Organism : Geobacter sulfurreducens | Module List :
GSU0707 sugE

sugE protein (NCBI)

CircVis
Functional Annotations (2)
Function System
Membrane transporters of cations and cationic drugs cog/ cog
integral to membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0707
(Mouseover regulator name to see its description)

GSU0707 is regulated by 20 influences and regulates 0 modules.
Regulators for GSU0707 sugE (20)
Regulator Module Operator
GSU1277 95 tf
GSU1569 95 tf
GSU1940 95 tf
GSU2716 95 tf
GSU2787 95 tf
GSU2987 95 tf
GSU3229 95 tf
GSU3370 95 tf
GSU0031 234 tf
GSU0300 234 tf
GSU0581 234 tf
GSU0682 234 tf
GSU1483 234 tf
GSU1617 234 tf
GSU1692 234 tf
GSU2753 234 tf
GSU2817 234 tf
GSU3045 234 tf
GSU3053 234 tf
GSU3324 234 tf

Warning: GSU0707 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
2350 2.70e+03 GgAGGTGg
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2351 4.30e+03 tCAaaAAAAATGC
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2628 1.20e+04 GGcacGtGGcc.tgA.gaGCgg
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2629 6.70e+03 tTgAggggaGacCgtCcGGggGc
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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 GSU0707

GSU0707 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Membrane transporters of cations and cationic drugs cog/ cog
integral to membrane go/ cellular_component
Module neighborhood information for GSU0707

GSU0707 has total of 50 gene neighbors in modules 95, 234
Gene neighbors (50)
Gene Common Name Description Module membership
GSU0031 hrcA heat-inducible transcription repressor HrcA (NCBI) 184, 234
GSU0061 GSU0061 hypothetical protein (VIMSS) 9, 95
GSU0116 GSU0116 transglycosylase (VIMSS) 95, 200
GSU0184 b2690 HAD-superfamily hydrolase, subfamily IA, variant 1 (NCBI) 45, 234
GSU0203 GSU0203 conserved hypothetical protein (VIMSS) 194, 234
GSU0214 GSU0214 conserved hypothetical protein (VIMSS) 6, 95
GSU0357 GSU0357 cytochrome c family protein (VIMSS) 6, 95
GSU0409 fliE flagellar hook-basal body complex protein FliE (NCBI) 41, 234
GSU0421 fliM flagellar motor switch protein FliM (NCBI) 234, 244
GSU0422 fliN flagellar motor switch protein FliN (NCBI) 181, 234
GSU0533 GSU0533 cytochrome c family protein, putative (NCBI) 54, 95
GSU0640 GSU0640 conserved hypothetical protein (VIMSS) 95, 158
GSU0684 cheW-2 purine-binding chemotaxis protein CheW (NCBI) 100, 234
GSU0706 GSU0706 major facilitator family transporter (VIMSS) 234, 275
GSU0707 sugE sugE protein (NCBI) 95, 234
GSU0708 GSU0708 multidrug resistance protein (VIMSS) 234, 244
GSU0724 GSU0724 conserved hypothetical protein (NCBI) 49, 234
GSU0806 citG ATP:dephospho-CoA triphosphoribosyl transferase (NCBI) 95, 133
GSU0843 GSU0843 NADH oxidase, putative (VIMSS) 9, 95
GSU0845 GSU0845 Rieske 2Fe-2S family protein (VIMSS) 9, 95
GSU0897 GSU0897 conserved hypothetical protein (VIMSS) 234, 244
GSU0904 GSU0904 HD domain protein (VIMSS) 234, 244
GSU0926 GSU0926 mce-related protein (NCBI) 20, 95
GSU1014 GSU1014 smr domain protein (VIMSS) 234, 240
GSU1171 GSU1171 conserved hypothetical protein (VIMSS) 195, 234
GSU1255 GSU1255 conserved hypothetical protein (NCBI) 95, 104
GSU1256 GSU1256 conserved domain protein (NCBI) 6, 95
GSU1303 GSU1303 methyl-accepting chemotaxis protein (VIMSS) 45, 234
GSU1399 corA-1 magnesium and cobalt transport protein CorA (NCBI) 234, 240
GSU1844 GSU1844 IPT/TIG domain protein, putative (VIMSS) 9, 95
GSU2199 GSU2199 conserved hypothetical protein (VIMSS) 95, 273
GSU2387 GSU2387 B12-binding domain (NCBI) 165, 234
GSU2509 GSU2509 glycosyl transferase, group 2 family protein (VIMSS) 9, 95
GSU2515 GSU2515 cytochrome c family protein, putative (NCBI) 9, 95
GSU2561 GSU2561 conserved domain protein (NCBI) 95, 193
GSU2593 GSU2593 ISGsu6, transposase OrfA (VIMSS) 234, 300
GSU2626 GSU2626 conserved hypothetical protein (VIMSS) 41, 234
GSU2640 GSU2640 hypothetical protein (VIMSS) 66, 95
GSU2641 GSU2641 hypothetical protein (VIMSS) 66, 95
GSU2755 GSU2755 periplasmic substrate-binding protein/sensor histidine kinase (VIMSS) 234, 244
GSU2775 GSU2775 hypothetical protein (VIMSS) 9, 95
GSU2787 GSU2787 transcriptional regulator, LysR family (VIMSS) 95, 224
GSU2896 GSU2896 ankyrin-related protein (VIMSS) 6, 95
GSU2903 GSU2903 conserved domain protein (VIMSS) 41, 234
GSU3032 GSU3032 hypothetical protein (VIMSS) 45, 234
GSU3048 flgH flagellar L-ring protein FlgH (NCBI) 95, 186
GSU3071 murD UDP-N-acetylmuramoylalanine--D-glutamate ligase (NCBI) 95, 264
GSU3115 GSU3115 hypothetical protein (VIMSS) 100, 234
GSU3128 GSU3128 hypothetical protein (VIMSS) 95, 183
GSU3238 GSU3238 Rieske 2Fe-2S family protein (VIMSS) 95, 264
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 GSU0707
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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