Organism : Bacillus cereus ATCC14579 | Module List :
BC5222

Transcriptional regulators, LysR family (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
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 BC5222
(Mouseover regulator name to see its description)

BC5222 is regulated by 16 influences and regulates 16 modules.
Regulators for BC5222 (16)
Regulator Module Operator
BC0648 96 tf
BC2340 96 tf
BC4181 96 tf
BC4670 96 tf
BC5175 96 tf
BC5222 96 tf
BC0433 76 tf
BC0566 76 tf
BC1335 76 tf
BC1439 76 tf
BC1603 76 tf
BC4124 76 tf
BC4670 76 tf
BC4703 76 tf
BC4826 76 tf
BC5222 76 tf

Warning: BC5222 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
4072 1.50e+01 atCCtCcTc.TctaT.tatat
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4073 4.30e+03 CGCGGCG
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4108 2.30e+01 ttAAATa.gGaAgaGgAG
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4109 3.70e+03 GCGGCG
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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 BC5222

BC5222 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BC5222

BC5222 has total of 54 gene neighbors in modules 76, 96
Gene neighbors (54)
Gene Common Name Description Module membership
BC0166 BC0166 hypothetical Cytosolic Protein (NCBI ptt file) 76, 462
BC0167 BC0167 Spore-specific N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 76, 462
BC0260 BC0260 UV-endonuclease (UvsE/Uve1/UvdE Family) (NCBI ptt file) 76, 241
BC0398 BC0398 Benzoate transport protein (NCBI ptt file) 76, 218
BC0463 BC0463 hypothetical protein (NCBI ptt file) 96, 175
BC0582 BC0582 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 96, 218
BC0608 BC0608 Nucleoside permease nupC (NCBI ptt file) 96, 280
BC0704 BC0704 None 31, 76
BC0782 BC0782 Spore germination protein, gerB family (NCBI ptt file) 96, 245
BC0856 BC0856 Transcriptional regulator, MarR family (NCBI ptt file) 33, 76
BC0968 BC0968 putative hydrolase (NCBI ptt file) 96, 487
BC1170 BC1170 putative hydrolase (NCBI ptt file) 76, 407
BC1171 BC1171 Glucose epimerase (NCBI ptt file) 76, 288
BC1201 BC1201 None 76, 179
BC1204 BC1204 Glycosyltransferase (NCBI ptt file) 76, 397
BC1293 BC1293 Ribosomal large subunit pseudouridine synthase D (NCBI ptt file) 76, 400
BC1362 BC1362 hypothetical protein (NCBI ptt file) 76, 288
BC1434 BC1434 Na+/H+ antiporter NhaC (NCBI ptt file) 76, 222
BC1439 BC1439 Two-component response regulator yvqC (NCBI ptt file) 76, 347
BC1479 BC1479 hypothetical Cytosolic Protein (NCBI ptt file) 96, 461
BC1480 BC1480 Cell wall endopeptidase, family M23/M37 (NCBI ptt file) 25, 96
BC1503 BC1503 hypothetical protein (NCBI ptt file) 76, 89
BC1631 BC1631 hypothetical protein (NCBI ptt file) 50, 76
BC1754 BC1754 hypothetical protein (NCBI ptt file) 13, 96
BC1900 BC1900 None 76, 127
BC1970 BC1970 hypothetical protein (NCBI ptt file) 76, 159
BC2212 BC2212 hypothetical protein (NCBI ptt file) 76, 517
BC2219 BC2219 Phenazine biosynthesis protein phzF (NCBI ptt file) 96, 506
BC2236 BC2236 None 96, 281
BC2328 BC2328 Pyruvate oxidase (NCBI ptt file) 96, 179
BC2359 BC2359 CAAX amino terminal protease family (NCBI ptt file) 76, 293
BC2473 BC2473 Beta-lactamase (NCBI ptt file) 96, 293
BC2555 BC2555 hypothetical protein (NCBI ptt file) 76, 468
BC2719 BC2719 Bacitracin transport ATP-binding protein bcrA (NCBI ptt file) 76, 276
BC2741 BC2741 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 76, 217
BC2838 BC2838 hypothetical protein (NCBI ptt file) 76, 218
BC2952 BC2952 enterotoxin / cell-wall binding protein (NCBI ptt file) 96, 150
BC2973 BC2973 Nucleoside permease nupC (NCBI ptt file) 96, 197
BC3033 BC3033 Transcriptional regulator, AraC family (NCBI ptt file) 76, 468
BC3038 BC3038 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 96, 153
BC3477 BC3477 Quinone oxidoreductase (NCBI ptt file) 72, 76
BC3515 BC3515 hypothetical Glycosyltransferase (NCBI ptt file) 25, 96
BC3557 BC3557 Squalene--hopene cyclase (NCBI ptt file) 76, 397
BC3776 BC3776 Stage V sporulation protein S (NCBI ptt file) 76, 481
BC3801 BC3801 Dipicolinate synthase, A chain (NCBI ptt file) 76, 407
BC3991 BC3991 phosphoesterase (NCBI ptt file) 96, 393
BC4281 BC4281 IG hypothetical 17696 (NCBI ptt file) 76, 288
BC4291 BC4291 hypothetical protein (NCBI ptt file) 31, 96
BC4612 BC4612 hypothetical protein (NCBI ptt file) 76, 141
BC5081 BC5081 NADH oxidase (NOXASE) (NCBI ptt file) 83, 96
BC5099 BC5099 hypothetical protein (NCBI ptt file) 76, 104
BC5181 BC5181 hypothetical protein (NCBI ptt file) 76, 77
BC5222 BC5222 Transcriptional regulators, LysR family (NCBI ptt file) 76, 96
BC5410 BC5410 FMN-dependent NADH-azoreductase (NCBI ptt file) 76, 353
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 BC5222
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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