Organism : Geobacter sulfurreducens | Module List :
conserved hypothetical protein (VIMSS)
Functional Annotations (1)
Regulation information for GSU1278(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 GSU1278
Module neighborhood information for GSU1278
|Gene||Common Name||Description||Module membership|
|GSU0095||GSU0095||conserved hypothetical protein TIGR00103 (VIMSS)||83, 170|
|GSU0114||atpC||ATP synthase F1, epsilon subunit (NCBI)||170, 230|
|GSU0117||GSU0117||aminotransferase, classes I and II (NCBI)||7, 248|
|GSU0191||GSU0191||cold-shock domain family protein (VIMSS)||16, 248|
|GSU0333||atpE||ATP synthase F0, C subunit (NCBI)||116, 170|
|GSU0335||GSU0335||hypothetical protein (VIMSS)||35, 170|
|GSU0336||GSU0336||hypothetical protein (VIMSS)||62, 170|
|GSU0337||hemL||glutamate-1-semialdehyde-2,1-aminomutase (NCBI)||139, 170|
|GSU0581||GSU0581||cold-shock domain family protein (VIMSS)||102, 248|
|GSU0906||rpsU-1||ribosomal protein S21 (NCBI)||11, 248|
|GSU1277||greA||transcription elongation factor GreA (NCBI)||19, 248|
|GSU1278||GSU1278||conserved hypothetical protein (VIMSS)||170, 248|
|GSU1317||ispB||octaprenyl-diphosphate synthase (NCBI)||233, 248|
|GSU1318||GSU1318||hypothetical protein (VIMSS)||83, 248|
|GSU1451||GSU1451||3-hydroxyisobutyrate dehydrogenase family protein (VIMSS)||170, 243|
|GSU1583||bioD||dethiobiotin synthase (NCBI)||120, 248|
|GSU1585||GSU1585||conserved hypothetical protein (VIMSS)||120, 248|
|GSU1586||nusA||N utilization substance protein A (NCBI)||120, 248|
|GSU1587||GSU1587||ribosomal protein L7Ae family protein (NCBI)||120, 248|
|GSU1588||infB||translation initiation factor IF-2 (NCBI)||120, 248|
|GSU1589||rbfA||ribosome-binding factor A (NCBI)||120, 248|
|GSU1591||truB||tRNA pseudouridine synthase B (NCBI)||120, 248|
|GSU1592||rpsO||ribosomal protein S15 (NCBI)||120, 248|
|GSU1593||pnp||polyribonucleotide nucleotidyltransferase (NCBI)||120, 248|
|GSU1637||pyrE||orotate phosphoribosyltransferase (NCBI)||170, 215|
|GSU1760||cyd-5||cytochrome c3 (NCBI)||30, 248|
|GSU1771||GSU1771||conserved domain protein (NCBI)||17, 170|
|GSU1792||clpP||ATP-dependent Clp protease, proteolytic subunit ClpP (VIMSS)||161, 170|
|GSU1793||tig||trigger factor (NCBI)||161, 170|
|GSU1794||GSU1794||HAM1 protein (NCBI)||158, 248|
|GSU1860||GSU1860||keto/oxoacid ferredoxin oxidoreductase, alpha subunit (VIMSS)||170, 239|
|GSU1861||GSU1861||keto/oxoacid ferredoxin oxidoreductase, beta subunit (VIMSS)||170, 199|
|GSU1863||GSU1863||transcriptional regulator, Ros/MucR family (VIMSS)||170, 215|
|GSU1882||ptsH||phosphocarrier protein HPr (NCBI)||168, 170|
|GSU1907||pssA||CDP-diacylglycerol--serineO-phosphatidyltransferase (NCBI)||102, 248|
|GSU1918||frr||ribosome recycling factor (NCBI)||230, 248|
|GSU1925||GSU1925||transport-associated domain protein (NCBI)||120, 248|
|GSU2072||GSU2072||1-acyl-sn-glycerol-3-phosphate acyltransferase, putative (VIMSS)||7, 248|
|GSU2245||GSU2245||UDP-N-acetylglucosamine 2-epimerase (VIMSS)||170, 316|
|GSU2625||GSU2625||transcriptional regulator, ArsR family (NCBI)||120, 248|
|GSU3006||cobB||cobyrinic acid a,c-diamide synthase (NCBI)||30, 248|
|GSU3298||GSU3298||transcriptional regulator, Cro/CI family (VIMSS)||7, 248|
|GSU3301||GSU3301||conserved hypothetical protein (NCBI)||106, 248|
|GSU3365||cysS||cysteinyl-tRNA synthetase (NCBI)||83, 248|
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.
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.
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.
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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