Organism : Bacillus cereus ATCC14579 | Module List :
Regulation information for BC4099(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 BC4099
|Gene||Common Name||Description||Module membership|
|BC0572||BC0572||Two-component response regulator (NCBI ptt file)||63, 286|
|BC0758||BC0758||Transcriptional regulator, MarR family (NCBI ptt file)||47, 286|
|BC0759||BC0759||Serine protease (NCBI ptt file)||233, 507|
|BC0761||BC0761||ABC transporter permease protein (NCBI ptt file)||286, 427|
|BC0762||BC0762||hypothetical protein (NCBI ptt file)||286, 427|
|BC0763||BC0763||ABC transporter permease protein (NCBI ptt file)||286, 427|
|BC0868||BC0868||NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (NCBI ptt file)||233, 507|
|BC1066||BC1066||Signal transduction protein TRAP (NCBI ptt file)||173, 233|
|BC1097||BC1097||hypothetical protein (NCBI ptt file)||63, 286|
|BC1098||BC1098||hypothetical protein (NCBI ptt file)||286, 427|
|BC1099||BC1099||hypothetical protein (NCBI ptt file)||26, 286|
|BC1269||BC1269||hypothetical protein (NCBI ptt file)||286, 427|
|BC1275||BC1275||Methyltransferase (NCBI ptt file)||47, 286|
|BC1484||BC1484||ATP-dependent DNA helicase recQ (NCBI ptt file)||286, 409|
|BC1519||BC1519||TPR-repeat-containing protein (NCBI ptt file)||286, 306|
|BC1588||BC1588||Secreted polysaccharide polymerase (NCBI ptt file)||286, 427|
|BC1803||BC1803||Manganese transport protein mntH (NCBI ptt file)||233, 287|
|BC1806||BC1806||2-dehydropantoate 2-reductase (NCBI ptt file)||107, 233|
|BC2114||BC2114||Glutathione peroxidase (NCBI ptt file)||48, 233|
|BC2407||BC2407||hypothetical protein (NCBI ptt file)||286, 453|
|BC2556||BC2556||DNA integration/recombination/invertion protein (NCBI ptt file)||286, 511|
|BC3026||BC3026||Tetracycline resistance protein tetP (NCBI ptt file)||286, 511|
|BC3053||BC3053||HesB-like protein (NCBI ptt file)||233, 287|
|BC3054||BC3054||IG hypothetical 18636 (NCBI ptt file)||233, 287|
|BC3107||BC3107||UvrC-like protein (NCBI ptt file)||286, 491|
|BC3478||BC3478||Phosphoglycerate mutase (NCBI ptt file)||233, 491|
|BC3483||BC3483||N-hydroxyarylamine O-acetyltransferase (NCBI ptt file)||77, 233|
|BC3484||BC3484||Oligoendopeptidase F (NCBI ptt file)||286, 439|
|BC3548||BC3548||Benzil reductase (NCBI ptt file)||233, 507|
|BC3727||BC3727||Formate transporter (NCBI ptt file)||47, 286|
|BC3743||BC3743||Peptidase T (NCBI ptt file)||77, 233|
|BC3747||BC3747||Sensory box/GGDEF family protein (NCBI ptt file)||63, 286|
|BC4001||BC4001||Transcriptional repressor PadR (NCBI ptt file)||1, 233|
|BC4092||BC4092||Stage II sporulation protein M (NCBI ptt file)||233, 511|
|BC4099||BC4099||hypothetical protein (NCBI ptt file)||233, 286|
|BC4340||BC4340||NAD(P)H nitroreductase (NCBI ptt file)||47, 286|
|BC4674||BC4674||Chorismate mutase (NCBI ptt file)||286, 288|
|BC4691||BC4691||Thioredoxin (NCBI ptt file)||233, 507|
|BC4729||BC4729||hypothetical protein (NCBI ptt file)||286, 427|
|BC4730||BC4730||Homoserine O-acetyltransferase (NCBI ptt file)||286, 398|
|BC5159||BC5159||Thioredoxin reductase (NCBI ptt file)||233, 507|
|BC5233||BC5233||D-alanine aminotransferase (NCBI ptt file)||233, 286|
|BC5400||BC5400||Bacitracin transport ATP-binding protein bcrA (NCBI ptt file)||237, 286|
|BC5441||BC5441||Autolysin sensor kinase (NCBI ptt file)||286, 414|
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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- 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.
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