Organism : Geobacter sulfurreducens | Module List :
GSU3374 rpe

ribulose-phosphate 3-epimerase (NCBI)

CircVis
Functional Annotations (9)
Function System
Pentose-5-phosphate-3-epimerase cog/ cog
ribulose-phosphate 3-epimerase activity go/ molecular_function
carbohydrate metabolic process go/ biological_process
Pentose phosphate pathway kegg/ kegg pathway
Pentose and glucuronate interconversions kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
rpe tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU3374
(Mouseover regulator name to see its description)

GSU3374 is regulated by 21 influences and regulates 0 modules.
Regulators for GSU3374 rpe (21)
Regulator Module Operator
GSU0013 125 tf
GSU0164 125 tf
GSU0178 125 tf
GSU0514 125 tf
GSU0534 125 tf
GSU0776 125 tf
GSU1345 125 tf
GSU2716 125 tf
GSU2779 125 tf
GSU2809 125 tf
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

Warning: GSU3374 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
2410 1.80e+00 aTGcaattGgaTTaTaCCGgc
Loader icon
2411 1.70e+01 aAtAAaAgAccCaCCgatttaaA
Loader icon
2480 2.90e+03 TCCcttCttCTttC
Loader icon
2481 3.90e+03 ctcatT.tgcTAtAct..c..tTt
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 GSU3374

GSU3374 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Pentose-5-phosphate-3-epimerase cog/ cog
ribulose-phosphate 3-epimerase activity go/ molecular_function
carbohydrate metabolic process go/ biological_process
Pentose phosphate pathway kegg/ kegg pathway
Pentose and glucuronate interconversions kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
rpe tigr/ tigrfam
Module neighborhood information for GSU3374

GSU3374 has total of 53 gene neighbors in modules 125, 160
Gene neighbors (53)
Gene Common Name Description Module membership
GSU0025 GSU0025 tolB protein (NCBI) 125, 184
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
GSU0457 GSU0457 lipoprotein, putative (VIMSS) 125, 164
GSU0458 GSU0458 (3R)-hydroxymyristoyl-(acyl-carrier-protein) dehydratase, putative (VIMSS) 125, 164
GSU0577 recO DNA repair protein RecO (NCBI) 160, 225
GSU0685 GSU0685 radical SAM domain protein (NCBI) 125, 309
GSU0776 GSU0776 sigma-54 dependent DNA-binding response regulator (VIMSS) 160, 184
GSU0846 acnA aconitate hydratase 1 (NCBI) 97, 160
GSU1025 GSU1025 conserved domain protein (NCBI) 59, 160
GSU1026 GSU1026 conserved hypothetical protein (VIMSS) 63, 160
GSU1165 ptsP phosphoenolpyruvate-protein phosphotransferase PtsP (NCBI) 19, 125
GSU1184 GSU1184 conserved hypothetical protein (VIMSS) 125, 223
GSU1196 GSU1196 hypothetical protein (VIMSS) 125, 201
GSU1198 serA D-3-phosphoglycerate dehydrogenase (NCBI) 125, 309
GSU1316 GSU1316 response regulator (VIMSS) 160, 258
GSU1706 panC pantoate--beta-alanine ligase (NCBI) 11, 125
GSU1707 GSU1707 group II decarboxylase (VIMSS) 125, 290
GSU1708 GSU1708 chlorohydrolase, Atz/Trz family (VIMSS) 125, 290
GSU1709 smpB SsrA-binding protein (NCBI) 125, 290
GSU1720 GSU1720 6-pyruvoyl tetrahydrobiopterin synthase family protein (NCBI) 57, 125
GSU1721 GSU1721 radical SAM domain protein (NCBI) 125, 309
GSU1722 GSU1722 creatinine amidohydrolase (VIMSS) 125, 309
GSU1938 GSU1938 hypothetical protein (VIMSS) 60, 160
GSU2201 GSU2201 cytochrome c family protein (NCBI) 20, 125
GSU2233 GSU2233 conserved hypothetical protein (VIMSS) 125, 309
GSU2429 GSU2429 PPIC-type PPIASE domain protein (NCBI) 125, 309
GSU2458 GSU2458 penicillin-binding protein, putative (NCBI) 160, 258
GSU2489 GSU2489 deoxyribonuclease, TatD family (VIMSS) 128, 160
GSU2492 GSU2492 sensory box histidine kinase (VIMSS) 99, 160
GSU2526 GSU2526 membrane protein, putative (VIMSS) 57, 125
GSU2527 GSU2527 nitrite/sulfite reductase domain protein (NCBI) 125, 262
GSU2859 tuf-1 translation elongation factor Tu (NCBI) 24, 160
GSU2871 tuf-2 translation elongation factor Tu (NCBI) 10, 160
GSU3049 GSU3049 hypothetical protein (VIMSS) 160, 164
GSU3112 GSU3112 cell division protein FtsK, putative (VIMSS) 128, 160
GSU3145 GSU3145 MOSC domain protein (VIMSS) 125, 273
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
GSU3336 GSU3336 hypothetical protein (NCBI) 3, 160
GSU3373 sun Sun protein (NCBI) 160, 336
GSU3374 rpe ribulose-phosphate 3-epimerase (NCBI) 125, 160
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 GSU3374
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