 24 gene neighbors in modules 182, 320
Gene neighbors (24)
Gene Common Name Description Module membership
GSU0066 GSU0066 AhpC/Tsa family protein, selenocysteine-containing (NCBI) 270, 320
GSU0067 GSU0067 carbonic anhydrase (NCBI) 270, 320
GSU0068 GSU0068 cytochrome c family protein (NCBI) 211, 320
GSU0193 GSU0193 L-sorbosone dehydrogenase, putative (NCBI) 182, 339
GSU0194 GSU0194 conserved hypothetical protein (VIMSS) 182, 339
GSU0195 GSU0195 conserved hypothetical protein (VIMSS) 270, 320
GSU0500 typA GTP-binding protein TypA (NCBI) 53, 320
GSU0802 GSU0802 oxidoreductase, short chain dehydrogenase/reductase family (NCBI) 182, 339
GSU0803 ppsA phosphoenolpyruvate synthase (NCBI) 182, 320
GSU0910 GSU0910 aldehyde:ferredoxin oxidoreductase, tungsten-containing (VIMSS) 182, 339
GSU0911 GSU0911 iron-sulfur cluster-binding protein (VIMSS) 182, 211
GSU2435 GSU2435 dehydrogenase complex E2 component, dihydrolipamide acetyltransferase (NCBI) 167, 182
GSU2436 GSU2436 dehydrogenase complex, E1 component, beta subunit (NCBI) 182, 237
GSU2444 GSU2444 sensor histidine kinase (VIMSS) 167, 320
GSU2447 GSU2447 conserved hypothetical protein (VIMSS) 167, 182
GSU2448 sucB 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase (NCBI) 167, 182
GSU2449 sucA 2-oxoglutarate dehydrogenase, E1 component (NCBI) 182, 237
GSU2681 GSU2681 iron-sulfur cluster-binding protein (VIMSS) 100, 320
GSU2872 GSU2872 electron transfer flavoprotein, Etf beta-subunit/FixA family (VIMSS) 175, 320
GSU3252 GSU3252 sensor histidine kinase (VIMSS) 279, 320
GSU3257 glgA-2 glycogen synthase (NCBI) 279, 320
GSU3258 GSU3258 hypothetical protein (VIMSS) 279, 320
GSU3290 GSU3290 conserved hypothetical protein (VIMSS) 175, 320
GSU3350 pleD sensor histidine kinase/GGDEF domain protein (NCBI) 182, 261
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 GSU0803
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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