Organism : Bacillus cereus ATCC14579 | Module List :
BC2760

Transcriptional regulator, TetR family (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2760
(Mouseover regulator name to see its description)

BC2760 is regulated by 20 influences and regulates 33 modules.
Regulators for BC2760 (20)
Regulator Module Operator
BC0566 309 tf
BC0742 309 tf
BC1059 309 tf
BC1363 309 tf
BC2469 309 tf
BC2517 309 tf
BC2760 309 tf
BC2964 309 tf
BC3588 309 tf
BC3904 309 tf
BC0230 314 tf
BC1080 314 tf
BC1329 314 tf
BC2410 314 tf
BC2760 314 tf
BC2801 314 tf
BC3588 314 tf
BC3904 314 tf
BC4930 314 tf
BC5205 314 tf

Warning: BC2760 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
4532 3.30e+01 CaCCTct
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4533 1.40e+03 AGGGgg
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4542 9.10e-02 AtAgaaaGaGg
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4543 6.50e+02 AGgAGA
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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 BC2760

BC2760 is enriched for 5 functions in 3 categories.
Module neighborhood information for BC2760

BC2760 has total of 28 gene neighbors in modules 309, 314
Gene neighbors (28)
Gene Common Name Description Module membership
BC0230 BC0230 Transcriptional regulator, LacI family (NCBI ptt file) 314, 398
BC0573 BC0573 Two component system histidine kinase (NCBI ptt file) 113, 314
BC0614 BC0614 Small, acid-soluble spore protein (NCBI ptt file) 61, 314
BC0623 BC0623 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 314, 398
BC0713 BC0713 ATP-binding protein (P-loop) (NCBI ptt file) 309, 314
BC1380 BC1380 hypothetical protein (NCBI ptt file) 114, 314
BC1899 BC1899 Phage protein (NCBI ptt file) 144, 309
BC1980 BC1980 AMP-(fatty)acid ligases (NCBI ptt file) 16, 309
BC2279 BC2279 hypothetical protein (NCBI ptt file) 309, 344
BC2760 BC2760 Transcriptional regulator, TetR family (NCBI ptt file) 309, 314
BC2768 BC2768 hypothetical Cytosolic Protein (NCBI ptt file) 314, 336
BC2769 BC2769 Acetyltransferase (NCBI ptt file) 314, 336
BC2788 BC2788 hypothetical protein (NCBI ptt file) 102, 314
BC2801 BC2801 DNA topology modulation protein (NCBI ptt file) 68, 314
BC2861 BC2861 Xaa-Pro dipeptidyl-peptidase (NCBI ptt file) 200, 309
BC3010 BC3010 Microbial collagenase (NCBI ptt file) 144, 309
BC3151 BC3151 Zwittermicin A resistance protein zmaR (NCBI ptt file) 309, 344
BC3173 BC3173 hypothetical protein (NCBI ptt file) 309, 349
BC3325 BC3325 hypothetical protein (NCBI ptt file) 136, 309
BC3383 BC3383 Bacillolysin (NCBI ptt file) 21, 309
BC3384 BC3384 Enhancin (NCBI ptt file) 21, 314
BC3686 BC3686 Phosphonates-binding protein (NCBI ptt file) 309, 344
BC3744 BC3744 hypothetical protein (NCBI ptt file) 95, 314
BC3832 BC3832 Nucleotide-binding SMF protein (NCBI ptt file) 314, 398
BC4659 BC4659 Acetyl-coenzyme A synthetase (NCBI ptt file) 314, 336
BC4711 BC4711 hypothetical protein (NCBI ptt file) 309, 378
BC4736 BC4736 VrrB (NCBI ptt file) 309, 508
BC4912 BC4912 hypothetical Membrane Spanning Protein (NCBI ptt file) 136, 309
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 BC2760
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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