Organism : Bacillus cereus ATCC14579 | Module List :
BC4433

Two-component response regulator yvcP (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4433
(Mouseover regulator name to see its description)

BC4433 is regulated by 22 influences and regulates 11 modules.
Regulators for BC4433 (22)
Regulator Module Operator
BC1329 229 tf
BC1603 229 tf
BC2401 229 tf
BC2469 229 tf
BC2517 229 tf
BC2549 229 tf
BC2631 229 tf
BC2988 229 tf
BC4029 229 tf
BC4433 229 tf
BC5176 229 tf
BC0648 307 tf
BC1731 307 tf
BC2178 307 tf
BC2410 307 tf
BC2936 307 tf
BC3084 307 tf
BC3702 307 tf
BC3922 307 tf
BC4433 307 tf
BC4672 307 tf
BC5402 307 tf

Warning: BC4433 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
4374 5.50e-03 ggGgaGAg
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4375 7.60e+01 ACAca.tGggcT.aTTcgG
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4528 3.70e+03 GGTGTGaAcGGG
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4529 2.70e+03 gAAAAgaGGaaaGGt
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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 BC4433

BC4433 is enriched for 6 functions in 3 categories.
Module neighborhood information for BC4433

BC4433 has total of 34 gene neighbors in modules 229, 307
Gene neighbors (34)
Gene Common Name Description Module membership
BC0379 BC0379 Methylthioribose salvage protein (NCBI ptt file) 307, 516
BC0673 BC0673 Flavin-dependent dehydrogenase (NCBI ptt file) 111, 229
BC0866 BC0866 Glutamate racemase (NCBI ptt file) 229, 244
BC0949 BC0949 hypothetical Membrane Spanning Protein (NCBI ptt file) 108, 307
BC1209 BC1209 O-antigen biosynthesis protein rfbC (NCBI ptt file) 229, 244
BC1681 BC1681 Tetracycline resistance determinant tetV (NCBI ptt file) 229, 378
BC1770 BC1770 hypothetical Membrane Associated Protein (NCBI ptt file) 114, 307
BC2161 BC2161 hypothetical protein (NCBI ptt file) 307, 437
BC2468 BC2468 Cell elongation specific D,D-transpeptidase (NCBI ptt file) 307, 424
BC2483 BC2483 None 229, 362
BC2638 BC2638 Spore germination protein LC (NCBI ptt file) 57, 229
BC2916 BC2916 hypothetical Membrane Spanning Protein (NCBI ptt file) 307, 525
BC2928 BC2928 hydrolase (NCBI ptt file) 253, 307
BC3007 BC3007 Acetylornithine aminotransferase (NCBI ptt file) 21, 229
BC3067 BC3067 Regulator of kinase autophosphorylation inhibitor (NCBI ptt file) 229, 392
BC3196 BC3196 hypothetical ATP-binding protein (NCBI ptt file) 229, 324
BC3440 BC3440 Beta-lactamase, type II (NCBI ptt file) 307, 437
BC3684 BC3684 Phosphonates transport system permease protein phnE (NCBI ptt file) 21, 229
BC3692 BC3692 hypothetical protein (NCBI ptt file) 202, 229
BC3994 BC3994 Exopolyphosphatase (NCBI ptt file) 112, 307
BC4188 BC4188 Stage III sporulation protein AF (NCBI ptt file) 136, 307
BC4430 BC4430 ABC transporter permease protein (NCBI ptt file) 229, 307
BC4431 BC4431 ABC transporter ATP-binding protein (NCBI ptt file) 229, 307
BC4433 BC4433 Two-component response regulator yvcP (NCBI ptt file) 229, 307
BC4463 BC4463 Stage II sporulation protein B (NCBI ptt file) 307, 437
BC4924 BC4924 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 23, 307
BC5015 BC5015 hypothetical exported repetitive protein (NCBI ptt file) 307, 362
BC5110 BC5110 hypothetical ATP-binding protein (NCBI ptt file) 229, 276
BC5292 BC5292 NADH-quinone oxidoreductase chain M (NCBI ptt file) 229, 490
BC5297 BC5297 NADH-quinone oxidoreductase chain H (NCBI ptt file) 229, 490
BC5298 BC5298 NADH-quinone oxidoreductase chain D (NCBI ptt file) 178, 229
BC5341 BC5341 Acyl-CoA dehydrogenase, short-chain specific (NCBI ptt file) 229, 469
BC5342 BC5342 Acyl-CoA dehydrogenase, short-chain specific (NCBI ptt file) 229, 469
BC5343 BC5343 3-hydroxybutyryl-CoA dehydrogenase (NCBI ptt file) 229, 469
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 BC4433
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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