Organism : Bacillus subtilis | Module List :
Regulation information for BSU31130(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 BSU31130
Module neighborhood information for BSU31130
|Gene||Common Name||Description||Module membership|
|BSU00570||yabM||putative exporter (RefSeq)||66, 409|
|BSU00580||yabN||putative fusion methylase and nucleotide pyrophosphohydrolase (RefSeq)||66, 193|
|BSU02270||pssA||phosphatidylserine synthase (RefSeq)||66, 212|
|BSU03100||ycgG||hypothetical protein (RefSeq)||216, 291|
|BSU05150||ydeC||putative transcriptional regulator (AraC/XylS family) (RefSeq)||157, 216|
|BSU05180||ydeF||putative PLP-dependent transcriptional regulator (RefSeq)||115, 216|
|BSU05600||ydgE||putative N-acetyltransferase (RefSeq)||111, 216|
|BSU05680||ydgK||putative efflux transporter (RefSeq)||14, 66|
|BSU06330||yeaC||hypothetical protein (RefSeq)||66, 142|
|BSU06340||yeaD||hypothetical protein (RefSeq)||66, 142|
|BSU06380||yebC||putative integral inner membrane protein (RefSeq)||14, 66|
|BSU07220||yetL||putative transcriptional regulator (MarR family) (RefSeq)||216, 378|
|BSU07500||yfmE||iron-dicitrate ABC transporter (permease) (RefSeq)||66, 151|
|BSU07980||pdaA||exported N-acetylmuramic acid deacetylase (RefSeq)||66, 293|
|BSU08340||padR||transcriptional regulator (RefSeq)||216, 258|
|BSU09000||yhbJ||putative integral inner membrane protein; putative exporter subunit (RefSeq)||66, 225|
|BSU09020||yhcB||putative oxidoreductase associated to oxygen stress (RefSeq)||14, 66|
|BSU11890||yjcK||putative ribosomal-protein-alanine N-acetyltransferase (RefSeq)||157, 216|
|BSU12060||yjdI||hypothetical protein (RefSeq)||49, 216|
|BSU13090||ykkC||efflux transporter (RefSeq)||37, 66|
|BSU13100||ykkD||efflux transporter (RefSeq)||66, 293|
|BSU13310||tnrA||nitrogen sensing transcriptional regulator (RefSeq)||216, 258|
|BSU13320||ykzB||hypothetical protein (RefSeq)||159, 216|
|BSU13770||ykvO||putative oxidoreductase (RefSeq)||44, 216|
|BSU13800||ykvR||hypothetical protein (RefSeq)||109, 216|
|BSU13820||ykvT||cell wall hydrolase related to spore cortex-lytic enzymes (RefSeq)||116, 216|
|BSU13880||glcT||transcriptional antiterminator (BglG family) (RefSeq)||66, 283|
|BSU18730||yoaS||hypothetical protein (RefSeq)||216, 327|
|BSU18750||yoaT||putative integral inner membrane protein (RefSeq)||216, 327|
|BSU19230||yocJ||azoreductase (RefSeq)||66, 164|
|BSU19530||yodA||putative tautomerase (RefSeq)||66, 322|
|BSU20040||nrdF||ribonucleotide-diphosphate reductase subunit beta (NCBI)||66, 102|
|BSU21730||ypmS||hypothetical protein (RefSeq)||66, 370|
|BSU22010||exoA||5'3'-exonuclease (RefSeq)||216, 226|
|BSU22160||yptA||hypothetical protein (RefSeq)||66, 67|
|BSU22300||yppC||hypothetical protein (RefSeq)||216, 308|
|BSU22970||ypbH||adaptor protein (RefSeq)||51, 216|
|BSU23600||yqxK||hypothetical protein (RefSeq)||66, 292|
|BSU23800||proI||pyrroline-5-carboxylate reductase (RefSeq)||66, 409|
|BSU26240||yqaO||conserved hypothetical protein; skin element (RefSeq)||64, 216|
|BSU26550||yrkD||hypothetical protein (RefSeq)||51, 216|
|BSU26630||yrdQ||putative transcriptional regulator (LysR family) (RefSeq)||216, 226|
|BSU27090||aapA||d-Serine/d-alanine/glycine permease (RefSeq)||38, 66|
|BSU27110||yrhO||putative transcriptional regulator (RefSeq)||216, 378|
|BSU27210||yrhF||hypothetical protein (RefSeq)||14, 66|
|BSU28600||yshB||putative integral inner membrane protein (RefSeq)||216, 226|
|BSU29970||ytkP||putative cysteine synthase-like protein (RefSeq)||66, 151|
|BSU31130||yubD||putative efflux transporter (RefSeq)||66, 216|
|BSU33030||yuxN||putative transcriptional regulator (RefSeq)||151, 216|
|BSU33100||liaF||integral inner membrane protein (RefSeq)||66, 319|
|BSU33990||yvbU||putative transcriptional regulator (LysR family) (RefSeq)||14, 66|
|BSU35740||tagD||glycerol-3-phosphate cytidylyltransferase (RefSeq)||216, 226|
|BSU36160||ywqM||putative transcriptional regulator (LysR family) (RefSeq)||49, 216|
|BSU36440||ywoH||putative transcriptional regulator (MarR family) (RefSeq)||51, 216|
|BSU36450||ywoG||putative efflux transporter (RefSeq)||51, 216|
|BSU36590||clsA||cardiolipin synthase (RefSeq)||66, 226|
|BSU36980||ywlA||putative integral inner membrane protein (RefSeq)||216, 378|
|BSU36990||ywkF||hypothetical protein (RefSeq)||14, 66|
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.
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.
- 2. Source gene
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