Organism : Bacillus cereus ATCC14579 | Module List :
BC1033

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 BC1033
(Mouseover regulator name to see its description)

BC1033 is regulated by 29 influences and regulates 20 modules.
Regulators for BC1033 (29)
Regulator Module Operator
BC0116 37 tf
BC0607 37 tf
BC1033 37 tf
BC1363 37 tf
BC3095 37 tf
BC3868 37 tf
BC3982 37 tf
BC4057 37 tf
BC4081 37 tf
BC4204 37 tf
BC4356 37 tf
BC4499 37 tf
BC5339 37 tf
BC5368 37 tf
BC0116 148 tf
BC0595 148 tf
BC1033 148 tf
BC1363 148 tf
BC1889 148 tf
BC2401 148 tf
BC3982 148 tf
BC4010 148 tf
BC4057 148 tf
BC4081 148 tf
BC4204 148 tf
BC4356 148 tf
BC5200 148 tf
BC5339 148 tf
BC5368 148 tf

Warning: BC1033 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
3996 5.40e-01 AtAgAGGa
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3997 1.10e+04 cCATCCCACc
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4212 1.60e+01 atAtaAaAAtaaGa..G
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4213 6.50e+03 AggAaGgg
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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 BC1033

BC1033 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 BC1033

BC1033 has total of 33 gene neighbors in modules 37, 148
Gene neighbors (33)
Gene Common Name Description Module membership
BC0449 BC0449 hypothetical protein (NCBI ptt file) 37, 147
BC0542 BC0542 Thiol-disulfide oxidoreductase BdbD (NCBI ptt file) 37, 382
BC0682 BC0682 Sortase (NCBI ptt file) 148, 442
BC0689 BC0689 Guanine-hypoxanthine permease (NCBI ptt file) 6, 148
BC0959 BC0959 hypothetical Membrane Spanning Protein (NCBI ptt file) 37, 214
BC1033 BC1033 Glycerol uptake operon antiterminator regulatory protein (NCBI ptt file) 37, 148
BC1074 BC1074 hypothetical protein (NCBI ptt file) 148, 440
BC1196 BC1196 hypothetical Cytosolic Protein (NCBI ptt file) 37, 442
BC1277 BC1277 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 148, 482
BC1599 BC1599 hypothetical Membrane Spanning Protein (NCBI ptt file) 8, 37
BC2096 BC2096 hypothetical protein (NCBI ptt file) 148, 260
BC2418 BC2418 hypothetical protein (NCBI ptt file) 148, 442
BC2703 BC2703 hypothetical protein (NCBI ptt file) 97, 148
BC2755 BC2755 Integral membrane protein (NCBI ptt file) 10, 148
BC2818 BC2818 hypothetical Cytosolic Protein (NCBI ptt file) 148, 249
BC2977 BC2977 Pyrroline-5-carboxylate reductase (NCBI ptt file) 148, 249
BC3335 BC3335 Protein tyrosine phosphatase (NCBI ptt file) 148, 382
BC3663 BC3663 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 37, 466
BC3975 BC3975 hydrolase (HAD superfamily) (NCBI ptt file) 148, 442
BC4018 BC4018 hypothetical Membrane Spanning Protein (NCBI ptt file) 37, 304
BC4020 BC4020 hypothetical protein (NCBI ptt file) 148, 442
BC4058 BC4058 hypothetical Cytosolic Protein (NCBI ptt file) 37, 147
BC4138 BC4138 Metal-dependent hydrolase (NCBI ptt file) 8, 37
BC4203 BC4203 Phosphoglycolate phosphatase (NCBI ptt file) 37, 466
BC4356 BC4356 Transcriptional regulator, MerR family (NCBI ptt file) 55, 148
BC4488 BC4488 hypothetical protein (NCBI ptt file) 37, 442
BC4669 BC4669 Large-conductance mechanosensitive channel (NCBI ptt file) 37, 466
BC5063 BC5063 UDP-N-acetylenolpyruvoylglucosamine reductase (NCBI ptt file) 37, 432
BC5064 BC5064 hypothetical protein (NCBI ptt file) 37, 249
BC5185 BC5185 Cell division protein ftsX (NCBI ptt file) 37, 399
BC5186 BC5186 Cell division ATP-binding protein ftsE (NCBI ptt file) 37, 433
BC5337 BC5337 hypothetical protein (NCBI ptt file) 148, 249
BC5384 BC5384 hypothetical Cytosolic Protein (NCBI ptt file) 37, 64
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 BC1033
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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