Organism : Bacillus cereus ATCC14579 | Module List :
BC5205

Transcriptional regulatory protein levR (NCBI ptt file)

CircVis
Functional Annotations (10)
Function System
Transcriptional antiterminator cog/ cog
nucleic acid binding go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
ATP-dependent helicase activity go/ molecular_function
transcription factor binding go/ molecular_function
phosphoenolpyruvate-dependent sugar phosphotransferase system go/ biological_process
integral to membrane go/ cellular_component
nucleoside-triphosphatase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC5205
(Mouseover regulator name to see its description)

BC5205 is regulated by 28 influences and regulates 35 modules.
Regulators for BC5205 (28)
Regulator Module Operator
BC0116 142 tf
BC3706 142 tf
BC3814 142 tf
BC3891 142 tf
BC3922 142 tf
BC4170 142 tf
BC4206 142 tf
BC4212 142 tf
BC4499 142 tf
BC5205 142 tf
BC5265 142 tf
BC5332 142 tf
BC5339 142 tf
BC0435 304 tf
BC0742 304 tf
BC0801 304 tf
BC1077 304 tf
BC1363 304 tf
BC1818 304 tf
BC2410 304 tf
BC2517 304 tf
BC3592 304 tf
BC4057 304 tf
BC4672 304 tf
BC4826 304 tf
BC4842 304 tf
BC5205 304 tf
BC5339 304 tf

Warning: BC5205 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
4200 2.60e+02 CCTCCc
Loader icon
4201 2.20e+03 AAaAAgAaAta.gc
Loader icon
4522 2.60e-04 aATAgAaggaG
Loader icon
4523 6.40e+03 CGCGCC
Loader icon
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 BC5205

BC5205 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Transcriptional antiterminator cog/ cog
nucleic acid binding go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
ATP-dependent helicase activity go/ molecular_function
transcription factor binding go/ molecular_function
phosphoenolpyruvate-dependent sugar phosphotransferase system go/ biological_process
integral to membrane go/ cellular_component
nucleoside-triphosphatase activity go/ molecular_function
Module neighborhood information for BC5205

BC5205 has total of 34 gene neighbors in modules 142, 304
Gene neighbors (34)
Gene Common Name Description Module membership
BC0232 BC0232 hypothetical Membrane Spanning Protein (NCBI ptt file) 142, 300
BC0459 BC0459 Bacterial/Archaeal Transporter family protein (NCBI ptt file) 304, 443
BC0588 BC0588 FdhD protein (fdsC) (NCBI ptt file) 15, 304
BC1077 BC1077 Transcriptional regulator, TetR family (NCBI ptt file) 304, 440
BC1548 BC1548 Endonuclease III (NCBI ptt file) 142, 269
BC1549 BC1549 hypothetical protein (NCBI ptt file) 142, 269
BC1620 BC1620 hypothetical membrane protein (NCBI ptt file) 221, 304
BC2008 BC2008 hypothetical protein (NCBI ptt file) 117, 304
BC2035 BC2035 Magnesium and cobalt transport protein corA (NCBI ptt file) 170, 304
BC2280 BC2280 hypothetical Membrane Spanning Protein (NCBI ptt file) 6, 304
BC2675 BC2675 Acetyltransferase (NCBI ptt file) 20, 304
BC2987 BC2987 hypothetical Membrane Spanning Protein (NCBI ptt file) 90, 304
BC2989 BC2989 hypothetical protein (NCBI ptt file) 90, 304
BC3229 BC3229 hypothetical Membrane Spanning Protein (NCBI ptt file) 27, 304
BC3604 BC3604 hypothetical Membrane Spanning Protein (NCBI ptt file) 142, 396
BC3705 BC3705 None 133, 142
BC3706 BC3706 Transcriptional regulator, MerR family (NCBI ptt file) 133, 142
BC3709 BC3709 hypothetical Membrane Spanning Protein (NCBI ptt file) 304, 388
BC3871 BC3871 Protein yicC (NCBI ptt file) 142, 275
BC3922 BC3922 Prespore specific transcriptional activator rsfA (NCBI ptt file) 92, 142
BC4017 BC4017 3-oxoacyl-[acyl-carrier protein] reductase (NCBI ptt file) 304, 480
BC4018 BC4018 hypothetical Membrane Spanning Protein (NCBI ptt file) 37, 304
BC4059 BC4059 hypothetical protein (NCBI ptt file) 170, 304
BC4107 BC4107 hypothetical Cytosolic Protein (NCBI ptt file) 227, 304
BC4519 BC4519 hypothetical Cytosolic Protein (NCBI ptt file) 90, 304
BC4734 BC4734 hypothetical protein (NCBI ptt file) 170, 304
BC4826 BC4826 hypothetical protein (NCBI ptt file) 100, 304
BC4842 BC4842 Transcriptional regulator, GntR family (NCBI ptt file) 100, 304
BC5205 BC5205 Transcriptional regulatory protein levR (NCBI ptt file) 142, 304
BC5330 BC5330 Thymidine kinase (NCBI ptt file) 133, 142
BC5423 BC5423 hypothetical Membrane Spanning Protein (NCBI ptt file) 304, 442
BC5449 BC5449 Conserved membrane protein (hemolysin III homolog) (NCBI ptt file) 88, 142
BC5487 BC5487 Jag protein (NCBI ptt file) 142, 396
BC5489 BC5489 Ribonuclease P protein component (NCBI ptt file) 142, 161
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 BC5205
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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