Organism : Geobacter sulfurreducens | Module List :
GSU3303

methylmalonyl-CoA epimerase (VIMSS)

CircVis
Functional Annotations (6)
Function System
Lactoylglutathione lyase and related lyases cog/ cog
lactoylglutathione lyase activity go/ molecular_function
methylmalonyl-CoA epimerase activity go/ molecular_function
carbohydrate metabolic process go/ biological_process
Pyruvate metabolism kegg/ kegg pathway
metmalonyl_epim tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU3303
(Mouseover regulator name to see its description)

GSU3303 is regulated by 15 influences and regulates 0 modules.
Regulators for GSU3303 (15)
Regulator Module Operator
GSU0018 230 tf
GSU1379 230 tf
GSU1483 230 tf
GSU2041 230 tf
GSU2237 230 tf
GSU3396 230 tf
GSU0031 106 tf
GSU0187 106 tf
GSU0581 106 tf
GSU0732 106 tf
GSU1201 106 tf
GSU1525 106 tf
GSU1692 106 tf
GSU2753 106 tf
GSU2964 106 tf

Warning: GSU3303 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
2372 2.60e+01 aAAg.GtTtG.CaTT
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2373 1.30e+02 TgGTgAtAAaA
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2620 5.80e+02 aatagtaTactGTatAcacaa
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2621 2.40e+04 GGcAAaGggGc
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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 GSU3303

GSU3303 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Lactoylglutathione lyase and related lyases cog/ cog
lactoylglutathione lyase activity go/ molecular_function
methylmalonyl-CoA epimerase activity go/ molecular_function
carbohydrate metabolic process go/ biological_process
Pyruvate metabolism kegg/ kegg pathway
metmalonyl_epim tigr/ tigrfam
Module neighborhood information for GSU3303

GSU3303 has total of 39 gene neighbors in modules 106, 230
Gene neighbors (39)
Gene Common Name Description Module membership
GSU0097 GSU0097 pyruvate ferredoxin/flavodoxin oxidoreductase (VIMSS) 30, 230
GSU0114 atpC ATP synthase F1, epsilon subunit (NCBI) 170, 230
GSU0179 GSU0179 NADPH-dependent FMN reductase domain protein (NCBI) 202, 230
GSU0215 folD-1 folD bifunctional protein (NCBI) 39, 106
GSU0342 nuoE-1 NADH dehydrogenase I, E subunit (NCBI) 230, 243
GSU0344 GSU0344 NADH dehydrogenase I, G subunit, putative (NCBI) 230, 305
GSU0391 GSU0391 Outer membrane efflux family protein (VIMSS) 216, 230
GSU0870 mutT mutator mutT protein (NCBI) 106, 306
GSU0882 GSU0882 conserved hypothetical protein (VIMSS) 31, 106
GSU1108 GSU1108 aldehyde dehydrogenase family protein (NCBI) 230, 327
GSU1201 greB transcription elongation factor GreB (NCBI) 106, 192
GSU1222 GSU1222 histone deacetylase/AcuC/AphA family protein (VIMSS) 106, 181
GSU1223 GSU1223 hypothetical protein (VIMSS) 106, 319
GSU1312 GSU1312 radical SAM domain protein, selenocysteine-containing (NCBI) 139, 230
GSU1319 GSU1319 sensor histidine kinase (VIMSS) 106, 181
GSU1365 GSU1365 Mrr restriction system protein, putative (NCBI) 83, 106
GSU1483 GSU1483 transcriptional regulator, MarR family (VIMSS) 137, 230
GSU1652 GSU1652 hypothetical protein (VIMSS) 106, 276
GSU1797 GSU1797 ComEA-related protein (VIMSS) 106, 306
GSU1806 GSU1806 hypothetical protein (VIMSS) 83, 106
GSU1908 GSU1908 phosphatidylserine decarboxylase, putative (NCBI) 39, 106
GSU1918 frr ribosome recycling factor (NCBI) 230, 248
GSU1927 GSU1927 sensory box/response regulator (VIMSS) 30, 106
GSU2104 GSU2104 lipoprotein, putative (VIMSS) 106, 276
GSU2601 GSU2601 TPR domain/SEC-C motif domain protein (NCBI) 39, 106
GSU2634 GSU2634 hypothetical protein (VIMSS) 195, 230
GSU2637 GSU2637 alcohol dehydrogenase, zinc-containing (VIMSS) 129, 230
GSU3037 fliD flagellar hook-associated protein 2 (NCBI) 150, 230
GSU3063 ftsZ cell division protein FtsZ (NCBI) 230, 264
GSU3123 GSU3123 aldehyde ferredoxin oxidoreductase domain protein (VIMSS) 137, 230
GSU3125 GSU3125 alcohol dehydrogenase, zinc-containing (VIMSS) 137, 230
GSU3299 mmdA carboxyl transferase domain protein (NCBI) 30, 106
GSU3300 GSU3300 biotin-requiring enzyme subunit (NCBI) 230, 327
GSU3301 GSU3301 conserved hypothetical protein (NCBI) 106, 248
GSU3303 GSU3303 methylmalonyl-CoA epimerase (VIMSS) 106, 230
GSU3305 GSU3305 hypothetical protein (VIMSS) 106, 162
GSU3306 GSU3306 hypothetical protein (VIMSS) 30, 106
GSU3464 gidA glucose inhibited division protein A (NCBI) 106, 209
GSU3466 GSU3466 membrane protein, putative (VIMSS) 230, 315
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 GSU3303
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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