Organism : Bacillus cereus ATCC14579 | Module List :
BC4672

Catabolite control protein A (NCBI ptt file)

CircVis
Functional Annotations (5)
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
ccpA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4672
(Mouseover regulator name to see its description)

BC4672 is regulated by 25 influences and regulates 41 modules.
Regulators for BC4672 (25)
Regulator Module Operator
BC0116 270 tf
BC0880 270 tf
BC1531 270 tf
BC1998 270 tf
BC3976 270 tf
BC4289 270 tf
BC4336 270 tf
BC4433 270 tf
BC4603 270 tf
BC4672 270 tf
BC5339 270 tf
BC0051 300 tf
BC0122 300 tf
BC0880 300 tf
BC2358 300 tf
BC2801 300 tf
BC3522 300 tf
BC4057 300 tf
BC4289 300 tf
BC4393 300 tf
BC4603 300 tf
BC4672 300 tf
BC5010 300 tf
BC5339 300 tf
BC5368 300 tf

Warning: BC4672 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
4456 1.00e+05 GAAGaAGG
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4457 7.40e+00 GgAggaAaAa
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4514 8.30e-01 AGgAGg
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4515 3.50e+03 GGGcGcaGG
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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 BC4672

BC4672 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
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
ccpA tigr/ tigrfam
Module neighborhood information for BC4672

BC4672 has total of 27 gene neighbors in modules 270, 300
Gene neighbors (27)
Gene Common Name Description Module membership
BC0108 BC0108 Glutamyl-tRNA synthetase (NCBI ptt file) 270, 471
BC0232 BC0232 hypothetical Membrane Spanning Protein (NCBI ptt file) 142, 300
BC0292 BC0292 hypothetical protein (NCBI ptt file) 126, 300
BC0293 BC0293 CAAX amino terminal protease family (NCBI ptt file) 81, 300
BC0779 BC0779 Thiol-disulfide oxdoreductase BdbC (NCBI ptt file) 300, 326
BC1417 BC1417 Phosphoglycerol transferase (NCBI ptt file) 300, 372
BC1465 BC1465 Lysyltransferase (NCBI ptt file) 201, 300
BC1526 BC1526 hypothetical Membrane Spanning Protein (NCBI ptt file) 64, 300
BC1546 BC1546 Aspartate aminotransferase (NCBI ptt file) 300, 471
BC2191 BC2191 Thymidylate synthase (NCBI ptt file) 300, 474
BC2200 BC2200 DegV family protein (NCBI ptt file) 226, 300
BC3803 BC3803 Zinc protease (NCBI ptt file) 170, 270
BC3822 BC3822 Ribosome Recycling Factor (RRF) (NCBI ptt file) 300, 471
BC3858 BC3858 Ribulose-phosphate 3-epimerase (NCBI ptt file) 270, 442
BC3906 BC3906 Cell division protein ftsZ (NCBI ptt file) 298, 300
BC3960 BC3960 hypothetical protein (NCBI ptt file) 270, 326
BC4051 BC4051 Transcription antiterminator, BglG family (NCBI ptt file) 270, 326
BC4274 BC4274 hypothetical protein (NCBI ptt file) 226, 270
BC4480 BC4480 Trigger factor, ppiase (NCBI ptt file) 270, 423
BC4672 BC4672 Catabolite control protein A (NCBI ptt file) 270, 300
BC4689 BC4689 tRNA binding domain protein (NCBI ptt file) 270, 527
BC4690 BC4690 hypothetical Cytosolic Protein (NCBI ptt file) 270, 527
BC4735 BC4735 hypothetical protein (NCBI ptt file) 226, 300
BC4835 BC4835 Two-component response regulator (NCBI ptt file) 270, 406
BC4836 BC4836 Two component system histidine kinase (NCBI ptt file) 270, 300
BC4898 BC4898 Glucose-6-phosphate isomerase (NCBI ptt file) 270, 326
BC5432 BC5432 Bactoprenol glucosyl transferase (NCBI ptt file) 201, 300
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 BC4672
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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