Organism : Bacillus cereus ATCC14579 | Module List :
BC3486

Transcriptional regulator, MerR family (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator, effector-binding domain/component cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3486
(Mouseover regulator name to see its description)

BC3486 is regulated by 18 influences and regulates 6 modules.
Regulators for BC3486 (18)
Regulator Module Operator
BC0648 502 tf
BC1282 502 tf
BC1699 502 tf
BC1710 502 tf
BC3486 502 tf
BC4001 502 tf
BC4672 502 tf
BC5363 502 tf
BC1080 472 tf
BC1115 472 tf
BC1329 472 tf
BC2410 472 tf
BC2469 472 tf
BC2517 472 tf
BC3486 472 tf
BC3587 472 tf
BC3588 472 tf
BC4336 472 tf

Warning: BC3486 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
4854 8.40e+03 GTatGaaggggTaG
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4855 8.40e+03 GCGCAC
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4914 2.60e-03 .gatA.Aaagaaaa.gag.aGaaG
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4915 1.40e+03 GGCGCG
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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 BC3486

BC3486 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Transcriptional regulator, effector-binding domain/component cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BC3486

BC3486 has total of 31 gene neighbors in modules 472, 502
Gene neighbors (31)
Gene Common Name Description Module membership
BC0551 BC0551 Glycosyltransferase (NCBI ptt file) 151, 472
BC0561 BC0561 Two-component response regulator (NCBI ptt file) 189, 472
BC1735 BC1735 Export ABC transporter permease protein (NCBI ptt file) 135, 502
BC1977 BC1977 Acetyltransferase (NCBI ptt file) 68, 472
BC2078 BC2078 hypothetical Membrane Spanning Protein (NCBI ptt file) 342, 502
BC2079 BC2079 hypothetical Membrane Associated Protein (NCBI ptt file) 342, 502
BC2080 BC2080 hypothetical Membrane Associated Protein (NCBI ptt file) 30, 502
BC2081 BC2081 DNA segregation ATPase and related proteins (FtsK/SpoIIIE family) (NCBI ptt file) 30, 502
BC2082 BC2082 hypothetical protein (NCBI ptt file) 342, 502
BC2083 BC2083 hypothetical protein (NCBI ptt file) 342, 502
BC2084 BC2084 hypothetical Cytosolic Protein (NCBI ptt file) 108, 502
BC2085 BC2085 hypothetical protein (NCBI ptt file) 30, 502
BC2140 BC2140 N-hydroxyarylamine O-acetyltransferase (NCBI ptt file) 398, 472
BC2360 BC2360 hypothetical protein (NCBI ptt file) 293, 502
BC2365 BC2365 Choloylglycine hydrolase (NCBI ptt file) 464, 502
BC2448 BC2448 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 444, 472
BC2472 BC2472 None 445, 502
BC2475 BC2475 hypothetical Membrane Spanning Protein (NCBI ptt file) 395, 502
BC2599 BC2599 holin (NCBI ptt file) 42, 472
BC2780 BC2780 hypothetical protein (NCBI ptt file) 101, 472
BC2859 BC2859 hypothetical protein (NCBI ptt file) 278, 472
BC2905 BC2905 hypothetical protein (NCBI ptt file) 101, 472
BC3239 BC3239 MafB-related protein (NCBI ptt file) 35, 472
BC3273 BC3273 hypothetical protein (NCBI ptt file) 60, 502
BC3274 BC3274 hypothetical protein (NCBI ptt file) 404, 502
BC3424 BC3424 None 38, 502
BC3485 BC3485 Agmatine deiminase (NCBI ptt file) 155, 502
BC3486 BC3486 Transcriptional regulator, MerR family (NCBI ptt file) 472, 502
BC3488 BC3488 hypothetical Membrane Spanning Protein (NCBI ptt file) 502, 504
BC3489 BC3489 Agmatine deiminase (NCBI ptt file) 502, 504
BC4013 BC4013 None 502, 519
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 BC3486
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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