Organism : Bacillus subtilis | Module List :
Regulation information for BSU05100(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 BSU05100
|Gene||Common Name||Description||Module membership|
|BSU02110||ybyB||hypothetical protein (RefSeq)||231, 299|
|BSU02590||ycbP||putative inner integral membrane protein (RefSeq)||137, 299|
|BSU02830||ycdF||putative dehydrogenase (RefSeq)||299, 391|
|BSU02840||ycdG||putative glycosidase (RefSeq)||147, 299|
|BSU03130||nadE||NAD synthetase (RefSeq)||29, 169|
|BSU04340||ydaP||pyruvate oxidase (RefSeq)||299, 320|
|BSU04380||ydaT||hypothetical protein (RefSeq)||203, 299|
|BSU04400||gsiB||general stress protein (RefSeq)||203, 299|
|BSU04410||ydbB||putative enzyme ; cupin family (RefSeq)||29, 353|
|BSU04420||ydbC||hypothetical protein (RefSeq)||29, 353|
|BSU05100||yddT||hypothetical protein (RefSeq)||29, 299|
|BSU07550||yflT||heat stress induced protein (RefSeq)||203, 299|
|BSU07850||yfkM||general stress protein 18 (RefSeq)||39, 299|
|BSU09390||ygxB||putative integral inner membrane protein (RefSeq)||147, 299|
|BSU09530||yhdN||aldo/keto reductase specific for NADPH (RefSeq)||149, 299|
|BSU10320||yhfP||putative oxidoreductase (RefSeq)||29, 252|
|BSU10430||yhxD||putative oxidoreductase (RefSeq)||147, 299|
|BSU13010||ykgB||putative 6-phosphogluconolactonase (RefSeq)||29, 113|
|BSU13160||ohrB||organic hydroperoxide resistance reductase B (RefSeq)||203, 299|
|BSU21320||yomL||conserved hypothetical protein; phage SPbeta (RefSeq)||29, 299|
|BSU24470||yqhS||3-dehydroquinate dehydratase (RefSeq)||29, 256|
|BSU28340||ysnF||putative stress response protein (RefSeq)||29, 299|
|BSU28410||gerE||transcriptional regulator (RefSeq)||29, 248|
|BSU30650||dps||DNA-protecting protein, ferritin (RefSeq)||29, 320|
|BSU32100||yumB||putative NAD-disulfide oxidoreductase (RefSeq)||29, 391|
|BSU32450||pucL||urate oxidase with peroxide reductase N-terminal domain (RefSeq)||29, 231|
|BSU32500||pucB||enzyme for molybdopterin cofactor synthesis required for xanthine dehydrogenase (RefSeq)||29, 231|
|BSU33620||yvaK||carboxylesterase (RefSeq)||29, 149|
|BSU34680||yvcT||putative 2-hydroxyacid dehydrogenase (RefSeq)||29, 169|
|BSU35970||ywsB||hypothetical protein (RefSeq)||29, 149|
|BSU36670||csbD||stress response protein (RefSeq)||203, 299|
|BSU37300||ywiC||putative integral inner membrane protein (RefSeq)||29, 238|
|BSU37940||ywdJ||putative purine/pyrimidine permease (RefSeq)||29, 243|
|BSU37950||ywdI||hypothetical protein (RefSeq)||29, 243|
|BSU38190||galT||galactose-1-phosphate uridylyltransferase (RefSeq)||29, 149|
|BSU38200||galK||galactokinase (RefSeq)||29, 183|
|BSU38620||yxlJ||3-methyladenine DNA glycosylase (RefSeq)||29, 59|
|BSU38980||scoB||succinyl CoA:3-oxoacid CoA-transferase (subunit B) (RefSeq)||29, 231|
|BSU39050||katE||catalase 2 (RefSeq)||147, 299|
|BSU39560||yxeG||putative integral inner membrane protein (RefSeq)||29, 233|
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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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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