Organism : Bacillus cereus ATCC14579 | Module List :
Regulation information for BC1830(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 BC1830
Module neighborhood information for BC1830
|Gene||Common Name||Description||Module membership|
|BC0034||BC0034||CsfB protein (NCBI ptt file)||217, 351|
|BC0047||BC0047||Sporulation-specific protease YabG (NCBI ptt file)||217, 393|
|BC0214||BC0214||hypothetical Membrane Spanning Protein (NCBI ptt file)||123, 498|
|BC0240||BC0240||hypothetical protein (NCBI ptt file)||123, 405|
|BC0288||BC0288||Ribosomal-protein-alanine acetyltransferase (NCBI ptt file)||217, 351|
|BC0319||BC0319||hypothetical protein (NCBI ptt file)||123, 415|
|BC0480||BC0480||hypothetical protein (NCBI ptt file)||217, 241|
|BC0818||BC0818||Oligopeptide transport system permease protein oppB (NCBI ptt file)||217, 351|
|BC0819||BC0819||Oligopeptide transport system permease protein oppC (NCBI ptt file)||162, 217|
|BC0870||BC0870||Multidrug resistance ABC transporter ATP-binding and permease protein (NCBI ptt file)||104, 217|
|BC0871||BC0871||Multidrug resistance ABC transporter ATP-binding and permease protein (NCBI ptt file)||104, 217|
|BC1141||BC1141||Spore germination protein PE (NCBI ptt file)||217, 351|
|BC1152||BC1152||Asparagine synthetase (NCBI ptt file)||136, 217|
|BC1243||BC1243||hypothetical protein (NCBI ptt file)||217, 377|
|BC1331||BC1331||Internalin (NCBI ptt file)||217, 419|
|BC1361||BC1361||CAAX amino terminal protease family (NCBI ptt file)||123, 363|
|BC1449||BC1449||cAMP-dependent protein kinase regulatory chain (NCBI ptt file)||217, 504|
|BC1508||BC1508||hypothetical protein (NCBI ptt file)||123, 155|
|BC1568||BC1568||Methionine aminopeptidase (NCBI ptt file)||217, 407|
|BC1613||BC1613||Zn-dependent hydrolase (NCBI ptt file)||123, 498|
|BC1678||BC1678||JEMB (NCBI ptt file)||9, 123|
|BC1679||BC1679||Small acid soluble spore protein (NCBI ptt file)||24, 123|
|BC1830||BC1830||Copper resistance protein A (NCBI ptt file)||123, 217|
|BC2363||BC2363||Aspartate-semialdehyde dehydrogenase (NCBI ptt file)||123, 453|
|BC2378||BC2378||Transporter, LysE family (NCBI ptt file)||217, 509|
|BC2404||BC2404||hypothetical Cytosolic Protein (NCBI ptt file)||217, 241|
|BC2417||BC2417||hypothetical protein (NCBI ptt file)||123, 217|
|BC2430||BC2430||Methyltransferase (NCBI ptt file)||217, 453|
|BC2465||BC2465||hypothetical protein (NCBI ptt file)||85, 217|
|BC2544||BC2544||ABC transporter permease protein (NCBI ptt file)||217, 351|
|BC2545||BC2545||hypothetical protein (NCBI ptt file)||136, 217|
|BC2643||BC2643||hydrolase (HAD superfamily) (NCBI ptt file)||123, 241|
|BC2711||BC2711||Bacitracin resistance protein (Putative undecaprenol kinase) (NCBI ptt file)||2, 217|
|BC2741||BC2741||Transporter, Drug/Metabolite Exporter family (NCBI ptt file)||76, 217|
|BC2744||BC2744||hypothetical protein (NCBI ptt file)||158, 217|
|BC3280||BC3280||hypothetical protein (NCBI ptt file)||136, 217|
|BC3458||BC3458||XpaF1 protein (NCBI ptt file)||56, 123|
|BC3474||BC3474||hypothetical protein (NCBI ptt file)||217, 351|
|BC3475||BC3475||hypothetical protein (NCBI ptt file)||3, 217|
|BC3593||BC3593||Transcriptional regulator, DeoR family (NCBI ptt file)||217, 351|
|BC3660||BC3660||hypothetical protein (NCBI ptt file)||123, 154|
|BC3667||BC3667||ABC transporter permease protein (NCBI ptt file)||2, 217|
|BC3967||BC3967||hypothetical protein (NCBI ptt file)||154, 217|
|BC4006||BC4006||hypothetical Cytosolic Protein (NCBI ptt file)||123, 238|
|BC4304||BC4304||hypothetical Cytosolic Protein (NCBI ptt file)||217, 272|
|BC4339||BC4339||LSU ribosomal protein L33P (NCBI ptt file)||46, 123|
|BC4450||BC4450||Phage integrase family protein (NCBI ptt file)||123, 464|
|BC4520||uvrC||excinuclease ABC subunit C (RefSeq)||217, 351|
|BC4607||BC4607||hypothetical protein (NCBI ptt file)||217, 339|
|BC4641||BC4641||hypothetical protein (NCBI ptt file)||154, 217|
|BC4779||BC4779||ABC transporter ATP-binding protein (NCBI ptt file)||123, 495|
|BC4788||BC4788||hypothetical protein (NCBI ptt file)||123, 487|
|BC4847||BC4847||D-alanyl-D-alanine carboxypeptidase (NCBI ptt file)||217, 361|
|BC4858||BC4858||DnaK suppressor protein (NCBI ptt file)||217, 241|
|BC5247||BC5247||hypothetical protein (NCBI ptt file)||123, 186|
|BC5250||BC5250||Competence transcription factor (NCBI ptt file)||123, 138|
|BC5284||BC5284||ABC transporter permease protein (NCBI ptt file)||123, 284|
|BC5285||BC5285||Bacitracin transport ATP-binding protein bcrA (NCBI ptt file)||123, 487|
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
- 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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