Organism : Bacillus cereus ATCC14579 | Module List :
BC0006

DNA gyrase subunit A (NCBI ptt file)

CircVis
Functional Annotations (7)
Function System
Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit cog/ cog
DNA topoisomerase (ATP-hydrolyzing) activity go/ molecular_function
ATP binding go/ molecular_function
chromosome go/ cellular_component
DNA topological change go/ biological_process
DNA unwinding involved in replication go/ biological_process
gyrA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0006
(Mouseover regulator name to see its description)

BC0006 is regulated by 21 influences and regulates 0 modules.
Regulators for BC0006 (21)
Regulator Module Operator
BC0051 357 tf
BC0122 357 tf
BC0123 357 tf
BC0518 357 tf
BC1059 357 tf
BC1710 357 tf
BC2340 357 tf
BC4072 357 tf
BC4703 357 tf
BC0122 75 tf
BC0518 75 tf
BC1841 75 tf
BC2672 75 tf
BC3706 75 tf
BC4057 75 tf
BC4072 75 tf
BC4076 75 tf
BC4499 75 tf
BC4652 75 tf
BC4703 75 tf
BC5332 75 tf

Warning: BC0006 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
4070 6.70e+02 GAAAGgtAgcGA
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4071 4.80e+02 aAGgaGGa
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4624 2.20e-01 AGatgctaggG
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4625 5.40e+02 AaGgGgtGcttgTTT
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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 BC0006

BC0006 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit cog/ cog
DNA topoisomerase (ATP-hydrolyzing) activity go/ molecular_function
ATP binding go/ molecular_function
chromosome go/ cellular_component
DNA topological change go/ biological_process
DNA unwinding involved in replication go/ biological_process
gyrA tigr/ tigrfam
Module neighborhood information for BC0006

BC0006 has total of 40 gene neighbors in modules 75, 357
Gene neighbors (40)
Gene Common Name Description Module membership
BC0006 BC0006 DNA gyrase subunit A (NCBI ptt file) 75, 357
BC0109 BC0109 Serine acetyltransferase (NCBI ptt file) 240, 357
BC0110 BC0110 Cysteinyl-tRNA synthetase (NCBI ptt file) 240, 357
BC0111 BC0111 hypothetical protein (NCBI ptt file) 240, 357
BC0112 BC0112 23S rRNA methyltransferase (NCBI ptt file) 240, 357
BC0113 BC0113 hypothetical Cytosolic Protein (NCBI ptt file) 357, 484
BC0122 BC0122 DNA-directed RNA polymerase beta chain (NCBI ptt file) 357, 366
BC0123 BC0123 DNA-directed RNA polymerase beta' chain (NCBI ptt file) 357, 366
BC0235 BC0235 hypothetical protein (NCBI ptt file) 67, 75
BC0894 BC0894 Polysaccharides export protein (NCBI ptt file) 8, 75
BC1108 BC1108 hypothetical protein (NCBI ptt file) 75, 276
BC1356 BC1356 Transcriptional regulator, GntR family (NCBI ptt file) 75, 241
BC1357 BC1357 ABC transporter ATP-binding protein (NCBI ptt file) 27, 75
BC1474 BC1474 ResB protein (NCBI ptt file) 150, 357
BC1475 BC1475 ResB protein (NCBI ptt file) 150, 357
BC1476 BC1476 Protein resC (NCBI ptt file) 150, 357
BC1761 BC1761 GTP-binding protein hflX (NCBI ptt file) 75, 517
BC1841 BC1841 Transcriptional regulators, LysR family (NCBI ptt file) 75, 388
BC2001 BC2001 Integral membrane protein (NCBI ptt file) 75, 230
BC2984 BC2984 Immune inhibitor A precursor (NCBI ptt file) 357, 509
BC3075 BC3075 EpiH/GdmH-related protein (NCBI ptt file) 75, 139
BC3941 BC3941 Cytochrome c oxidase polypeptide IVB (NCBI ptt file) 357, 405
BC3942 BC3942 Cytochrome c oxidase polypeptide III (NCBI ptt file) 357, 405
BC3943 BC3943 Cytochrome c oxidase polypeptide I (NCBI ptt file) 161, 357
BC3944 BC3944 Cytochrome c oxidase polypeptide II (NCBI ptt file) 161, 357
BC4076 BC4076 Acetoin transport repressor (NCBI ptt file) 60, 75
BC4283 BC4283 ATP-dependent RNA helicase (NCBI ptt file) 69, 75
BC4492 BC4492 putative phosphoesterase (NCBI ptt file) 182, 357
BC4494 BC4494 Ribonuclease PH (NCBI ptt file) 313, 357
BC4499 BC4499 Transcriptional regulator, TetR family (NCBI ptt file) 75, 432
BC5236 BC5236 Diguanylate cyclase/phosphodiesterase domain 1 (GGDEF) (NCBI ptt file) 27, 75
BC5238 BC5238 Glycine betaine transporter (NCBI ptt file) 67, 75
BC5305 BC5305 ATP synthase epsilon chain (NCBI ptt file) 182, 357
BC5306 BC5306 ATP synthase beta chain (NCBI ptt file) 182, 357
BC5307 BC5307 ATP synthase gamma chain (NCBI ptt file) 182, 357
BC5308 BC5308 F0F1 ATP synthase subunit alpha (RefSeq) 182, 357
BC5419 BC5419 N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase (NCBI ptt file) 75, 479
BC5420 BC5420 Glycosyltransferase (NCBI ptt file) 67, 75
BC5443 BC5443 Glycine betaine transporter (NCBI ptt file) 75, 462
BC5451 BC5451 ATP-dependent RNA helicase (NCBI ptt file) 8, 75
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 BC0006
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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