Organism : Bacillus cereus ATCC14579 | Module List :
Regulation information for BC3996(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 BC3996
|Gene||Common Name||Description||Module membership|
|BC0193||BC0193||hypothetical protein (NCBI ptt file)||343, 440|
|BC0349||BC0349||hypothetical protein (NCBI ptt file)||20, 163|
|BC0360||BC0360||Aminopeptidase (NCBI ptt file)||20, 488|
|BC0651||BC0651||Two component system histidine kinase (NCBI ptt file)||440, 478|
|BC0652||BC0652||Two-component response regulator (NCBI ptt file)||228, 440|
|BC0766||BC0766||Methylthioribose transport system permease protein (NCBI ptt file)||20, 63|
|BC0781||BC0781||hypothetical protein (NCBI ptt file)||20, 364|
|BC0986||BC0986||Response regulator aspartate phosphatase (NCBI ptt file)||20, 416|
|BC1014||BC1014||Quinone oxidoreductase (NCBI ptt file)||364, 440|
|BC1074||BC1074||hypothetical protein (NCBI ptt file)||148, 440|
|BC1075||BC1075||Beta-lactamase repressor (NCBI ptt file)||219, 440|
|BC1077||BC1077||Transcriptional regulator, TetR family (NCBI ptt file)||304, 440|
|BC1130||BC1130||hypothetical protein (NCBI ptt file)||9, 440|
|BC1172||BC1172||ComZ protein (NCBI ptt file)||20, 477|
|BC1178||BC1178||hypothetical protein (NCBI ptt file)||20, 73|
|BC1336||BC1336||Sporulation kinase D (NCBI ptt file)||6, 440|
|BC1431||BC1431||Cell wall endopeptidase, family M23/M37 (NCBI ptt file)||20, 416|
|BC1624||BC1624||hydrolase (HAD superfamily) (NCBI ptt file)||20, 227|
|BC1769||BC1769||hypothetical protein (NCBI ptt file)||20, 26|
|BC1889||BC1889||Phage protein (NCBI ptt file)||20, 254|
|BC2364||BC2364||hypothetical protein (NCBI ptt file)||6, 20|
|BC2558||BC2558||Transcriptional regulator (NCBI ptt file)||7, 440|
|BC2671||BC2671||ThiJ/PfpI family (NCBI ptt file)||20, 90|
|BC2675||BC2675||Acetyltransferase (NCBI ptt file)||20, 304|
|BC2749||BC2749||Acetyltransferase (NCBI ptt file)||20, 146|
|BC2750||BC2750||hypothetical protein (NCBI ptt file)||20, 279|
|BC2797||BC2797||Acetyltransferase (NCBI ptt file)||6, 20|
|BC2809||BC2809||Phosphinothricin N-acetyltransferase (NCBI ptt file)||20, 258|
|BC2988||BC2988||Transcriptional regulator, Cro/CI family (NCBI ptt file)||100, 440|
|BC2996||BC2996||Transcriptional regulator, PadR family (NCBI ptt file)||7, 440|
|BC3226||BC3226||hypothetical protein (NCBI ptt file)||440, 449|
|BC3279||BC3279||hypothetical protein (NCBI ptt file)||7, 440|
|BC3334||BC3334||2-haloalkanoic acid dehalogenase (NCBI ptt file)||15, 440|
|BC3421||BC3421||Transcriptional regulator, MarR family (NCBI ptt file)||20, 485|
|BC3460||BC3460||Short chain dehydrogenase (NCBI ptt file)||20, 478|
|BC3518||BC3518||Response regulator aspartate phosphatase (NCBI ptt file)||20, 163|
|BC3592||BC3592||Transcriptional regulator, TetR family (NCBI ptt file)||20, 354|
|BC3636||BC3636||hypothetical Cytosolic Protein (NCBI ptt file)||308, 440|
|BC3996||BC3996||hypothetical Exported Protein (NCBI ptt file)||20, 440|
|BC4035||BC4035||Aspartate aminotransferase (NCBI ptt file)||20, 408|
|BC4123||BC4123||Lipase/Acylhydrolase with GDSL-like motif (NCBI ptt file)||20, 343|
|BC4146||BC4146||Protein erfK/srfK precursor (NCBI ptt file)||20, 63|
|BC4337||BC4337||hypothetical Membrane Spanning Protein (NCBI ptt file)||440, 443|
|BC4453||BC4453||Phage protein (NCBI ptt file)||62, 440|
|BC4532||BC4532||hypothetical protein (NCBI ptt file)||7, 440|
|BC4660||BC4660||Acetoin utilization protein acuA (NCBI ptt file)||440, 478|
|BC4908||BC4908||hypothetical Membrane Associated Protein (NCBI ptt file)||20, 284|
|BC4929||BC4929||Macrolide-efflux protein (NCBI ptt file)||20, 100|
|BC4931||BC4931||hypothetical Cytosolic Protein (NCBI ptt file)||20, 316|
|BC4933||BC4933||Methyltransferase (NCBI ptt file)||303, 440|
|BC4947||BC4947||hypothetical protein (NCBI ptt file)||20, 63|
|BC5011||BC5011||hypothetical protein (NCBI ptt file)||422, 440|
|BC5046||BC5046||Lysine decarboxylase family (NCBI ptt file)||20, 284|
|BC5352||BC5352||two-component response regulator YocG (NCBI)||41, 440|
|BC5353||BC5353||Two-component sensor kinase yocF (NCBI ptt file)||41, 440|
|BC5424||BC5424||Methyl-accepting chemotaxis protein (NCBI ptt file)||416, 440|
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.
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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.
- 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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