Organism : Geobacter sulfurreducens | Module List :
GSU3207 gpmA

phosphoglycerate mutase, 2,3-bisphosphoglycerate-independent (NCBI)

CircVis
Functional Annotations (13)
Function System
Phosphoglyceromutase cog/ cog
cytoplasm go/ cellular_component
glucose catabolic process go/ biological_process
sulfuric ester hydrolase activity go/ molecular_function
manganese ion binding go/ molecular_function
2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity go/ molecular_function
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity go/ molecular_function
Glycolysis / Gluconeogenesis kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
pgm_bpd_ind tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU3207
(Mouseover regulator name to see its description)

GSU3207 is regulated by 18 influences and regulates 0 modules.
Regulators for GSU3207 gpmA (18)
Regulator Module Operator
GSU0770 160 tf
GSU0776 160 tf
GSU0836 160 tf
GSU1495 160 tf
GSU2033 160 tf
GSU2571 160 tf
GSU2670 160 tf
GSU2753 160 tf
GSU2941 160 tf
GSU2980 160 tf
GSU3457 160 tf
GSU0280 9 tf
GSU0598 9 tf
GSU0776 9 tf
GSU1072 9 tf
GSU1250 9 tf
GSU1268 9 tf
GSU2670 9 tf

Warning: GSU3207 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
2178 2.70e+02 aCAaGgAGGAaA
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2179 4.60e+03 tttTTTCATtA
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2480 2.90e+03 TCCcttCttCTttC
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2481 3.90e+03 ctcatT.tgcTAtAct..c..tTt
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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 GSU3207

GSU3207 is enriched for 13 functions in 3 categories.
Enrichment Table (13)
Function System
Phosphoglyceromutase cog/ cog
cytoplasm go/ cellular_component
glucose catabolic process go/ biological_process
sulfuric ester hydrolase activity go/ molecular_function
manganese ion binding go/ molecular_function
2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity go/ molecular_function
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity go/ molecular_function
Glycolysis / Gluconeogenesis kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
pgm_bpd_ind tigr/ tigrfam
Module neighborhood information for GSU3207

GSU3207 has total of 59 gene neighbors in modules 9, 160
Gene neighbors (59)
Gene Common Name Description Module membership
GSU0061 GSU0061 hypothetical protein (VIMSS) 9, 95
GSU0073 GSU0073 outer membrane protein, putative (VIMSS) 160, 275
GSU0074 elbB enhancing lycopene biosynthesis protein 2 (NCBI) 160, 279
GSU0135 hemB delta-aminolevulinic acid dehydratase (NCBI) 91, 160
GSU0153 argG argininosuccinate synthase (NCBI) 160, 258
GSU0155 GSU0155 hypothetical protein (VIMSS) 160, 289
GSU0451 tcrA DNA-binding response regulator (NCBI) 160, 210
GSU0452 GSU0452 sensor histidine kinase (VIMSS) 4, 160
GSU0453 pfs MTA/SAH nucleosidase (NCBI) 127, 160
GSU0454 GSU0454 conserved hypothetical protein (VIMSS) 99, 160
GSU0542 GSU0542 GGDEF domain protein (NCBI) 9, 66
GSU0577 recO DNA repair protein RecO (NCBI) 160, 225
GSU0599 GSU0599 sensor histidine kinase (VIMSS) 9, 275
GSU0692 GSU0692 carbohydrate kinase, PfkB family (VIMSS) 9, 157
GSU0776 GSU0776 sigma-54 dependent DNA-binding response regulator (VIMSS) 160, 184
GSU0843 GSU0843 NADH oxidase, putative (VIMSS) 9, 95
GSU0845 GSU0845 Rieske 2Fe-2S family protein (VIMSS) 9, 95
GSU0846 acnA aconitate hydratase 1 (NCBI) 97, 160
GSU0858 GSU0858 TonB-dependent receptor, putative (VIMSS) 9, 164
GSU0895 GSU0895 GAF domain/GGDEF domain protein (NCBI) 9, 331
GSU0948 GSU0948 ABC transporter, permease protein, putative (VIMSS) 9, 224
GSU1025 GSU1025 conserved domain protein (NCBI) 59, 160
GSU1026 GSU1026 conserved hypothetical protein (VIMSS) 63, 160
GSU1316 GSU1316 response regulator (VIMSS) 160, 258
GSU1439 GSU1439 hypothetical protein (VIMSS) 9, 90
GSU1477 lemA LemA family protein (NCBI) 9, 292
GSU1844 GSU1844 IPT/TIG domain protein, putative (VIMSS) 9, 95
GSU1938 GSU1938 hypothetical protein (VIMSS) 60, 160
GSU2097 GSU2097 carbon monoxide dehydrogenase accessory protein, putative (NCBI) 9, 269
GSU2361 GSU2361 alpha amylase family protein (VIMSS) 9, 142
GSU2425 GSU2425 O-acetyl-L-homoserine sulfhydrylase (NCBI) 9, 91
GSU2458 GSU2458 penicillin-binding protein, putative (NCBI) 160, 258
GSU2479 GSU2479 hypothetical protein (VIMSS) 6, 9
GSU2489 GSU2489 deoxyribonuclease, TatD family (VIMSS) 128, 160
GSU2492 GSU2492 sensory box histidine kinase (VIMSS) 99, 160
GSU2493 GSU2493 NHL repeat domain protein (NCBI) 9, 341
GSU2509 GSU2509 glycosyl transferase, group 2 family protein (VIMSS) 9, 95
GSU2510 GSU2510 hypothetical protein (VIMSS) 9, 79
GSU2515 GSU2515 cytochrome c family protein, putative (NCBI) 9, 95
GSU2529 fusA-2 translation elongation factor G (NCBI) 9, 46
GSU2775 GSU2775 hypothetical protein (VIMSS) 9, 95
GSU2776 GSU2776 conserved hypothetical protein (NCBI) 1, 9
GSU2859 tuf-1 translation elongation factor Tu (NCBI) 24, 160
GSU2871 tuf-2 translation elongation factor Tu (NCBI) 10, 160
GSU2880 GSU2880 cytochrome c biogenesis protein, CcmF/CcyK/CcsA family (VIMSS) 9, 269
GSU3049 GSU3049 hypothetical protein (VIMSS) 160, 164
GSU3112 GSU3112 cell division protein FtsK, putative (VIMSS) 128, 160
GSU3207 gpmA phosphoglycerate mutase, 2,3-bisphosphoglycerate-independent (NCBI) 9, 160
GSU3209 GSU3209 iojap-related protein (VIMSS) 160, 335
GSU3210 nadD nicotinate (nicotinamide) nucleotide adenylyltransferase (NCBI) 160, 214
GSU3211 proA gamma-glutamyl phosphate reductase (NCBI) 160, 321
GSU3212 proB glutamate 5-kinase (NCBI) 121, 160
GSU3313 GSU3313 thiolase, putative (NCBI) 9, 66
GSU3336 GSU3336 hypothetical protein (NCBI) 3, 160
GSU3373 sun Sun protein (NCBI) 160, 336
GSU3374 rpe ribulose-phosphate 3-epimerase (NCBI) 125, 160
GSU3420 GSU3420 lipid A biosynthesis lauroyl acyltransferase, putative (VIMSS) 9, 66
GSU3423 tkt transketolase (NCBI) 9, 84
GSU3434 nuoI-2 NADH dehydrogenase I, I subunit (NCBI) 160, 275
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 GSU3207
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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