Organism : Geobacter sulfurreducens | Module List :
GSU2716 sfsA

sugar fermentation stimulation protein (NCBI)

CircVis
Functional Annotations (2)
Function System
DNA-binding protein, stimulates sugar fermentation cog/ cog
sfsA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2716
(Mouseover regulator name to see its description)

GSU2716 is regulated by 17 influences and regulates 20 modules.
Regulators for GSU2716 sfsA (17)
Regulator Module Operator
GSU0164 300 tf
GSU1270 300 tf
GSU2202 300 tf
GSU2716 300 tf
GSU2779 300 tf
GSU3217 300 tf
GSU0041 226 tf
GSU0266 226 tf
GSU1115 226 tf
GSU1320 226 tf
GSU1382 226 tf
GSU1495 226 tf
GSU1569 226 tf
GSU2716 226 tf
GSU2915 226 tf
GSU3387 226 tf
GSU3421 226 tf

Warning: GSU2716 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
2612 1.20e+03 cTG.a.AA.aA
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2613 3.60e+04 ATaAATAATA
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2758 1.40e-07 AaaTtgaCcc.tTCttccTCTaTC
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2759 1.00e-06 CCGacCCTcCAGGtCGgCtAg
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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 GSU2716

GSU2716 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
DNA-binding protein, stimulates sugar fermentation cog/ cog
sfsA tigr/ tigrfam
Module neighborhood information for GSU2716

GSU2716 has total of 47 gene neighbors in modules 226, 300
Gene neighbors (47)
Gene Common Name Description Module membership
GSU0044 GSU0044 salmonella virulence plasmid 65kDa B protein /YD repeat protein (NCBI) 274, 300
GSU0045 GSU0045 hypothetical protein (VIMSS) 232, 300
GSU0048 GSU0048 integrase (NCBI) 287, 300
GSU0137 GSU0137 hypothetical protein (NCBI) 198, 226
GSU0223 GSU0223 protoheme IX farnesyl transferase, putative (VIMSS) 257, 300
GSU0369 GSU0369 FlhB domain protein, putative (NCBI) 293, 300
GSU0545 GSU0545 membrane protein, putative (VIMSS) 226, 252
GSU0595 GSU0595 hypothetical protein (NCBI) 300, 337
GSU0624 GSU0624 glycosyl transferase, group 1 family protein (VIMSS) 131, 226
GSU0889 GSU0889 Acylphosphatase (VIMSS) 213, 226
GSU0931 GSU0931 Rhodanese-like domain protein (VIMSS) 104, 226
GSU1034 GSU1034 None 287, 300
GSU1078 GSU1078 chromosomal replication initiator protein DnaA, truncation (NCBI) 226, 260
GSU1172 mviN virulence factor mviN protein (NCBI) 295, 300
GSU1270 pyrR pyrimidine operon regulatory protein PyrR (NCBI) 281, 300
GSU1329 gltX tRNA synthetases class I (E and Q), catalytic domain protein (NCBI) 15, 300
GSU1383 dnaQ exonuclease (NCBI) 287, 300
GSU1480 GSU1480 drug resistance transporter, EmrB/QacA family (VIMSS) 131, 226
GSU1539 xth exodeoxyribonuclease III (NCBI) 274, 300
GSU1565 GSU1565 hypothetical protein (VIMSS) 276, 300
GSU1680 GSU1680 conserved hypothetical protein (VIMSS) 59, 300
GSU1703 pfk 6-phosphofructokinase (NCBI) 204, 300
GSU1748 GSU1748 RNA methyltransferase, TrmA family (VIMSS) 70, 226
GSU1822 mutS DNA mismatch repair protein MutS (NCBI) 163, 226
GSU2080 GSU2080 rod shape-determining protein MreD, putative (VIMSS) 137, 300
GSU2166 GSU2166 hypothetical protein (VIMSS) 1, 300
GSU2204 GSU2204 cytochrome c family protein, putative (NCBI) 300, 327
GSU2205 GSU2205 hypothetical protein (VIMSS) 300, 337
GSU2210 GSU2210 cytochrome c family protein (NCBI) 218, 226
GSU2326 GSU2326 outer membrane lipoprotein (VIMSS) 118, 226
GSU2336 otsB trehalose-phosphatase (NCBI) 296, 300
GSU2400 GSU2400 conserved hypothetical protein (VIMSS) 104, 226
GSU2578 cheW-9 purine-binding chemotaxis protein CheW (NCBI) 79, 300
GSU2592 GSU2592 hypothetical protein (VIMSS) 68, 300
GSU2593 GSU2593 ISGsu6, transposase OrfA (VIMSS) 234, 300
GSU2594 GSU2594 ISGsu6, transposase OrfB (VIMSS) 287, 300
GSU2716 sfsA sugar fermentation stimulation protein (NCBI) 226, 300
GSU2818 GSU2818 membrane protein, putative (VIMSS) 110, 226
GSU2890 GSU2890 cytochrome c biogenesis protein, CcmF/CcyK/CcsA family (VIMSS) 130, 300
GSU2957 GSU2957 thioredoxin family protein (VIMSS) 146, 300
GSU3050 GSU3050 flagella basal body P-ring formation protein flgA, putative (VIMSS) 165, 226
GSU3184 GSU3184 hypothetical protein (VIMSS) 181, 300
GSU3186 GSU3186 conserved hypothetical protein (VIMSS) 213, 300
GSU3264 GSU3264 membrane protein, putative (VIMSS) 295, 300
GSU3286 hemD uroporphyrinogen III synthase/methyltransferase (NCBI) 89, 300
GSU3354 GSU3354 MutT/nudix family protein (VIMSS) 226, 293
GSU3390 GSU3390 membrane protein, putative (VIMSS) 104, 226
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 GSU2716
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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