Organism : Geobacter sulfurreducens | Module List :
Regulation information for GSU1618(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 GSU1618
|Gene||Common Name||Description||Module membership|
|GSU0124||GSU0124||competence protein F, putative (VIMSS)||59, 261|
|GSU0134||GSU0134||metallo-beta-lactamase family protein (NCBI)||38, 59|
|GSU0235||GSU0235||S1 RNA binding domain protein (VIMSS)||59, 298|
|GSU0258||GSU0258||hypothetical protein (VIMSS)||59, 222|
|GSU0269||GSU0269||conserved hypothetical protein (VIMSS)||59, 137|
|GSU0435||GSU0435||MSHA biogenesis protein MshE, putative (VIMSS)||79, 272|
|GSU0498||GSU0498||hypothetical protein (VIMSS)||153, 272|
|GSU0597||GSU0597||hypothetical protein (VIMSS)||45, 59|
|GSU0766||GSU0766||methyl-accepting chemotaxis protein, putative (VIMSS)||82, 272|
|GSU0855||GSU0855||membrane protein, TerC family (NCBI)||59, 71|
|GSU0900||GSU0900||hypothetical protein (VIMSS)||79, 272|
|GSU0947||GSU0947||ABC transporter, ATP-binding protein (VIMSS)||272, 293|
|GSU1025||GSU1025||conserved domain protein (NCBI)||59, 160|
|GSU1049||GSU1049||conserved hypothetical protein (NCBI)||21, 272|
|GSU1050||GSU1050||sensory box histidine kinase (VIMSS)||21, 272|
|GSU1145||cheB-2||protein-glutamate methylesterase (NCBI)||241, 272|
|GSU1299||cheW||purine-binding chemotaxis protein CheW (NCBI)||59, 157|
|GSU1342||GSU1342||transcriptional regulator, LysR family (VIMSS)||127, 272|
|GSU1343||GSU1343||isochorismatase family protein (NCBI)||127, 272|
|GSU1372||GSU1372||3-hydroxyisobutyrate dehydrogenase family protein (VIMSS)||59, 304|
|GSU1373||GSU1373||hypothetical protein (VIMSS)||59, 321|
|GSU1618||GSU1618||hypothetical protein (VIMSS)||59, 272|
|GSU1619||cheY-4||chemotaxis protein CheY (NCBI)||59, 304|
|GSU1620||GSU1620||iron-sulfur cluster binding protein, putative (VIMSS)||59, 272|
|GSU1621||GSU1621||conserved domain protein (VIMSS)||59, 272|
|GSU1622||GSU1622||L-lactate permease (VIMSS)||59, 272|
|GSU1623||GSU1623||glycolate oxidase subunit GlcD, putative (VIMSS)||59, 272|
|GSU1624||GSU1624||glycolate oxidase iron-sulfur subunit, putative (NCBI)||59, 272|
|GSU1671||GSU1671||response regulator/GGDEF domain protein (NCBI)||59, 224|
|GSU1680||GSU1680||conserved hypothetical protein (VIMSS)||59, 300|
|GSU1751||GSU1751||hypothetical protein (VIMSS)||59, 141|
|GSU2077||GSU2077||hypothetical protein (VIMSS)||59, 194|
|GSU2125||GSU2125||conserved domain protein (VIMSS)||59, 222|
|GSU2135||GSU2135||heavy metal efflux pump, CzcA family (VIMSS)||59, 113|
|GSU2218||cheW-6||chemotaxis protein CheW (NCBI)||59, 321|
|GSU2334||GSU2334||hypothetical protein (VIMSS)||59, 147|
|GSU2369||GSU2369||hypothetical protein (VIMSS)||59, 79|
|GSU2416||cheW-8||chemotaxis protein CheW (NCBI)||59, 79|
|GSU2450||GSU2450||conserved hypothetical protein (VIMSS)||51, 59|
|GSU2452||GSU2452||copper-translocating P-type ATPase (VIMSS)||40, 59|
|GSU2454||GSU2454||membrane protein, putative (VIMSS)||59, 144|
|GSU2477||GSU2477||TPR domain/radical SAM/B12 binding domain protein (NCBI)||59, 198|
|GSU2511||GSU2511||sensory box/GGDEF family protein (VIMSS)||272, 337|
|GSU2973||GSU2973||lipoprotein, putative (VIMSS)||59, 296|
|GSU3023||GSU3023||glycosyl transferase, group 1/2 family protein (VIMSS)||78, 272|
|GSU3025||GSU3025||heptosyltransferase family protein (VIMSS)||27, 272|
|GSU3417||GSU3417||dioxygenase, putative (VIMSS)||21, 59|
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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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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