Organism : Geobacter sulfurreducens | Module List :
Regulation information for GSU0226(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|
Functional Enrichment for GSU0226
Module neighborhood information for GSU0226
|Gene||Common Name||Description||Module membership|
|GSU0087||GSU0087||heterodisulfide reductase, iron-sulfur binding subunit, putative (VIMSS)||126, 214|
|GSU0089||GSU0089||heterodisulfide reductase subunit (VIMSS)||126, 291|
|GSU0090||GSU0090||heterodisulfide reductase subunit (VIMSS)||126, 214|
|GSU0091||GSU0091||heterodisulfide reductase subunit (VIMSS)||126, 214|
|GSU0213||GSU0213||radical SAM domain protein (NCBI)||126, 323|
|GSU0226||GSU0226||L-lactate permease, putative (VIMSS)||126, 164|
|GSU0227||GSU0227||type II DNA modification methyltransferase, putative (NCBI)||164, 253|
|GSU0457||GSU0457||lipoprotein, putative (VIMSS)||125, 164|
|GSU0458||GSU0458||(3R)-hydroxymyristoyl-(acyl-carrier-protein) dehydratase, putative (VIMSS)||125, 164|
|GSU0524||GSU0524||conserved hypothetical protein (VIMSS)||47, 164|
|GSU0526||GSU0526||conserved hypothetical protein (VIMSS)||126, 281|
|GSU0541||polA||DNA polymerase I (NCBI)||164, 183|
|GSU0825||GSU0825||pirin family protein (VIMSS)||126, 183|
|GSU0841||GSU0841||sigma-54 dependent DNA-binding response regulator (VIMSS)||164, 281|
|GSU0854||GSU0854||membrane protein (NCBI)||65, 164|
|GSU0858||GSU0858||TonB-dependent receptor, putative (VIMSS)||9, 164|
|GSU0860||GSU0860||methylenetetrahydrofolate reductase family protein (VIMSS)||126, 144|
|GSU0862||folD-2||folD bifunctional protein (NCBI)||46, 126|
|GSU0932||uraA||uracil permease (NCBI)||147, 164|
|GSU0934||GSU0934||hypothetical protein (VIMSS)||8, 164|
|GSU0997||mutM||formamidopyrimidine-DNA glycosylase (NCBI)||40, 164|
|GSU1009||hflX||GTP-binding protein (NCBI)||164, 253|
|GSU1053||GSU1053||sensory box protein (VIMSS)||122, 126|
|GSU1124||coaBC||phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase (NCBI)||126, 295|
|GSU1180||ftsH-1||cell division protein FtsH (NCBI)||112, 126|
|GSU1274||GSU1274||radical SAM domain protein (NCBI)||126, 208|
|GSU1297||GSU1297||ISGsu2, transposase (VIMSS)||72, 164|
|GSU1298||GSU1298||methyl-accepting chemotaxis protein (VIMSS)||126, 183|
|GSU1377||GSU1377||3-hydroxybutyryl-CoA dehydratase (VIMSS)||11, 126|
|GSU1461||pyrF||orotidine 5`-phosphate decarboxylase (NCBI)||126, 233|
|GSU1535||recD||exodeoxyribonuclease V, alpha subunit (NCBI)||126, 336|
|GSU1562||GSU1562||conserved hypothetical protein TIGR00106 (VIMSS)||164, 253|
|GSU1563||GSU1563||hypothetical protein (VIMSS)||97, 164|
|GSU2047||GSU2047||conserved hypothetical protein (VIMSS)||26, 126|
|GSU2050||secA||preprotein translocase, SecA subunit (NCBI)||91, 126|
|GSU2102||GSU2102||pyruvate formate-lyase-activating enzyme, putative (VIMSS)||126, 183|
|GSU2214||cheB-3||protein-glutamate methylesterase (NCBI)||126, 295|
|GSU2222||cheA-2||chemotaxis protein CheA (NCBI)||126, 222|
|GSU2239||GSU2239||conserved hypothetical protein TIGR00255 (VIMSS)||47, 164|
|GSU2272||GSU2272||lipoprotein, putative (VIMSS)||80, 126|
|GSU2337||GSU2337||glycosyl transferase, group 20 family protein (NCBI)||47, 164|
|GSU2414||GSU2414||membrane protein, putative (VIMSS)||164, 183|
|GSU2674||GSU2674||hypothetical protein (VIMSS)||164, 323|
|GSU2683||panE||2-dehydropantoate 2-reductase (VIMSS)||47, 164|
|GSU2736||GSU2736||hypothetical protein (VIMSS)||164, 327|
|GSU2879||leuB||3-isopropylmalate dehydrogenase (NCBI)||126, 233|
|GSU3049||GSU3049||hypothetical protein (VIMSS)||160, 164|
|GSU3062||GSU3062||radical SAM domain protein (NCBI)||42, 126|
|GSU3133||GSU3133||penicillin-binding protein, 1A family (VIMSS)||47, 164|
|GSU3147||mobB||molybdopterin-guanine dinucleotide biosynthesis protein MobB (NCBI)||164, 201|
|GSU3260||GSU3260||phosphoserine aminotransferase, putative (VIMSS)||35, 126|
|GSU3314||GSU3314||lipoprotein, putative (VIMSS)||164, 183|
|GSU3371||GSU3371||AP endonuclease, family 2 (NCBI)||47, 164|
|GSU3411||pcrA||ATP-dependent DNA helicase PcrA, putative (NCBI)||164, 281|
|GSU3421||GSU3421||transcriptional regulator, Crp/Fnr family (VIMSS)||126, 164|
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.
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.
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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.
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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.
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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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