Organism : Bacillus cereus ATCC14579 | Module List :
Replication initiation and membrane attachment protein (NCBI ptt file)
Functional Annotations (1)
|Replication initiation/membrane attachment protein||cog/ cog|
Regulation information for BC4580(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 BC4580
|Replication initiation/membrane attachment protein||cog/ cog|
Module neighborhood information for BC4580
|Gene||Common Name||Description||Module membership|
|BC0024||BC0024||DNA polymerase III subunit gamma/tau (NCBI ptt file)||88, 252|
|BC0186||BC0186||hypothetical Membrane Spanning Protein (NCBI ptt file)||450, 451|
|BC0187||BC0187||hypothetical Membrane Associated Protein (NCBI ptt file)||450, 451|
|BC0286||BC0286||ATP/GTP hydrolase (NCBI ptt file)||252, 351|
|BC0341||BC0341||NAD-dependent DNA ligase (NCBI ptt file)||252, 351|
|BC0468||BC0468||DNA-3-methyladenine glycosylase II (NCBI ptt file)||242, 252|
|BC0497||BC0497||Cell division inhibitor (NCBI ptt file)||222, 252|
|BC0609||BC0609||Lactoylglutathione lyase (NCBI ptt file)||252, 329|
|BC0624||BC0624||von Willebrand factor type A domain protein (NCBI ptt file)||450, 451|
|BC0625||BC0625||NorQ protein (NCBI ptt file)||450, 451|
|BC0694||BC0694||Na+/H+ antiporter NapA (NCBI ptt file)||243, 252|
|BC1035||BC1035||Glycerol kinase (NCBI ptt file)||252, 329|
|BC1300||BC1300||Two-component response regulator (NCBI ptt file)||252, 329|
|BC1301||BC1301||Two component system histidine kinase (NCBI ptt file)||252, 329|
|BC1485||BC1485||ATP-dependent DNA helicase recQ (NCBI ptt file)||268, 450|
|BC1486||BC1486||CAAX amino terminal protease family (NCBI ptt file)||268, 450|
|BC1488||BC1488||phosphoesterase (NCBI ptt file)||268, 450|
|BC1489||BC1489||Transcriptional regulator, MerR family (NCBI ptt file)||268, 450|
|BC1531||BC1531||hypothetical Transcriptional Regulatory Protein (NCBI ptt file)||439, 450|
|BC1532||BC1532||Dihydrodipicolinate reductase (NCBI ptt file)||450, 527|
|BC1533||BC1533||Methylglyoxal synthase (NCBI ptt file)||240, 450|
|BC1534||BC1534||Lmbe-related protein (NCBI ptt file)||240, 450|
|BC1535||BC1535||Glycosyltransferase (NCBI ptt file)||240, 450|
|BC1536||BC1536||Poly(A) polymerase (NCBI ptt file)||240, 450|
|BC1540||BC1540||3-methyl-2-oxobutanoate hydroxymethyltransferase (NCBI ptt file)||329, 450|
|BC1541||BC1541||Pantoate--beta-alanine ligase (NCBI ptt file)||329, 450|
|BC1542||BC1542||Aspartate 1-decarboxylase (NCBI ptt file)||329, 450|
|BC1742||BC1742||Two component system histidine kinase (NCBI ptt file)||252, 361|
|BC1743||BC1743||Two-component response regulator (NCBI ptt file)||243, 252|
|BC1804||BC1804||Rhodanese-related sulfurtransferases (NCBI ptt file)||252, 467|
|BC2293||BC2293||hypothetical protein (NCBI ptt file)||450, 511|
|BC3843||BC3843||Signal recognition particle, subunit Ffh/SRP54 (NCBI ptt file)||252, 476|
|BC3920||BC3920||2-dehydropantoate 2-reductase (NCBI ptt file)||268, 450|
|BC4180||BC4180||Methylenetetrahydrofolate dehydrogenase (NADP+) (NCBI ptt file)||371, 450|
|BC4181||BC4181||N utilization substance protein B (NCBI ptt file)||450, 451|
|BC4295||BC4295||DNA repair protein recO (NCBI ptt file)||252, 257|
|BC4315||BC4315||Coproporphyrinogen oxidase, anaerobic (NCBI ptt file)||243, 252|
|BC4440||BC4440||Stage IV sporulation protein FB (NCBI ptt file)||252, 285|
|BC4579||BC4579||Primosomal protein dnaI (NCBI ptt file)||252, 351|
|BC4580||BC4580||Replication initiation and membrane attachment protein (NCBI ptt file)||252, 450|
|BC4605||BC4605||DNA polymerase III alpha subunit (NCBI ptt file)||268, 450|
|BC4673||BC4673||hypothetical protein (NCBI ptt file)||243, 252|
|BC5182||BC5182||Multidrug resistance ABC transporter ATP-binding and permease protein (NCBI ptt file)||252, 467|
|BC5457||BC5457||hypothetical protein (NCBI ptt file)||143, 252|
|BC5460||BC5460||hypothetical protein (NCBI ptt file)||252, 288|
|BC5462||BC5462||Two-component sensor kinase yycG (NCBI ptt file)||252, 374|
|BC5485||BC5485||Glucose inhibited division protein A (NCBI ptt file)||240, 252|
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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