Organism : Bacillus cereus ATCC14579
| Module List :
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Regulation information for BC2851
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
BC0410 | 199 | tf |
BC1047 | 199 | tf |
BC2766 | 199 | tf |
BC3224 | 199 | tf |
BC3244 | 199 | tf |
BC3332 | 199 | tf |
BC3653 | 199 | tf |
BC4570 | 199 | tf |
BC4960 | 199 | tf |
BC1083 | 516 | tf |
BC1335 | 516 | tf |
BC2178 | 516 | tf |
BC2469 | 516 | tf |
BC2794 | 516 | tf |
BC2837 | 516 | tf |
BC3039 | 516 | tf |
BC3160 | 516 | tf |
BC3588 | 516 | tf |
BC4474 | 516 | tf |
BC4661 | 516 | tf |
BC5251 | 516 | tf |
BC5340 | 516 | tf |
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Motif information (de novo identified motifs for modules)
There are 4 motifs predicted.
Motif Id | e-value | Consensus | Motif Logo |
---|---|---|---|
4314 | 1.50e-08 | atGaAAGCGtt |
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4315 | 7.80e-05 | aAGGaGGagtt |
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4942 | 2.70e-06 | AtgaAAaCGctTaC |
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4943 | 9.00e-04 | aGgGGGgA |
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Module neighborhood information for BC2851
Gene | Common Name | Description | Module membership |
---|---|---|---|
BC0373 | BC0373 | Na+/H+ antiporter NnaC (NCBI ptt file) | 197, 199 |
BC0378 | BC0378 | 5-methylthioribose kinase (NCBI ptt file) | 387, 516 |
BC0379 | BC0379 | Methylthioribose salvage protein (NCBI ptt file) | 307, 516 |
BC0380 | BC0380 | L-fuculose phosphate aldolase (NCBI ptt file) | 387, 516 |
BC0560 | BC0560 | Two component system histidine kinase (NCBI ptt file) | 489, 516 |
BC0620 | BC0620 | Ubiquinone/menaquinone biosynthesis methyltransferase UBIE (NCBI ptt file) | 199, 248 |
BC0643 | BC0643 | Arginine permease (NCBI ptt file) | 199, 473 |
BC0808 | BC0808 | PTS system, diacetylchitobiose-specific IIB component (NCBI ptt file) | 387, 516 |
BC0809 | BC0809 | PTS system, diacetylchitobiose-specific IIC component (NCBI ptt file) | 199, 387 |
BC0900 | BC0900 | hypothetical protein (NCBI ptt file) | 199, 225 |
BC0979 | BC0979 | Dihydroxyacetone kinase (NCBI ptt file) | 72, 199 |
BC0981 | BC0981 | Dihydroxyacetone kinase (NCBI ptt file) | 199, 220 |
BC1034 | BC1034 | Glycerol uptake facilitator protein (NCBI ptt file) | 199, 516 |
BC1047 | BC1047 | Protease production regulatory protein hpr (NCBI ptt file) | 30, 199 |
BC1083 | BC1083 | Transcriptional regulator, LacI family (NCBI ptt file) | 387, 516 |
BC1185 | BC1185 | Oligopeptide-binding protein oppA (NCBI ptt file) | 199, 387 |
BC1328 | BC1328 | Saccharopine dehydrogenase [NADP+, L-lysine forming] (NCBI ptt file) | 469, 516 |
BC1333 | BC1333 | CBS domain containing protein (NCBI ptt file) | 100, 199 |
BC1389 | BC1389 | Proton/sodium-glutamate symport protein (NCBI ptt file) | 199, 264 |
BC1596 | BC1596 | Transporter, Drug/Metabolite Exporter family (NCBI ptt file) | 199, 381 |
BC1625 | BC1625 | Chemotaxis motA protein (NCBI ptt file) | 30, 199 |
BC1626 | BC1626 | Chemotaxis motB protein (NCBI ptt file) | 30, 199 |
BC1823 | BC1823 | Cytidine deaminase (NCBI ptt file) | 199, 250 |
BC2238 | BC2238 | hypothetical protein (NCBI ptt file) | 387, 516 |
BC2329 | BC2329 | Zinc uptake transporter (NCBI ptt file) | 199, 250 |
BC2617 | BC2617 | Cysteine dioxygenase (NCBI ptt file) | 199, 327 |
BC2766 | BC2766 | Sigma-54-dependent transcriptional activator (NCBI ptt file) | 199, 415 |
BC2851 | BC2851 | hypothetical protein (NCBI ptt file) | 199, 516 |
BC2962 | BC2962 | Sugar transport system permease protein (NCBI ptt file) | 199, 334 |
BC2965 | BC2965 | Sugar (pentulose and hexulose) kinases (NCBI ptt file) | 186, 199 |
BC3113 | BC3113 | Two-component response regulator ycbB (NCBI ptt file) | 30, 199 |
BC3180 | BC3180 | Low temperature requirement protein A (NCBI ptt file) | 199, 410 |
BC3185 | BC3185 | hypothetical protein (NCBI ptt file) | 197, 199 |
BC3189 | BC3189 | Serine transporter (NCBI ptt file) | 199, 213 |
BC3197 | BC3197 | Tetracycline resistance determinant tetV (NCBI ptt file) | 324, 516 |
BC3224 | BC3224 | Transcriptional regulator, ArsR family (NCBI ptt file) | 199, 264 |
BC3225 | BC3225 | Macrolide-efflux protein (NCBI ptt file) | 199, 401 |
BC3452 | BC3452 | hypothetical protein (NCBI ptt file) | 199, 225 |
BC3495 | BC3495 | Glycerophosphoryl diester phosphodiesterase (NCBI ptt file) | 199, 213 |
BC3531 | BC3531 | Acetyltransferase (NCBI ptt file) | 23, 516 |
BC3631 | BC3631 | Medium-chain-fatty-acid--CoA ligase (NCBI ptt file) | 199, 213 |
BC3718 | BC3718 | PTS system, fructose-specific IIABC component (NCBI ptt file) | 387, 516 |
BC4241 | BC4241 | hypothetical protein (NCBI ptt file) | 7, 199 |
BC4591 | BC4591 | MaoC family protein (NCBI ptt file) | 199, 334 |
BC4661 | BC4661 | Acetoin utilization acuB protein (NCBI ptt file) | 30, 516 |
BC4662 | BC4662 | Acetoin utilization acuC protein (NCBI ptt file) | 424, 516 |
BC4780 | BC4780 | ABC transporter permease protein (NCBI ptt file) | 141, 199 |
BC4784 | BC4784 | hypothetical protein (NCBI ptt file) | 199, 504 |
BC4841 | BC4841 | 2-keto-3-deoxygluconate permease (NCBI ptt file) | 384, 516 |
BC4843 | BC4843 | 2-dehydro-3-deoxygluconokinase (NCBI ptt file) | 387, 516 |
BC4844 | BC4844 | 4-Hydroxy-2-oxoglutarate aldolase (NCBI ptt file) | 387, 516 |
BC4845 | BC4845 | L-seryl-tRNA(Sec) selenium transferase (NCBI ptt file) | 387, 516 |
BC4846 | BC4846 | Dihydroorotase (NCBI ptt file) | 387, 516 |
BC5209 | BC5209 | 6-phospho-beta-glucosidase (NCBI ptt file) | 54, 516 |
BC5211 | BC5211 | PTS system, lichenan oligosaccharide-specific IIC component (NCBI ptt file) | 387, 516 |
BC5217 | BC5217 | PTS system, lichenan oligosaccharide-specific IIB component (NCBI ptt file) | 199, 339 |
BC5228 | BC5228 | L-lactate permease (NCBI ptt file) | 387, 516 |
BC5320 | BC5320 | PTS system, glucose-specific IIA component (NCBI ptt file) | 74, 199 |
BC5438 | BC5438 | Murein hydrolase export regulator (NCBI ptt file) | 199, 434 |
BC5439 | BC5439 | Murein hydrolase exporter (NCBI ptt file) | 197, 199 |
Gene Page Help
Network Tab
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.
Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.
Regulation Tab
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".
For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.
Motifs Tab
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.
Functions Tab
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.
Help Tab
This help page. More general help can be accessed by clicking help menu in the main navigation bar.
CircVis
Our 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;![](/static/images/help_images/circvis-help.png)
- 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
- 6. Visualisation legend
Social Tab
Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.
Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.
In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.