Organism : Bacillus cereus ATCC14579 | Module List :
BC5250

Competence transcription factor (NCBI ptt file)

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC5250
(Mouseover regulator name to see its description)

BC5250 is regulated by 20 influences and regulates 18 modules.
Regulators for BC5250 (20)
Regulator Module Operator
BC0607 138 tf
BC1337 138 tf
BC2770 138 tf
BC2964 138 tf
BC3084 138 tf
BC4336 138 tf
BC4930 138 tf
BC5171 138 tf
BC5173 138 tf
BC5250 138 tf
BC5363 138 tf
BC0213 123 tf
BC0648 123 tf
BC1477 123 tf
BC3903 123 tf
BC3982 123 tf
BC4181 123 tf
BC4603 123 tf
BC5175 123 tf
BC5250 123 tf

Warning: BC5250 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
4162 2.10e-11 aaaGGaGG
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4163 1.50e+04 GaGAGCGCC
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4192 3.60e-01 aaAAGGgG
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4193 1.30e+04 GCATGAcGcc
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for BC5250

Warning: No Functional annotations were found!

Module neighborhood information for BC5250

BC5250 has total of 36 gene neighbors in modules 123, 138
Gene neighbors (36)
Gene Common Name Description Module membership
BC0214 BC0214 hypothetical Membrane Spanning Protein (NCBI ptt file) 123, 498
BC0240 BC0240 hypothetical protein (NCBI ptt file) 123, 405
BC0319 BC0319 hypothetical protein (NCBI ptt file) 123, 415
BC0675 BC0675 hypothetical protein (NCBI ptt file) 85, 138
BC1280 BC1280 hypothetical protein (NCBI ptt file) 128, 138
BC1361 BC1361 CAAX amino terminal protease family (NCBI ptt file) 123, 363
BC1508 BC1508 hypothetical protein (NCBI ptt file) 123, 155
BC1613 BC1613 Zn-dependent hydrolase (NCBI ptt file) 123, 498
BC1678 BC1678 JEMB (NCBI ptt file) 9, 123
BC1679 BC1679 Small acid soluble spore protein (NCBI ptt file) 24, 123
BC1830 BC1830 Copper resistance protein A (NCBI ptt file) 123, 217
BC2363 BC2363 Aspartate-semialdehyde dehydrogenase (NCBI ptt file) 123, 453
BC2417 BC2417 hypothetical protein (NCBI ptt file) 123, 217
BC2487 BC2487 3-hydroxybutyryl-CoA dehydratase (NCBI ptt file) 138, 464
BC2560 BC2560 hypothetical protein (NCBI ptt file) 138, 184
BC2561 BC2561 Phage protein (NCBI ptt file) 138, 184
BC2564 BC2564 Phage protein (NCBI ptt file) 138, 184
BC2582 BC2582 Terminase small subunit (NCBI ptt file) 138, 364
BC2643 BC2643 hydrolase (HAD superfamily) (NCBI ptt file) 123, 241
BC3458 BC3458 XpaF1 protein (NCBI ptt file) 56, 123
BC3650 BC3650 Imidazolonepropionase (NCBI ptt file) 138, 337
BC3651 BC3651 Urocanate hydratase (NCBI ptt file) 138, 337
BC3660 BC3660 hypothetical protein (NCBI ptt file) 123, 154
BC4006 BC4006 hypothetical Cytosolic Protein (NCBI ptt file) 123, 238
BC4339 BC4339 LSU ribosomal protein L33P (NCBI ptt file) 46, 123
BC4450 BC4450 Phage integrase family protein (NCBI ptt file) 123, 464
BC4779 BC4779 ABC transporter ATP-binding protein (NCBI ptt file) 123, 495
BC4788 BC4788 hypothetical protein (NCBI ptt file) 123, 487
BC5009 BC5009 Methyl-accepting chemotaxis protein (NCBI ptt file) 138, 434
BC5213 BC5213 Spermidine synthase (NCBI ptt file) 138, 250
BC5214 BC5214 S-adenosylmethionine decarboxylase proenzyme (NCBI ptt file) 138, 225
BC5247 BC5247 hypothetical protein (NCBI ptt file) 123, 186
BC5248 BC5248 hypothetical protein (NCBI ptt file) 138, 355
BC5250 BC5250 Competence transcription factor (NCBI ptt file) 123, 138
BC5284 BC5284 ABC transporter permease protein (NCBI ptt file) 123, 284
BC5285 BC5285 Bacitracin transport ATP-binding protein bcrA (NCBI ptt file) 123, 487
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.

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.

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;
  • 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
Comments for BC5250
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

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;
  • 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