Organism : Geobacter sulfurreducens | Module List :
Regulation information for GSU3039(Mouseover regulator name to see its description)
Motif information (de novo identified motifs for modules)
There are 4 motifs predicted.
|Motif Id||e-value||Consensus||Motif Logo|
Module neighborhood information for GSU3039
|Gene||Common Name||Description||Module membership|
|GSU0138||prfC||peptide chain release factor 3 (NCBI)||140, 275|
|GSU0167||GSU0167||conserved hypothetical protein, truncation (NCBI)||62, 140|
|GSU0311||GSU0311||hypothetical protein (VIMSS)||78, 97|
|GSU0490||GSU0490||acetyl-CoA hydrolase/transferase family protein (VIMSS)||140, 225|
|GSU0602||GSU0602||conserved hypothetical protein (VIMSS)||140, 275|
|GSU0649||rnhB||ribonuclease HII (NCBI)||42, 140|
|GSU0659||GSU0659||polysaccharide deacetylase domain protein (VIMSS)||14, 97|
|GSU0731||lpxC||UDP-3-0-acyl N-acetylglucosamine deacetylase (NCBI)||16, 140|
|GSU0738||GSU0738||hypothetical protein (VIMSS)||97, 186|
|GSU0812||GSU0812||nitrogen regulation protein NtrY, putative (VIMSS)||140, 285|
|GSU0834||GSU0834||hypothetical protein (VIMSS)||140, 190|
|GSU0844||GSU0844||potassium uptake protein, Trk family (VIMSS)||46, 97|
|GSU0846||acnA||aconitate hydratase 1 (NCBI)||97, 160|
|GSU1046||GSU1046||conserved hypothetical protein (VIMSS)||97, 127|
|GSU1563||GSU1563||hypothetical protein (VIMSS)||97, 164|
|GSU1654||GSU1654||response regulator, putative (NCBI)||4, 140|
|GSU1769||GSU1769||conserved hypothetical protein (VIMSS)||97, 113|
|GSU1823||GSU1823||hypothetical protein (VIMSS)||8, 140|
|GSU2142||GSU2142||hypothetical protein (VIMSS)||97, 311|
|GSU2238||gmk||guanylate kinase (NCBI)||140, 267|
|GSU2313||GSU2313||response regulator (VIMSS)||70, 140|
|GSU2316||GSU2316||mechanosensitive ion channel family protein (NCBI)||140, 257|
|GSU2347||GSU2347||conserved hypothetical protein (VIMSS)||97, 190|
|GSU2348||GSU2348||conserved hypothetical protein (VIMSS)||49, 97|
|GSU2362||GSU2362||transcriptional regulator, MarR family (VIMSS)||140, 159|
|GSU2403||GSU2403||hypothetical protein (VIMSS)||65, 97|
|GSU2404||GSU2404||pentapeptide repeat domain protein (VIMSS)||97, 325|
|GSU2482||kdpC||potassium-transporting ATPase, C subunit (NCBI)||49, 97|
|GSU2506||GSU2506||sensory box protein/sigma-54 dependent DNA-binding response regulator (NCBI)||97, 341|
|GSU2514||GSU2514||hypothetical protein (VIMSS)||128, 140|
|GSU2560||GSU2560||hypothetical protein (NCBI)||140, 216|
|GSU2562||sixA||phosphohistidine phosphatase SixA (NCBI)||140, 157|
|GSU2587||GSU2587||transcriptional regulator, MarR family (VIMSS)||140, 183|
|GSU2680||GSU2680||conserved hypothetical protein (VIMSS)||140, 225|
|GSU2710||GSU2710||hypothetical protein (NCBI)||140, 335|
|GSU2749||GSU2749||NOL1/NOP2/sun family protein (VIMSS)||130, 140|
|GSU2752||GSU2752||hypothetical protein (VIMSS)||90, 97|
|GSU2761||GSU2761||FAD-dependent glycerol-3-phosphate dehydrogenase subunit (VIMSS)||42, 140|
|GSU2815||GSU2815||sensory box histidine kinase (VIMSS)||97, 317|
|GSU2826||GSU2826||membrane protein, putative (VIMSS)||140, 275|
|GSU2884||GSU2884||cytochrome c family protein (VIMSS)||2, 97|
|GSU2885||GSU2885||NHL repeat domain protein (VIMSS)||2, 97|
|GSU2893||GSU2893||hypothetical protein (VIMSS)||130, 140|
|GSU2978||GSU2978||hypothetical protein (VIMSS)||133, 140|
|GSU3011||GSU3011||hypothetical protein (VIMSS)||97, 101|
|GSU3039||GSU3039||hypothetical protein (VIMSS)||97, 140|
|GSU3069||murG||UDP-N-acetylglucosamine--N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase (NCBI)||140, 264|
|GSU3072||mraY||phospho-N-acetylmuramoyl-pentapeptide-transferase (NCBI)||140, 264|
|GSU3104||prfA||peptide chain release factor 1 (NCBI)||82, 140|
|GSU3107||rpmE||ribosomal protein L31 (NCBI)||113, 140|
|GSU3158||cysM||cysteine synthase b (VIMSS)||140, 258|
|GSU3215||GSU3215||hypothetical protein (VIMSS)||113, 140|
|GSU3319||ppiA||peptidyl-prolyl cis-trans isomerase A (NCBI)||97, 317|
|GSU3409||GSU3409||hypothetical protein (VIMSS)||97, 206|
|GSU3410||GSU3410||hypothetical protein (VIMSS)||97, 206|
|GSU3412||GSU3412||hypothetical protein (VIMSS)||49, 140|
|GSU3455||GSU3455||ABC transporter, permease protein, ABC-2 family (VIMSS)||129, 140|
Gene Page Help
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.
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Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.
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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.
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CircVisOur 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.
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