Organism : Bacillus cereus ATCC14579 | Module List :
BC3792

Transcriptional regulator, GntR family (NCBI ptt file)

CircVis
Functional Annotations (4)
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
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3792
(Mouseover regulator name to see its description)

BC3792 is regulated by 28 influences and regulates 15 modules.
Regulators for BC3792 (28)
Regulator Module Operator
BC0116 283 tf
BC0123 283 tf
BC0410 283 tf
BC0473 283 tf
BC0613 283 tf
BC2794 283 tf
BC3095 283 tf
BC3792 283 tf
BC3826 283 tf
BC4057 283 tf
BC4091 283 tf
BC4603 283 tf
BC5205 283 tf
BC5250 283 tf
BC0116 234 tf
BC0123 234 tf
BC0410 234 tf
BC2166 234 tf
BC3095 234 tf
BC3720 234 tf
BC3792 234 tf
BC4001 234 tf
BC4010 234 tf
BC4091 234 tf
BC4570 234 tf
BC4611 234 tf
BC4714 234 tf
BC4832 234 tf

Warning: BC3792 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
4384 1.90e-02 gaGGgGG
Loader icon
4385 5.50e+01 TGtaagCGTTtTcAtAA
Loader icon
4482 2.30e-03 agaGagGG
Loader icon
4483 8.50e+03 aAaAgaGa
Loader icon
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 BC3792

BC3792 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
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
Module neighborhood information for BC3792

BC3792 has total of 43 gene neighbors in modules 234, 283
Gene neighbors (43)
Gene Common Name Description Module membership
BC0258 BC0258 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D- alanyl ligase (NCBI ptt file) 283, 311
BC0297 BC0297 Guanine-hypoxanthine permease (NCBI ptt file) 234, 283
BC0323 BC0323 Phosphoribosylaminoimidazole carboxylase catalytic subunit (NCBI ptt file) 92, 283
BC0324 BC0324 Phosphoribosylaminoimidazole carboxylase ATPase subunit (NCBI ptt file) 92, 283
BC0325 BC0325 Adenylosuccinate lyase (NCBI ptt file) 92, 283
BC0363 BC0363 Nucleoside permease nupC (NCBI ptt file) 234, 382
BC0579 BC0579 Malate-sodium symport (NCBI ptt file) 234, 257
BC0580 BC0580 NAD-dependent malic enzyme (NCBI ptt file) 234, 250
BC0592 BC0592 Alanine dehydrogenase (NCBI ptt file) 234, 387
BC0611 BC0611 Aspartate ammonia-lyase (NCBI ptt file) 31, 234
BC0631 BC0631 PTS system, trehalose-specific IIBC component (NCBI ptt file) 283, 387
BC0632 BC0632 Trehalose-6-phosphate hydrolase (NCBI ptt file) 283, 387
BC0807 BC0807 PTS system, diacetylchitobiose-specific IIA component (NCBI ptt file) 234, 387
BC1068 BC1068 Uroporphyrinogen decarboxylase (NCBI ptt file) 283, 311
BC1369 BC1369 Protein dltD precursor (NCBI ptt file) 201, 283
BC1370 BC1370 D-alanyl carrier protein (NCBI ptt file) 201, 283
BC1569 BC1569 Xanthine phosphoribosyltransferase (NCBI ptt file) 234, 283
BC1570 BC1570 Xanthine permease (NCBI ptt file) 234, 283
BC1741 BC1741 NAD-dependent malic enzyme (NCBI ptt file) 134, 234
BC2722 BC2722 dATP pyrophosphohydrolase (NCBI ptt file) 38, 283
BC2723 BC2723 D-amino acid dehydrogenase small subunit (NCBI ptt file) 50, 283
BC2724 BC2724 LAAC (NCBI ptt file) 234, 276
BC3109 BC3109 Pyrroline-5-carboxylate reductase (NCBI ptt file) 234, 487
BC3203 BC3203 hypothetical Exported Protein (NCBI ptt file) 234, 417
BC3707 BC3707 Aluminum resistance protein (NCBI ptt file) 236, 283
BC3719 BC3719 1-phosphofructokinase (NCBI ptt file) 234, 481
BC3720 BC3720 Fructose repressor (NCBI ptt file) 234, 263
BC3788 BC3788 Nucleoside transport system permease protein (NCBI ptt file) 139, 234
BC3789 BC3789 None 139, 234
BC3790 BC3790 Nucleoside transport ATP-binding protein (NCBI ptt file) 234, 283
BC3791 BC3791 Nucleoside-binding protein (NCBI ptt file) 234, 283
BC3792 BC3792 Transcriptional regulator, GntR family (NCBI ptt file) 234, 283
BC3912 BC3912 UDP-N-acetylmuramoylalanine--D-glutamate ligase (NCBI ptt file) 283, 382
BC3916 BC3916 Division specific D,D-transpeptidase / Cell division protein ftsI (NCBI ptt file) 283, 479
BC4083 BC4083 Guanine-hypoxanthine permease (NCBI ptt file) 283, 290
BC4229 BC4229 hypothetical protein (NCBI ptt file) 198, 234
BC4762 BC4762 Phosphoenolpyruvate carboxykinase [ATP] (NCBI ptt file) 234, 400
BC4814 BC4814 hypothetical protein (NCBI ptt file) 234, 387
BC4832 BC4832 Transcriptional regulator, AraC family (NCBI ptt file) 155, 234
BC5259 BC5259 ABC transporter substrate-binding protein (NCBI ptt file) 213, 283
BC5260 BC5260 hypothetical Exported Protein (NCBI ptt file) 283, 290
BC5261 BC5261 Two component system histidine kinase (NCBI ptt file) 213, 283
BC5262 BC5262 Two-component response regulator (NCBI ptt file) 50, 283
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 BC3792
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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