Organism : Bacillus subtilis | Module List :
BSU08100 acoR

transcriptional regulator (RefSeq)

CircVis
Functional Annotations (7)
Function System
Transcriptional activator of acetoin/glycerol metabolism cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU08100
(Mouseover regulator name to see its description)

BSU08100 is regulated by 14 influences and regulates 13 modules.
Regulators for BSU08100 acoR (14)
Regulator Module Operator
BSU08100 321 tf
BSU19030 321 tf
BSU29700 321 tf
BSU35910 321 tf
BSU02000 277 tf
BSU02160 277 tf
BSU05970 277 tf
BSU06540 277 tf
BSU08100 277 tf
BSU09830 277 tf
BSU25760 277 tf
BSU30150 277 tf
BSU36420 277 tf
BSU37620 277 tf

Warning: BSU08100 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
5492 1.40e+03 gCaAAagcgtG
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5493 5.60e+03 agaagGaGGtGcA
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5580 3.70e-09 TtttAaAGCGcTTTCAacaTaGT
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5581 3.00e-04 CccgTaTatacAggtaGTcAacac
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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 BSU08100

BSU08100 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Transcriptional activator of acetoin/glycerol metabolism cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
Module neighborhood information for BSU08100

BSU08100 has total of 35 gene neighbors in modules 277, 321
Gene neighbors (35)
Gene Common Name Description Module membership
BSU07270 yfnH putative sugar-phosphate cytidylyltransferase (RefSeq) 156, 277
BSU07280 yfnG putative CDP-sugar-dehydratase/epimerase (RefSeq) 277, 281
BSU07290 yfnF putative glycosyltransferase (RefSeq) 277, 281
BSU07300 yfnE putative glycosyltransferase (complex carbohydrate synthase) (RefSeq) 277, 281
BSU07760 yfkT putative spore germination integral inner membrane protein (RefSeq) 59, 321
BSU07770 yfkS hypothetical protein (RefSeq) 59, 321
BSU07780 yfkR putative spore germination protein (RefSeq) 278, 321
BSU07790 yfkQ putative spore germination protein (RefSeq) 278, 321
BSU07800 treP phosphotransferase system (PTS) trehalose-specific enzyme IIBC component (RefSeq) 61, 321
BSU07810 treA trehalose-6-phosphate hydrolase (RefSeq) 61, 321
BSU07820 treR transcriptional regulator (GntR family) (RefSeq) 10, 321
BSU08070 acoB acetoin dehydrogenase E1 component (TPP-dependent beta subunit) (RefSeq) 17, 277
BSU08080 acoC branched-chain alpha-keto acid dehydrogenase subunit E2 (RefSeq) 17, 277
BSU08090 acoL dihydrolipoamide dehydrogenase (RefSeq) 17, 277
BSU08100 acoR transcriptional regulator (RefSeq) 277, 321
BSU10960 yitE putative integral inner membrane protein (RefSeq) 277, 286
BSU11790 yjcA sporulation-specific protein (RefSeq) 108, 277
BSU13290 ykzD hypothetical protein (RefSeq) 8, 277
BSU13830 ykvU spore membrane protein involved in germination (RefSeq) 277, 286
BSU13840 stoA thiol-disulfide isomerase (RefSeq) 277, 286
BSU17570 xynP putative H+-xyloside symporter (RefSeq) 321, 405
BSU17580 xynB xylan beta-1,4-xylosidase (RefSeq) 168, 321
BSU23440 spoVAA stage V sporulation protein AA (RefSeq) 277, 367
BSU25820 yqcI hypothetical protein (RefSeq) 277, 282
BSU27690 yrzE putative integral inner membrane protein (RefSeq) 277, 286
BSU27980 spoIVFA regulator of SpoIVFB (stage IV sporulation) (RefSeq) 277, 286
BSU28060 spoIIB spatial and temporal regulator of the dissolution of septal peptidoglycan during engulfment (stage II sporulation) (RefSeq) 33, 277
BSU29680 acsA acetyl-CoA synthetase (RefSeq) 134, 321
BSU29690 acuA protein acetyltransferase (RefSeq) 321, 330
BSU29700 acuB component of the acetoin degradation regulation pathway (RefSeq) 321, 330
BSU29710 acuC protein deacetylase (RefSeq) 321, 330
BSU38560 licH 6-phospho-beta-glucosidase (RefSeq) 186, 321
BSU38570 licA phosphotransferase system (PTS) lichenan-specific enzyme IIA component (RefSeq) 186, 321
BSU38580 licC phosphotransferase system (PTS) lichenan-specific enzyme IIC component (RefSeq) 186, 321
BSU38590 licB phosphotransferase system (PTS) lichenan-specific enzyme IIB component (RefSeq) 186, 321
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 BSU08100
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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