Organism : Bacillus cereus ATCC14579 | Module List :
Transcriptional regulator, XRE family (NCBI ptt file)
Functional Annotations (1)
|sequence-specific DNA binding||go/ molecular_function|
Regulation information for BC1680(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 BC1680
|sequence-specific DNA binding||go/ molecular_function|
Module neighborhood information for BC1680
|Gene||Common Name||Description||Module membership|
|BC0290||BC0290||ABC transporter ATP-binding protein uup (NCBI ptt file)||1, 475|
|BC0335||BC0335||hypothetical protein (NCBI ptt file)||166, 337|
|BC0336||BC0336||Somatin-like protein (NCBI ptt file)||103, 337|
|BC0626||BC0626||Cardiolipin synthetase (NCBI ptt file)||1, 224|
|BC1150||BC1150||IG hypothetical 15940 (NCBI ptt file)||126, 337|
|BC1432||BC1432||Proton/sodium-glutamate symport protein (NCBI ptt file)||133, 337|
|BC1680||BC1680||Transcriptional regulator, XRE family (NCBI ptt file)||1, 337|
|BC1755||BC1755||UDP-galactose-lipid carrier transferase (NCBI ptt file)||26, 337|
|BC2009||BC2009||hypothetical protein (NCBI ptt file)||1, 438|
|BC2665||BC2665||Teicoplanin resistance protein vanZ (NCBI ptt file)||97, 337|
|BC2717||BC2717||hypothetical protein (NCBI ptt file)||100, 337|
|BC2718||BC2718||hypothetical protein (NCBI ptt file)||100, 337|
|BC2817||BC2817||hypothetical protein (NCBI ptt file)||337, 354|
|BC2841||BC2841||hypothetical protein (NCBI ptt file)||296, 337|
|BC2842||BC2842||hypothetical protein (NCBI ptt file)||296, 337|
|BC3061||BC3061||Penicillin-binding protein (NCBI ptt file)||24, 337|
|BC3389||BC3389||Transcriptional regulator, MarR family (NCBI ptt file)||1, 74|
|BC3437||BC3437||hypothetical Cytosolic Protein (NCBI ptt file)||313, 337|
|BC3508||BC3508||hypothetical protein (NCBI ptt file)||128, 337|
|BC3599||BC3599||Succinyl-CoA synthetase, alpha subunit-related enzymes (NCBI ptt file)||1, 51|
|BC3616||BC3616||Aconitate hydratase (NCBI ptt file)||1, 475|
|BC3648||BC3648||CarD-like transcriptional regulator (NCBI ptt file)||98, 337|
|BC3650||BC3650||Imidazolonepropionase (NCBI ptt file)||138, 337|
|BC3651||BC3651||Urocanate hydratase (NCBI ptt file)||138, 337|
|BC3652||BC3652||Histidine ammonia-lyase (NCBI ptt file)||186, 337|
|BC3740||BC3740||ADA regulatory protein (NCBI ptt file)||224, 337|
|BC3741||BC3741||O6-methylguanine-DNA methyltransferase (NCBI ptt file)||224, 337|
|BC3742||BC3742||DNA-3-methyladenine glycosylase II (NCBI ptt file)||327, 337|
|BC4001||BC4001||Transcriptional repressor PadR (NCBI ptt file)||1, 233|
|BC4106||BC4106||Alpha/beta hydrolase (NCBI ptt file)||1, 438|
|BC4124||BC4124||Transcriptional regulator, MarR family (NCBI ptt file)||166, 337|
|BC4152||BC4152||hypothetical protein (NCBI ptt file)||166, 337|
|BC4153||BC4153||Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file)||88, 337|
|BC4245||BC4245||hypothetical protein (NCBI ptt file)||28, 337|
|BC4259||BC4259||hypothetical Membrane Spanning Protein (NCBI ptt file)||1, 166|
|BC4454||BC4454||hypothetical protein (NCBI ptt file)||313, 337|
|BC4631||BC4631||hypothetical protein (NCBI ptt file)||1, 438|
|BC4714||BC4714||CarD-like transcriptional regulator (NCBI ptt file)||1, 119|
|BC4790||BC4790||hypothetical Cytosolic Protein (NCBI ptt file)||1, 438|
|BC4935||BC4935||HESB protein (NCBI ptt file)||1, 119|
|BC4952||BC4952||NifU protein (NCBI ptt file)||1, 216|
|BC4953||BC4953||hypothetical protein (NCBI ptt file)||285, 337|
|BC4973||BC4973||Lipoic acid synthetase (NCBI ptt file)||1, 118|
|BC5045||BC5045||hypothetical protein (NCBI ptt file)||1, 284|
|BC5047||BC5047||IG hypothetical 16995 (NCBI ptt file)||1, 74|
|BC5048||BC5048||Ferritin (NCBI ptt file)||1, 337|
|BC5128||BC5128||SsrA-binding protein (NCBI ptt file)||1, 505|
|BC5142||BC5142||Glutaredoxin (NCBI ptt file)||1, 28|
|BC5143||BC5143||RNA polymerase sigma-54 factor rpoN (NCBI ptt file)||1, 28|
|BC5170||BC5170||Integral membrane protein (NCBI ptt file)||7, 337|
|BC5171||BC5171||Transcriptional regulator, MerR family (NCBI ptt file)||7, 337|
|BC5172||BC5172||hypothetical protein (NCBI ptt file)||337, 475|
|BC5197||BC5197||Transcriptional regulator, MarR family (NCBI ptt file)||1, 119|
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.
You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".
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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)
- 4. Interactions between source and target genes for a particular module
- 5. Module(s) that source gene and target genes belong to
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