Organism : Geobacter sulfurreducens | Module List :
Regulation information for GSU2369(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 GSU2369
|Gene||Common Name||Description||Module membership|
|GSU0063||GSU0063||conserved hypothetical protein (VIMSS)||79, 141|
|GSU0124||GSU0124||competence protein F, putative (VIMSS)||59, 261|
|GSU0134||GSU0134||metallo-beta-lactamase family protein (NCBI)||38, 59|
|GSU0225||GSU0225||hypothetical protein (VIMSS)||79, 84|
|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|
|GSU0314||GSU0314||general secretion protein E N-terminal domain protein (NCBI)||79, 278|
|GSU0435||GSU0435||MSHA biogenesis protein MshE, putative (VIMSS)||79, 272|
|GSU0597||GSU0597||hypothetical protein (VIMSS)||45, 59|
|GSU0683||GSU0683||methyl-accepting chemotaxis protein, putative (VIMSS)||45, 79|
|GSU0691||GSU0691||translation initation factor SUI1, putative (NCBI)||71, 79|
|GSU0701||GSU0701||cytochrome c family protein (NCBI)||79, 206|
|GSU0820||sppA-1||signal peptide peptidase SppA, 36K type (NCBI)||36, 79|
|GSU0855||GSU0855||membrane protein, TerC family (NCBI)||59, 71|
|GSU0900||GSU0900||hypothetical protein (VIMSS)||79, 272|
|GSU1025||GSU1025||conserved domain protein (NCBI)||59, 160|
|GSU1299||cheW||purine-binding chemotaxis protein CheW (NCBI)||59, 157|
|GSU1302||GSU1302||sensor histidine kinase/response regulator (VIMSS)||79, 180|
|GSU1327||GSU1327||homocysteine S-methyltransferase domain protein (VIMSS)||79, 260|
|GSU1372||GSU1372||3-hydroxyisobutyrate dehydrogenase family protein (VIMSS)||59, 304|
|GSU1373||GSU1373||hypothetical protein (VIMSS)||59, 321|
|GSU1418||GSU1418||hypothetical protein (VIMSS)||78, 79|
|GSU1570||GSU1570||membrane protein, TerC family (NCBI)||15, 79|
|GSU1572||GSU1572||ribD domain protein (NCBI)||51, 79|
|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|
|GSU2095||GSU2095||NADH oxidase, putative (VIMSS)||1, 79|
|GSU2125||GSU2125||conserved domain protein (VIMSS)||59, 222|
|GSU2135||GSU2135||heavy metal efflux pump, CzcA family (VIMSS)||59, 113|
|GSU2173||GSU2173||lipoprotein, putative (VIMSS)||79, 274|
|GSU2218||cheW-6||chemotaxis protein CheW (NCBI)||59, 321|
|GSU2289||GSU2289||nicotinate phosphoribosyltransferase, putative (NCBI)||46, 79|
|GSU2334||GSU2334||hypothetical protein (VIMSS)||59, 147|
|GSU2358||GSU2358||isoamylase family protein (VIMSS)||79, 142|
|GSU2360||GSU2360||maltooligosyltrehalose synthase, putative (VIMSS)||63, 79|
|GSU2369||GSU2369||hypothetical protein (VIMSS)||59, 79|
|GSU2384||GSU2384||sensor histidine kinase (VIMSS)||79, 269|
|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|
|GSU2453||GSU2453||membrane protein, putative (VIMSS)||51, 79|
|GSU2454||GSU2454||membrane protein, putative (VIMSS)||59, 144|
|GSU2477||GSU2477||TPR domain/radical SAM/B12 binding domain protein (NCBI)||59, 198|
|GSU2510||GSU2510||hypothetical protein (VIMSS)||9, 79|
|GSU2531||GSU2531||sensory box histidine kinase (VIMSS)||79, 82|
|GSU2578||cheW-9||purine-binding chemotaxis protein CheW (NCBI)||79, 300|
|GSU2582||GSU2582||hypothetical protein (VIMSS)||79, 151|
|GSU2646||GSU2646||hypothetical protein (VIMSS)||79, 304|
|GSU2931||GSU2931||hypothetical protein (VIMSS)||70, 79|
|GSU2973||GSU2973||lipoprotein, putative (VIMSS)||59, 296|
|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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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.
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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.
- 2. Source gene
- 3. Target genes (other module members)
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- 5. Module(s) that source gene and target genes belong to
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