Organism : Bacillus cereus ATCC14579 | Module List :
BC0613

Transcriptional regulator, ArsR family (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Predicted 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
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0613
(Mouseover regulator name to see its description)

BC0613 is regulated by 28 influences and regulates 33 modules.
Regulators for BC0613 (28)
Regulator Module Operator
BC0059 335 tf
BC0099 335 tf
BC0518 335 tf
BC0595 335 tf
BC0613 335 tf
BC0954 335 tf
BC1033 335 tf
BC1296 335 tf
BC1302 335 tf
BC1356 335 tf
BC4211 335 tf
BC4314 335 tf
BC4703 335 tf
BC0613 438 tf
BC0648 438 tf
BC1710 438 tf
BC2386 438 tf
BC2794 438 tf
BC3194 438 tf
BC3690 438 tf
BC4001 438 tf
BC4076 438 tf
BC4211 438 tf
BC4570 438 tf
BC4652 438 tf
BC4670 438 tf
BC4703 438 tf
BC5481 438 tf

Warning: BC0613 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
4582 1.80e+00 cCtCCTcA
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4583 2.10e+01 cTTTGaCcttttTTgacca
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4786 2.80e-04 a.AttTcTCCctctT
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4787 9.10e+03 GCCGccTCc
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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 BC0613

BC0613 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted 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
Module neighborhood information for BC0613

BC0613 has total of 50 gene neighbors in modules 335, 438
Gene neighbors (50)
Gene Common Name Description Module membership
BC0099 BC0099 Transcriptional regulator ctsR (NCBI ptt file) 335, 483
BC0100 BC0100 ClpC ATPase (NCBI ptt file) 335, 483
BC0101 BC0101 Arginine kinase (NCBI ptt file) 335, 483
BC0102 BC0102 Negative regulator of genetic competence clpC/mecB (NCBI ptt file) 335, 483
BC0195 BC0195 3-oxoacyl-[acyl-carrier protein] reductase (NCBI ptt file) 335, 483
BC0294 groES co-chaperonin GroES (RefSeq) 164, 335
BC0376 BC0376 Alkyl hydroperoxide reductase subunit F (NCBI ptt file) 335, 483
BC0377 BC0377 Alkyl hydroperoxide reductase C22 (NCBI ptt file) 335, 483
BC0385 BC0385 Thioredoxin reductase (NCBI ptt file) 48, 335
BC0393 BC0393 Sporulation kinase (NCBI ptt file) 261, 438
BC0503 BC0503 hypothetical Membrane Spanning Protein (NCBI ptt file) 335, 483
BC0518 BC0518 Peroxide operon regulator (NCBI ptt file) 247, 335
BC0595 BC0595 Cadmium efflux system accessory protein (NCBI ptt file) 335, 475
BC0596 BC0596 Zinc-transporting ATPase (NCBI ptt file) 335, 475
BC0613 BC0613 Transcriptional regulator, ArsR family (NCBI ptt file) 335, 438
BC0707 BC0707 Ferrous iron transport protein B (NCBI ptt file) 194, 335
BC0708 BC0708 Ferrous iron transport protein B (NCBI ptt file) 194, 335
BC0709 BC0709 Ferrous iron transport protein A (NCBI ptt file) 194, 335
BC1165 BC1165 hydrolase (HAD superfamily) (NCBI ptt file) 335, 483
BC1168 BC1168 ClpB protein (NCBI ptt file) 335, 483
BC1190 BC1190 genetic competence negative regulator mecA (NCBI ptt file) 268, 438
BC1296 BC1296 (S)-2-hydroxy-acid oxidase subunit GlcF (NCBI ptt file) 247, 335
BC1712 BC1712 Fumarate hydratase (NCBI ptt file) 335, 438
BC1787 BC1787 hypothetical protein (NCBI ptt file) 305, 438
BC1952 BC1952 Nitroreductase family protein (NCBI ptt file) 335, 483
BC2009 BC2009 hypothetical protein (NCBI ptt file) 1, 438
BC2199 BC2199 hypothetical protein (NCBI ptt file) 119, 438
BC2213 BC2213 Pyrazinamidase (NCBI ptt file) 119, 438
BC2214 BC2214 Small heat shock protein (NCBI ptt file) 335, 483
BC2277 BC2277 hypothetical protein (NCBI ptt file) 414, 438
BC2386 BC2386 RNA polymerase ECF-type sigma factor (NCBI ptt file) 438, 449
BC3000 BC3000 Proline/betaine transporter (NCBI ptt file) 414, 438
BC3605 BC3605 hypothetical Cytosolic Protein (NCBI ptt file) 438, 507
BC3723 BC3723 hypothetical protein (NCBI ptt file) 335, 483
BC3995 BC3995 hypothetical Cytosolic Protein (NCBI ptt file) 74, 438
BC4106 BC4106 Alpha/beta hydrolase (NCBI ptt file) 1, 438
BC4211 BC4211 Transcriptional regulator, LacI family (NCBI ptt file) 335, 483
BC4272 BC4272 Superoxide dismutase [Mn] (NCBI ptt file) 262, 438
BC4631 BC4631 hypothetical protein (NCBI ptt file) 1, 438
BC4634 BC4634 Protein ecsC (NCBI ptt file) 194, 438
BC4636 BC4636 MutT/nudix family protein (NCBI ptt file) 119, 438
BC4785 BC4785 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 274, 438
BC4790 BC4790 hypothetical Cytosolic Protein (NCBI ptt file) 1, 438
BC4937 BC4937 hypothetical protein (NCBI ptt file) 31, 438
BC4988 BC4988 hypothetical protein (NCBI ptt file) 385, 438
BC5007 BC5007 IG hypothetical 17029 (NCBI ptt file) 438, 507
BC5152 BC5152 ATP-dependent Clp protease proteolytic subunit (NCBI ptt file) 335, 483
BC5240 BC5240 hypothetical protein (NCBI ptt file) 335, 483
BC5336 BC5336 Sporulation initiation phosphotransferase F (NCBI ptt file) 438, 475
BC5437 BC5437 hypothetical Membrane Spanning Protein (NCBI ptt file) 119, 438
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 BC0613
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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