Organism : Bacillus cereus ATCC14579 | Module List :
BC3497

Transcriptional regulator, ArsR family (NCBI ptt file)

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

Cytoscape Web
Regulation information for BC3497
(Mouseover regulator name to see its description)

BC3497 is regulated by 27 influences and regulates 11 modules.
Regulators for BC3497 (27)
Regulator Module Operator
BC0123 146 tf
BC0882 146 tf
BC0950 146 tf
BC0953 146 tf
BC0993 146 tf
BC1915 146 tf
BC2298 146 tf
BC2442 146 tf
BC2558 146 tf
BC2738 146 tf
BC3069 146 tf
BC3244 146 tf
BC3400 146 tf
BC3493 146 tf
BC3497 146 tf
BC3589 146 tf
BC4072 146 tf
BC4474 146 tf
BC0649 63 tf
BC0758 63 tf
BC0950 63 tf
BC2444 63 tf
BC2794 63 tf
BC3160 63 tf
BC3244 63 tf
BC3493 63 tf
BC3497 63 tf

Warning: BC3497 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
4046 1.20e+04 GaGgaggA
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4047 1.90e+04 CAGCGCCc
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4208 4.00e+03 gGGAGAg
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4209 2.70e+04 CCCCcTTtTgT
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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 BC3497

BC3497 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BC3497

BC3497 has total of 60 gene neighbors in modules 63, 146
Gene neighbors (60)
Gene Common Name Description Module membership
BC0013 BC0013 Inosine-5'-monophosphate dehydrogenase (NCBI ptt file) 63, 137
BC0456 BC0456 Signal peptidase I (NCBI ptt file) 146, 163
BC0565 BC0565 Ankyrin (NCBI ptt file) 63, 265
BC0572 BC0572 Two-component response regulator (NCBI ptt file) 63, 286
BC0649 BC0649 Transcriptional regulator, DeoR family (NCBI ptt file) 63, 246
BC0766 BC0766 Methylthioribose transport system permease protein (NCBI ptt file) 20, 63
BC0890 BC0890 Long-chain-fatty-acid--CoA ligase (NCBI ptt file) 146, 279
BC0950 BC0950 Transcriptional regulator, copG family (NCBI ptt file) 85, 146
BC1040 BC1040 hypothetical protein (NCBI ptt file) 9, 146
BC1097 BC1097 hypothetical protein (NCBI ptt file) 63, 286
BC1229 BC1229 hypothetical protein (NCBI ptt file) 26, 146
BC1258 BC1258 hypothetical protein (NCBI ptt file) 63, 427
BC1601 BC1601 hypothetical protein (NCBI ptt file) 7, 146
BC1774 BC1774 Peptide methionine sulfoxide reductase (NCBI ptt file) 63, 260
BC1840 BC1840 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 63, 141
BC1912 BC1912 Phage protein (NCBI ptt file) 63, 137
BC1913 BC1913 Phage protein (NCBI ptt file) 63, 137
BC1914 BC1914 Phage protein (NCBI ptt file) 63, 146
BC2040 BC2040 putative spore coat protein (NCBI ptt file) 146, 225
BC2054 BC2054 Glutamyl-tRNA(Gln) amidotransferase subunit A (NCBI ptt file) 146, 427
BC2298 BC2298 Transcriptional repressor (NCBI ptt file) 146, 225
BC2315 BC2315 DinB protein (NCBI ptt file) 63, 163
BC2428 BC2428 hypothetical protein (NCBI ptt file) 63, 225
BC2494 BC2494 Aminoglycoside N6'-acetyltransferase (NCBI ptt file) 146, 163
BC2539 BC2539 Two-component sensor kinase yxdK (NCBI ptt file) 6, 63
BC2603 BC2603 hypothetical protein (NCBI ptt file) 63, 299
BC2740 BC2740 Protein translocase subunit SecY (NCBI ptt file) 6, 63
BC2749 BC2749 Acetyltransferase (NCBI ptt file) 20, 146
BC2776 BC2776 Dihydrolipoamide dehydrogenase (NCBI ptt file) 146, 427
BC2794 BC2794 RNA polymerase ECF-type sigma factor (NCBI ptt file) 63, 105
BC2829 BC2829 putative Metal-dependent phosphohydrolase (NCBI ptt file) 146, 299
BC2981 BC2981 hypothetical protein (NCBI ptt file) 146, 334
BC3148 BC3148 Streptothricin acetyltransferase (NCBI ptt file) 63, 364
BC3316 BC3316 Regulatory protein (NCBI ptt file) 72, 146
BC3339 BC3339 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 52, 146
BC3426 BC3426 RNA polymerase sigma-I factor (NCBI ptt file) 146, 163
BC3497 BC3497 Transcriptional regulator, ArsR family (NCBI ptt file) 63, 146
BC3498 BC3498 Quinone oxidoreductase (NCBI ptt file) 63, 465
BC3555 BC3555 Aldehyde dehydrogenase (NCBI ptt file) 146, 294
BC3584 BC3584 Oligopeptide-binding protein oppA (NCBI ptt file) 55, 63
BC3645 BC3645 CcdC protein (NCBI ptt file) 63, 285
BC3724 BC3724 GABA-specific permease (NCBI ptt file) 146, 163
BC3747 BC3747 Sensory box/GGDEF family protein (NCBI ptt file) 63, 286
BC3876 BC3876 hypothetical protein (NCBI ptt file) 63, 228
BC4014 BC4014 Neopullulanase (NCBI ptt file) 63, 299
BC4131 BC4131 hypothetical protein (NCBI ptt file) 63, 299
BC4146 BC4146 Protein erfK/srfK precursor (NCBI ptt file) 20, 63
BC4147 BC4147 Integral membrane protein (NCBI ptt file) 63, 482
BC4169 BC4169 hypothetical protein (NCBI ptt file) 146, 163
BC4305 BC4305 hypothetical Cytosolic Protein (NCBI ptt file) 63, 72
BC4464 BC4464 Folylpolyglutamate synthase (NCBI ptt file) 48, 63
BC4514 BC4514 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 63, 288
BC4666 BC4666 Two component system histidine kinase (NCBI ptt file) 63, 308
BC4712 BC4712 hypothetical Cytosolic Protein (NCBI ptt file) 146, 227
BC4839 BC4839 ABC transporter ATP-binding protein (NCBI ptt file) 63, 453
BC4946 BC4946 hypothetical protein (NCBI ptt file) 63, 330
BC4947 BC4947 hypothetical protein (NCBI ptt file) 20, 63
BC5049 BC5049 hypothetical Membrane Spanning Protein (NCBI ptt file) 146, 209
BC5068 BC5068 CrcB family protein (NCBI ptt file) 63, 285
BC5448 BC5448 UDP-glucose 4-epimerase (NCBI ptt file) 146, 263
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 BC3497
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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