Organism : Geobacter sulfurreducens | Module List :
Regulation information for GSU2155(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 GSU2155
|Gene||Common Name||Description||Module membership|
|GSU0072||GSU0072||hypothetical protein (VIMSS)||70, 281|
|GSU0429||GSU0429||conserved hypothetical protein (VIMSS)||135, 275|
|GSU0570||GSU0570||conserved hypothetical protein (VIMSS)||47, 70|
|GSU0638||GSU0638||conserved hypothetical protein (VIMSS)||70, 158|
|GSU0639||GSU0639||hypothetical protein (NCBI)||70, 158|
|GSU1030||GSU1030||methyl-accepting chemotaxis protein (VIMSS)||70, 269|
|GSU1072||GSU1072||transcriptional regulator, IclR family (VIMSS)||57, 135|
|GSU1182||malQ||4-alpha-glucanotransferase (NCBI)||70, 269|
|GSU1186||GSU1186||hypothetical protein (VIMSS)||70, 269|
|GSU1405||GSU1405||hypothetical protein (VIMSS)||70, 281|
|GSU1523||surE||stationary-phase survival protein SurE (NCBI)||47, 70|
|GSU1574||GSU1574||hypothetical protein (VIMSS)||70, 281|
|GSU1713||GSU1713||conserved hyothetical protein, truncation (VIMSS)||70, 304|
|GSU1748||GSU1748||RNA methyltransferase, TrmA family (VIMSS)||70, 226|
|GSU1749||GSU1749||hypothetical protein (VIMSS)||11, 70|
|GSU1750||infA||translation initiation factor IF-1 (NCBI)||70, 314|
|GSU2005||GSU2005||branched-chain amino acid ABC transporter, periplasmic amino acid-binding protein, putative (NCBI)||135, 142|
|GSU2006||GSU2006||branched-chain amino acid ABC transporter, permease protein (NCBI)||135, 142|
|GSU2007||GSU2007||branched-chain amino acid ABC transporter, permease protein (NCBI)||135, 142|
|GSU2008||GSU2008||branched-chain amino acid ABC transporter, ATP-binding protein (NCBI)||135, 142|
|GSU2009||GSU2009||branched-chain amino acid ABC transporter, ATP-binding protein (VIMSS)||135, 142|
|GSU2010||GSU2010||CBS domain protein (VIMSS)||135, 142|
|GSU2119||GSU2119||integrative genetic element Gsu56, integrase (VIMSS)||70, 274|
|GSU2120||ihfA-2||integration host factor, alpha subunit (NCBI)||70, 274|
|GSU2151||ssb-1||single-strand binding protein (NCBI)||6, 70|
|GSU2153||GSU2153||hypothetical protein (VIMSS)||70, 337|
|GSU2155||GSU2155||hypothetical protein (VIMSS)||70, 135|
|GSU2156||GSU2156||hypothetical protein (VIMSS)||1, 70|
|GSU2157||nrd||conserved domain protein (NCBI)||70, 153|
|GSU2313||GSU2313||response regulator (VIMSS)||70, 140|
|GSU2353||GSU2353||conserved hypothetical protein (VIMSS)||32, 70|
|GSU2355||GSU2355||hypothetical protein (VIMSS)||6, 135|
|GSU2417||GSU2417||hypothetical protein (VIMSS)||57, 135|
|GSU2419||GSU2419||nickel-dependent hydrogenase, large subunit (VIMSS)||78, 135|
|GSU2557||GSU2557||polysaccharide deacetylase family protein (NCBI)||122, 135|
|GSU2768||GSU2768||hypothetical protein (VIMSS)||122, 135|
|GSU2929||GSU2929||conserved hypothetical protein (NCBI)||47, 70|
|GSU2931||GSU2931||hypothetical protein (VIMSS)||70, 79|
|GSU3016||GSU3016||hypothetical protein (VIMSS)||122, 135|
|GSU3120||GSU3120||conserved hypothetical protein (VIMSS)||122, 135|
|GSU3167||GSU3167||hypothetical protein (VIMSS)||70, 130|
|GSU3169||GSU3169||conserved domain protein (NCBI)||70, 269|
|GSU3218||GSU3218||cytochrome c family protein (NCBI)||135, 155|
|GSU3355||GSU3355||hypothetical protein (VIMSS)||135, 246|
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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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.
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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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- 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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