Organism : Bacillus cereus ATCC14579 | Module List :
BC0566

Glycerol uptake operon antiterminator regulatory protein (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Glycerol-3-phosphate responsive antiterminator (mRNA-binding) cog/ cog
regulation of transcription, DNA-dependent go/ biological_process
response to biotic stimulus go/ biological_process
transcription regulator activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0566
(Mouseover regulator name to see its description)

BC0566 is regulated by 20 influences and regulates 22 modules.
Regulators for BC0566 (20)
Regulator Module Operator
BC0566 523 tf
BC0742 523 tf
BC0840 523 tf
BC0848 523 tf
BC2469 523 tf
BC2964 523 tf
BC3155 523 tf
BC3320 523 tf
BC3903 523 tf
BC4505 523 tf
BC5205 523 tf
BC0566 65 tf
BC0840 65 tf
BC0848 65 tf
BC1037 65 tf
BC2964 65 tf
BC3095 65 tf
BC3155 65 tf
BC3792 65 tf
BC3903 65 tf

Warning: BC0566 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
4050 3.10e+02 GGGaGGaGA
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4051 2.50e+02 gGAGagag
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4956 5.90e-01 aaAGGaGAaag
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4957 8.50e+03 CCTaaGGGGG
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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 BC0566

BC0566 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Glycerol-3-phosphate responsive antiterminator (mRNA-binding) cog/ cog
regulation of transcription, DNA-dependent go/ biological_process
response to biotic stimulus go/ biological_process
transcription regulator activity go/ molecular_function
Module neighborhood information for BC0566

BC0566 has total of 41 gene neighbors in modules 65, 523
Gene neighbors (41)
Gene Common Name Description Module membership
BC0566 BC0566 Glycerol uptake operon antiterminator regulatory protein (NCBI ptt file) 65, 523
BC0567 BC0567 SN-glycerol-3-phosphate transport ATP-binding protein ugpC (NCBI ptt file) 65, 523
BC0568 BC0568 SN-glycerol-3-phosphate transport system permease protein ugpA (NCBI ptt file) 65, 523
BC0569 BC0569 SN-glycerol-3-phosphate transport system permease protein ugpE (NCBI ptt file) 65, 523
BC0570 BC0570 Glycerol-3-phosphate-binding protein (NCBI ptt file) 65, 523
BC0710 BC0710 Phosphate-binding protein (NCBI ptt file) 65, 86
BC0711 BC0711 Phosphate transport system permease protein pstC (NCBI ptt file) 65, 86
BC0712 BC0712 Phosphate transport system permease protein pstA (NCBI ptt file) 65, 86
BC0794 BC0794 Hydroxyacylglutathione hydrolase (NCBI ptt file) 338, 523
BC0795 BC0795 Molybdopterin biosynthesis MoeB protein (NCBI ptt file) 338, 523
BC0796 BC0796 Rhodanese-related sulfurtransferases (NCBI ptt file) 338, 523
BC0797 BC0797 Molybdopterin biosynthesis MoeB protein (NCBI ptt file) 338, 523
BC0798 BC0798 NADH dehydrogenase (NCBI ptt file) 338, 523
BC0973 BC0973 hypothetical Membrane Spanning Protein (NCBI ptt file) 65, 509
BC1028 BC1028 hypothetical protein (NCBI ptt file) 65, 523
BC1323 BC1323 2-aminoethylphosphonate-binding protein (NCBI ptt file) 65, 523
BC1324 BC1324 2-aminoethylphosphonate transport ATP-binding protein phnT (NCBI ptt file) 65, 523
BC1325 BC1325 2-aminoethylphosphonate transport system permease protein phnU (NCBI ptt file) 65, 523
BC1365 BC1365 Isochorismatase (NCBI ptt file) 338, 523
BC1684 BC1684 ABC transporter ATP-binding protein (NCBI ptt file) 469, 523
BC1685 BC1685 ABC transporter substrate-binding protein (NCBI ptt file) 469, 523
BC1705 BC1705 Low-affinity zinc transport protein (NCBI ptt file) 65, 523
BC1845 BC1845 hypothetical protein (NCBI ptt file) 80, 523
BC2041 BC2041 hypothetical protein (NCBI ptt file) 65, 523
BC2131 BC2131 hypothetical protein (NCBI ptt file) 65, 86
BC3447 BC3447 CzcD accessory protein (NCBI ptt file) 65, 86
BC3729 BC3729 Acetyltransferase (NCBI ptt file) 86, 523
BC3730 BC3730 Copper-importing ATPase (NCBI ptt file) 305, 523
BC3731 BC3731 COP associated protein (NCBI ptt file) 305, 523
BC4265 BC4265 Phosphate transport system protein phoU (NCBI ptt file) 65, 456
BC4266 BC4266 Phosphate transport ATP-binding protein pstB (NCBI ptt file) 65, 86
BC4267 BC4267 Phosphate transport system permease protein pstA (NCBI ptt file) 65, 86
BC4268 BC4268 Phosphate transport system permease protein pstC (NCBI ptt file) 65, 86
BC4269 BC4269 Phosphate-binding protein (NCBI ptt file) 65, 86
BC4342 BC4342 hypothetical protein (NCBI ptt file) 46, 523
BC4343 BC4343 Alkaline phosphatase (NCBI ptt file) 65, 86
BC4755 BC4755 Phosphatidylglycerophosphatase B (NCBI ptt file) 65, 86
BC4756 BC4756 Glycosyltransferase (NCBI ptt file) 65, 86
BC4769 BC4769 Collagen triple helix repeat protein (NCBI ptt file) 65, 86
BC5021 BC5021 hypothetical protein (NCBI ptt file) 46, 65
BC5072 BC5072 ABC transporter ATP-binding protein (NCBI ptt file) 65, 509
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 BC0566
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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