Organism : Bacillus cereus ATCC14579 | Module List :
BC1337

Transcriptional regulator, MarR family (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
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 BC1337
(Mouseover regulator name to see its description)

BC1337 is regulated by 32 influences and regulates 23 modules.
Regulators for BC1337 (32)
Regulator Module Operator
BC0057 479 tf
BC0122 479 tf
BC0123 479 tf
BC1080 479 tf
BC1337 479 tf
BC1363 479 tf
BC2218 479 tf
BC2362 479 tf
BC3653 479 tf
BC3814 479 tf
BC3922 479 tf
BC3982 479 tf
BC4010 479 tf
BC4057 479 tf
BC5265 479 tf
BC0116 432 tf
BC0122 432 tf
BC0518 432 tf
BC0598 432 tf
BC0607 432 tf
BC0954 432 tf
BC1337 432 tf
BC2362 432 tf
BC2672 432 tf
BC2770 432 tf
BC3062 432 tf
BC3400 432 tf
BC3826 432 tf
BC3982 432 tf
BC4010 432 tf
BC4057 432 tf
BC4499 432 tf

Warning: BC1337 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
4774 3.80e+00 Aa.aGaGG.at
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4775 8.50e+03 CGGcCcc
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4868 3.80e-01 aaaGgAGg
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4869 6.30e+03 GGGAGGG
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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 BC1337

BC1337 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
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 BC1337

BC1337 has total of 35 gene neighbors in modules 432, 479
Gene neighbors (35)
Gene Common Name Description Module membership
BC0303 BC0303 Alpha/beta hydrolase (NCBI ptt file) 10, 432
BC0365 BC0365 Nitrogen regulation protein NIFR3 (NCBI ptt file) 399, 432
BC0607 BC0607 Transcriptional regulator, LytR family (NCBI ptt file) 159, 432
BC0656 BC0656 Glycerol-3-phosphate transporter (NCBI ptt file) 221, 479
BC0703 BC0703 Sodium/proline symporter (NCBI ptt file) 431, 479
BC0902 BC0902 S-layer protein / N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 425, 432
BC1217 BC1217 hypothetical protein (NCBI ptt file) 256, 479
BC1247 BC1247 hypothetical protein (NCBI ptt file) 92, 432
BC1337 BC1337 Transcriptional regulator, MarR family (NCBI ptt file) 432, 479
BC1430 BC1430 Sodium-dependent tryptophan transporter (NCBI ptt file) 412, 479
BC1473 BC1473 ResA protein (NCBI ptt file) 27, 479
BC2185 BC2185 Protein ecsB (NCBI ptt file) 341, 432
BC2391 BC2391 hypothetical protein (NCBI ptt file) 388, 432
BC2554 BC2554 hypothetical protein (NCBI ptt file) 257, 432
BC2704 BC2704 Serine protease (NCBI ptt file) 432, 460
BC2907 BC2907 hypothetical Membrane Spanning Protein (NCBI ptt file) 27, 479
BC3708 BC3708 GTP-binding protein hflX (NCBI ptt file) 176, 432
BC3804 BC3804 Chitooligosaccharide deacetylase (NCBI ptt file) 476, 479
BC3816 BC3816 DNA polymerase III alpha subunit (NCBI ptt file) 182, 479
BC3868 BC3868 DNA-directed RNA polymerase omega chain (NCBI ptt file) 275, 479
BC3916 BC3916 Division specific D,D-transpeptidase / Cell division protein ftsI (NCBI ptt file) 283, 479
BC3940 BC3940 CtaG protein (NCBI ptt file) 385, 479
BC3969 BC3969 hypothetical protein (NCBI ptt file) 394, 479
BC4010 BC4010 Transcriptional regulator, LacI family (NCBI ptt file) 139, 432
BC4499 BC4499 Transcriptional regulator, TetR family (NCBI ptt file) 75, 432
BC4552 BC4552 None 145, 479
BC4837 BC4837 ABC transporter permease protein (NCBI ptt file) 312, 479
BC5026 BC5026 hypothetical protein (NCBI ptt file) 67, 432
BC5027 BC5027 Protein erfK/srfK precursor (NCBI ptt file) 67, 432
BC5063 BC5063 UDP-N-acetylenolpyruvoylglucosamine reductase (NCBI ptt file) 37, 432
BC5289 BC5289 hypothetical protein (NCBI ptt file) 319, 432
BC5290 BC5290 hypothetical protein (NCBI ptt file) 319, 432
BC5371 BC5371 Spermidine synthase (NCBI ptt file) 399, 479
BC5407 BC5407 Chloride channel protein (NCBI ptt file) 67, 432
BC5419 BC5419 N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase (NCBI ptt file) 75, 479
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 BC1337
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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