Organism : Bacillus cereus ATCC14579 | Module List :
BC2656

Cobalt transport protein cbiQ (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
ABC-type cobalt transport system, permease component CbiQ and related transporters cog/ cog
cobalt ion transport go/ biological_process
cobalamin biosynthetic process go/ biological_process
cobalt ion transmembrane transporter activity go/ molecular_function
ABC transporters kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2656
(Mouseover regulator name to see its description)

BC2656 is regulated by 20 influences and regulates 0 modules.
Regulators for BC2656 (20)
Regulator Module Operator
BC2470 468 tf
BC2551 468 tf
BC3033 468 tf
BC3160 468 tf
BC4001 468 tf
BC4010 468 tf
BC4474 468 tf
BC5463 468 tf
BC0613 506 tf
BC1302 506 tf
BC2351 506 tf
BC2766 506 tf
BC2794 506 tf
BC2903 506 tf
BC3039 506 tf
BC4256 506 tf
BC4433 506 tf
BC4570 506 tf
BC4661 506 tf
BC4670 506 tf

Warning: BC2656 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
4846 1.40e+04 gaAtaGgaagt
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4847 3.10e+01 cgca.gAatGatgAGgggTt
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4922 7.00e+02 CCG.CAcgAcATGagtCc
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4923 2.60e+03 aGgAaGggGgaag
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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 BC2656

BC2656 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
ABC-type cobalt transport system, permease component CbiQ and related transporters cog/ cog
cobalt ion transport go/ biological_process
cobalamin biosynthetic process go/ biological_process
cobalt ion transmembrane transporter activity go/ molecular_function
ABC transporters kegg/ kegg pathway
Module neighborhood information for BC2656

BC2656 has total of 34 gene neighbors in modules 468, 506
Gene neighbors (34)
Gene Common Name Description Module membership
BC0314 BC0314 Glycosyltransferase (NCBI ptt file) 9, 506
BC0475 BC0475 None 97, 468
BC0562 BC0562 Ca2+/citrate complex secondary transporter (NCBI ptt file) 341, 468
BC0971 BC0971 Carboxylic ester hydrolase (NCBI ptt file) 250, 468
BC1126 BC1126 S-layer homology domain (NCBI ptt file) 213, 506
BC1245 BC1245 hypothetical protein (NCBI ptt file) 186, 468
BC1250 BC1250 hypothetical protein (NCBI ptt file) 179, 468
BC1462 BC1462 None 256, 468
BC1750 BC1750 hypothetical protein (NCBI ptt file) 405, 506
BC1893 BC1893 Scaffold protein (NCBI ptt file) 141, 468
BC2034 BC2034 Export protein for polysaccharides and teichoic acids (NCBI ptt file) 230, 506
BC2219 BC2219 Phenazine biosynthesis protein phzF (NCBI ptt file) 96, 506
BC2321 BC2321 tRNA pseudouridine synthase A (NCBI ptt file) 10, 468
BC2402 BC2402 Tetracycline resistance protein (NCBI ptt file) 130, 468
BC2555 BC2555 hypothetical protein (NCBI ptt file) 76, 468
BC2656 BC2656 Cobalt transport protein cbiQ (NCBI ptt file) 468, 506
BC2690 BC2690 Quaternary ammonium compound-resistance protein (NCBI ptt file) 443, 468
BC2765 BC2765 hypothetical protein (NCBI ptt file) 415, 506
BC3033 BC3033 Transcriptional regulator, AraC family (NCBI ptt file) 76, 468
BC3211 BC3211 NADPH-cytochrome P450 reductase (NCBI ptt file) 484, 506
BC3236 BC3236 hypothetical Cytosolic Protein (NCBI ptt file) 225, 468
BC3257 BC3257 N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 134, 468
BC3278 BC3278 hypothetical protein (NCBI ptt file) 26, 506
BC3342 BC3342 hypothetical Membrane Spanning Protein (NCBI ptt file) 389, 506
BC3622 BC3622 Multidrug resistance protein B (NCBI ptt file) 263, 468
BC3759 BC3759 6-phospho-beta-glucosidase (NCBI ptt file) 165, 506
BC4164 BC4164 hypothetical protein (NCBI ptt file) 179, 506
BC4537 BC4537 Bacitracin transport ATP-binding protein bcrA (NCBI ptt file) 376, 506
BC4829 BC4829 Ribosomal RNA adenine dimethylase (NCBI ptt file) 402, 468
BC4927 BC4927 Cell surface protein (NCBI ptt file) 130, 506
BC5212 BC5212 None 31, 468
BC5225 BC5225 Cytochrome d ubiquinol oxidase subunit II (NCBI ptt file) 402, 468
BC5350 BC5350 Transcriptional activator plcR (NCBI ptt file) 139, 506
BC5385 BC5385 Prespore specific transcriptional activator rsfA (NCBI ptt file) 468, 475
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 BC2656
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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