Organism : Bacillus cereus ATCC14579 | Module List :
Ribose transport ATP-binding protein rbsA (NCBI ptt file)
Functional Annotations (4)
|ABC-type sugar transport system, ATPase component||cog/ cog|
|ATP binding||go/ molecular_function|
|monosaccharide-transporting ATPase activity||go/ molecular_function|
|ABC transporters||kegg/ kegg pathway|
Regulation information for BC0662(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 BC0662
Module neighborhood information for BC0662
|Gene||Common Name||Description||Module membership|
|BC0192||BC0192||Acylamino-acid-releasing enzyme (NCBI ptt file)||375, 524|
|BC0326||BC0326||phosphoribosylaminoimidazole-succinocarboxamidesynthase (RefSeq)||424, 524|
|BC0327||BC0327||Phosphorybosylformylglycinamidine synthetase, PurS component (NCBI ptt file)||72, 524|
|BC0328||BC0328||Phosphoribosylformylglycinamidine synthase (NCBI ptt file)||72, 524|
|BC0329||BC0329||Phosphoribosylformylglycinamidine synthase (NCBI ptt file)||424, 524|
|BC0331||BC0331||Phosphoribosylformylglycinamidine cyclo-ligase (NCBI ptt file)||424, 524|
|BC0332||BC0332||Phosphoribosylglycinamide formyltransferase (NCBI ptt file)||424, 524|
|BC0659||BC0659||Ribose operon repressor (NCBI ptt file)||417, 524|
|BC0660||BC0660||Ribokinase (NCBI ptt file)||417, 524|
|BC0661||BC0661||High affinity ribose transport protein rbsD (NCBI ptt file)||417, 524|
|BC0662||BC0662||Ribose transport ATP-binding protein rbsA (NCBI ptt file)||417, 524|
|BC0663||BC0663||Ribose transport system permease protein rbsC (NCBI ptt file)||104, 417|
|BC0918||BC0918||IG hypothetical 23633 (NCBI ptt file)||401, 524|
|BC1019||BC1019||phosphoesterase (NCBI ptt file)||50, 524|
|BC1477||BC1477||Transcriptional regulatory protein resD (NCBI ptt file)||117, 417|
|BC1517||BC1517||3-dehydroquinate synthase (NCBI ptt file)||83, 524|
|BC1522||BC1522||Menaquinol-cytochrome c reductase iron-sulfur subunit (NCBI ptt file)||83, 524|
|BC1544||BC1544||hypothetical protein (NCBI ptt file)||308, 417|
|BC1545||BC1545||hypothetical protein (NCBI ptt file)||308, 417|
|BC1572||BC1572||putative GTPases (dynamin-related) (NCBI ptt file)||417, 451|
|BC1795||BC1795||hypothetical protein (NCBI ptt file)||460, 524|
|BC2149||BC2149||hypothetical protein (NCBI ptt file)||334, 417|
|BC2150||BC2150||metal-dependent phosphohydrolase (NCBI ptt file)||193, 417|
|BC2151||BC2151||ABC transporter ATP-binding protein uup (NCBI ptt file)||193, 417|
|BC2397||BC2397||ATPase family protein (NCBI ptt file)||437, 524|
|BC2839||BC2839||Sarcosine oxidase alpha subunit (NCBI ptt file)||267, 524|
|BC2869||BC2869||N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase (NCBI ptt file)||279, 524|
|BC3203||BC3203||hypothetical Exported Protein (NCBI ptt file)||234, 417|
|BC3964||BC3964||hypothetical protein (NCBI ptt file)||417, 485|
|BC3965||BC3965||hypothetical protein (NCBI ptt file)||197, 417|
|BC3966||BC3966||hypothetical protein (NCBI ptt file)||417, 485|
|BC4065||BC4065||Stage V sporulation protein AE (NCBI ptt file)||355, 524|
|BC4069||BC4069||Stage V sporulation protein AB (NCBI ptt file)||424, 524|
|BC4177||BC4177||Dimethylallyltransferase (NCBI ptt file)||22, 417|
|BC4302||BC4302||PhoH protein (NCBI ptt file)||193, 417|
|BC4487||BC4487||Superfamily I DNA and RNA helicases (NCBI ptt file)||518, 524|
|BC4560||BC4560||Phenylalanyl-tRNA synthetase beta chain (NCBI ptt file)||412, 417|
|BC4561||BC4561||Phenylalanyl-tRNA synthetase alpha chain (NCBI ptt file)||412, 417|
|BC4685||BC4685||Nicotinate phosphoribosyltransferase (NCBI ptt file)||22, 417|
|BC5334||BC5334||UDP-N-acetylglucosamine 1-carboxyvinyltransferase (NCBI ptt file)||54, 524|
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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