Organism : Bacillus cereus ATCC14579 | Module List :
BC2442

Transcriptional regulator, LuxR family (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2442
(Mouseover regulator name to see its description)

BC2442 is regulated by 31 influences and regulates 7 modules.
Regulators for BC2442 (31)
Regulator Module Operator
BC0405 187 tf
BC1131 187 tf
BC3062 187 tf
BC3163 187 tf
BC3758 187 tf
BC4076 187 tf
BC4240 187 tf
BC4256 187 tf
BC4425 187 tf
BC4652 187 tf
BC4708 187 tf
BC4902 187 tf
BC5010 187 tf
BC5409 187 tf
BC5481 187 tf
BC0047 184 tf
BC0230 184 tf
BC0680 184 tf
BC0993 184 tf
BC1337 184 tf
BC1695 184 tf
BC1699 184 tf
BC1987 184 tf
BC2109 184 tf
BC3072 184 tf
BC3105 184 tf
BC3175 184 tf
BC3693 184 tf
BC4081 184 tf
BC5173 184 tf
BC5368 184 tf

Warning: BC2442 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
4284 4.60e+03 GGcGGTGc
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4285 1.30e+04 ccGCACC
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4290 7.40e-07 aaaagGA.gAg
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4291 2.40e+04 CGctCTTGCC
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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 BC2442

BC2442 is enriched for 4 functions in 2 categories.
Enrichment Table (4)
Function System
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for BC2442

BC2442 has total of 46 gene neighbors in modules 184, 187
Gene neighbors (46)
Gene Common Name Description Module membership
BC0052 BC0052 Translation initiation inhibitor (NCBI ptt file) 187, 401
BC0291 BC0291 AT-rich DNA-binding protein (NCBI ptt file) 119, 187
BC0405 BC0405 Arginine repressor, argR (NCBI ptt file) 100, 187
BC0680 BC0680 Transcriptional regulator, PBSX family (NCBI ptt file) 184, 248
BC1018 BC1018 hypothetical protein (NCBI ptt file) 184, 496
BC1117 BC1117 hypothetical protein (NCBI ptt file) 184, 496
BC1131 BC1131 Cold shock protein (NCBI ptt file) 187, 477
BC1268 BC1268 hypothetical protein (NCBI ptt file) 17, 184
BC1463 BC1463 Purine nucleoside phosphorylase (NCBI ptt file) 28, 187
BC1515 BC1515 Nucleoside diphosphate kinase (NCBI ptt file) 187, 227
BC1702 BC1702 hypothetical protein (NCBI ptt file) 184, 497
BC1820 BC1820 Deoxyribose-phosphate aldolase (NCBI ptt file) 187, 401
BC1961 BC1961 hypothetical Membrane Spanning Protein (NCBI ptt file) 184, 497
BC2215 BC2215 Mechanosensitive ion channel (NCBI ptt file) 28, 187
BC2419 BC2419 Phage protein (NCBI ptt file) 184, 464
BC2442 BC2442 Transcriptional regulator, LuxR family (NCBI ptt file) 184, 187
BC2546 BC2546 hypothetical protein (NCBI ptt file) 187, 190
BC2559 BC2559 Phage protein (NCBI ptt file) 184, 504
BC2560 BC2560 hypothetical protein (NCBI ptt file) 138, 184
BC2561 BC2561 Phage protein (NCBI ptt file) 138, 184
BC2562 BC2562 Phage protein (NCBI ptt file) 184, 464
BC2563 BC2563 Phage replication protein (NCBI ptt file) 184, 464
BC2564 BC2564 Phage protein (NCBI ptt file) 138, 184
BC2565 BC2565 Phage protein (NCBI ptt file) 184, 464
BC2567 BC2567 Phage protein (NCBI ptt file) 184, 463
BC2826 BC2826 Manganese-dependent inorganic pyrophosphatase (NCBI ptt file) 187, 227
BC3352 BC3352 hypothetical protein (NCBI ptt file) 184, 497
BC3661 BC3661 CcdC protein (NCBI ptt file) 166, 187
BC4046 BC4046 hypothetical protein (NCBI ptt file) 28, 187
BC4093 BC4093 Ribosomal-protein-serine acetyltransferase (NCBI ptt file) 187, 401
BC4120 BC4120 hypothetical protein (NCBI ptt file) 141, 184
BC4197 BC4197 Protein Translation Elongation Factor P (EF-P) (NCBI ptt file) 187, 350
BC4252 BC4252 hypothetical protein (NCBI ptt file) 184, 205
BC4425 BC4425 hypothetical transcriptional regulator (NCBI ptt file) 28, 187
BC4529 BC4529 None 184, 504
BC4625 BC4625 Universal stress protein family (NCBI ptt file) 129, 187
BC4760 BC4760 Acetyltransferase (NCBI ptt file) 187, 296
BC4860 BC4860 hypothetical protein (NCBI ptt file) 187, 381
BC4978 BC4978 hypothetical protein (NCBI ptt file) 184, 469
BC5173 BC5173 Transcriptional regulator, PBSX family (NCBI ptt file) 184, 504
BC5190 BC5190 Probable Sigma (54) modulation protein / SSU ribosomal protein S30P (NCBI ptt file) 129, 187
BC5323 BC5323 hypothetical protein (NCBI ptt file) 126, 187
BC5374 BC5374 Glycerophosphoryl diester phosphodiesterase (NCBI ptt file) 129, 187
BC5378 BC5378 4-oxalocrotonate tautomerase (NCBI ptt file) 187, 401
BC5409 BC5409 Catabolite gene activator (NCBI ptt file) 187, 380
BC5444 BC5444 Nitric oxide synthase (NCBI ptt file) 187, 290
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 BC2442
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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