Organism : Bacillus subtilis | Module List :
BSU40250 yycR

putative dehydrogenase (RefSeq)

CircVis
Functional Annotations (9)
Function System
Threonine dehydrogenase and related Zn-dependent dehydrogenases cog/ cog
electron transport go/ biological_process
zinc ion binding go/ molecular_function
formaldehyde dehydrogenase activity go/ molecular_function
Chloroalkane and chloroalkene degradation kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
fdhA_non_GSH tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU40250
(Mouseover regulator name to see its description)

BSU40250 is regulated by 26 influences and regulates 0 modules.
Regulators for BSU40250 yycR (26)
Regulator Module Operator
BSU01010 287 tf
BSU01640 287 tf
BSU01810 287 tf
BSU02680 287 tf
BSU09330 287 tf
BSU10860 287 tf
BSU16600 287 tf
BSU24320 287 tf
BSU37160 287 tf
BSU38600 287 tf
BSU05050 136 tf
BSU05640 136 tf
BSU07590 136 tf
BSU09330 136 tf
BSU09510 136 tf
BSU09650 136 tf
BSU09990 136 tf
BSU10150 136 tf
BSU10860 136 tf
BSU15330 136 tf
BSU19030 136 tf
BSU23450 136 tf
BSU28550 136 tf
BSU29690 136 tf
BSU29740 136 tf
BSU33740 136 tf

Warning: BSU40250 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
5224 5.90e-01 AaAAAggagagGcgt
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5225 1.00e+03 gcgGaAaGgcgtT
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5512 4.90e-05 AAGGaGaG
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5513 2.20e+02 CATAaa.TagaaaGagGTgTta
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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 BSU40250

BSU40250 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Threonine dehydrogenase and related Zn-dependent dehydrogenases cog/ cog
electron transport go/ biological_process
zinc ion binding go/ molecular_function
formaldehyde dehydrogenase activity go/ molecular_function
Chloroalkane and chloroalkene degradation kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
fdhA_non_GSH tigr/ tigrfam
Module neighborhood information for BSU40250

BSU40250 has total of 42 gene neighbors in modules 136, 287
Gene neighbors (42)
Gene Common Name Description Module membership
BSU02090 ybxI exported beta-lactamase (RefSeq) 171, 287
BSU03010 amhX amidohydrolase (RefSeq) 101, 136
BSU05220 ydeJ putative lipoprotein (RefSeq) 171, 287
BSU07440 yfmK putative acetyltransferase (RefSeq) 171, 287
BSU09670 dat D-alanine aminotransferase (RefSeq) 101, 136
BSU10300 aprE serine alkaline protease (subtilisin E) (RefSeq) 114, 287
BSU12920 dppA D-alanyl-aminopeptidase (RefSeq) 134, 136
BSU12930 dppB dipeptide ABC transporter (permease) (RefSeq) 134, 136
BSU12940 dppC dipeptide ABC transporter (permease) (RefSeq) 134, 136
BSU12950 dppD dipeptide ABC transporter (ATP-binding protein) (RefSeq) 134, 136
BSU12960 dppE dipeptide ABC transporter (dipeptide-binding lipoprotein) (RefSeq) 134, 136
BSU12970 ykfA putative L,D-carboxypeptidase (RefSeq) 134, 136
BSU12980 ykfB L-Ala-D/L-Glu epimerase (RefSeq) 134, 136
BSU12990 ykfC cell wall endopeptidase (RefSeq) 134, 136
BSU13000 ykfD putative cell wall oligopeptide ABC transporter (ATP binding protein) (RefSeq) 134, 136
BSU13940 ykwB putative acetyltransferase (RefSeq) 171, 287
BSU18350 dacC D-alanyl-D-alanine carboxypeptidase (RefSeq) 136, 287
BSU18360 yoxA putative epimerase (RefSeq) 136, 287
BSU18370 yoeA putative efflux transporter (RefSeq) 171, 287
BSU26370 yqaC hypothetical protein (RefSeq) 171, 287
BSU28420 ysmA hypothetical protein (RefSeq) 171, 287
BSU30360 yttA hypothetical protein (RefSeq) 171, 287
BSU31330 yugN hypothetical protein (RefSeq) 134, 136
BSU31340 yugM putative transporter (RefSeq) 134, 136
BSU31945 BSU31945 None 69, 287
BSU35980 ywsA hypothetical protein (RefSeq) 134, 136
BSU36640 ureC urease subunit alpha (RefSeq) 101, 136
BSU36650 ureB urease (beta subunit) (RefSeq) 101, 136
BSU36660 ureA urease subunit gamma (RefSeq) 101, 136
BSU38470 ywaD double-zinc aminopeptidase (RefSeq) 101, 287
BSU39330 abnB arabinan endo-1,5-alpha-L-arabinosidase (RefSeq) 136, 323
BSU40022 BSU40022 None 117, 287
BSU40250 yycR putative dehydrogenase (RefSeq) 136, 287
BSU40290 yycN putative N-acetyltransferase (RefSeq) 114, 287
BSU40300 rapG response regulator aspartate phosphatase (RefSeq) 101, 287
BSU40630 yybI inner spore coat protein (RefSeq) 114, 287
BSU40640 yybH hypothetical protein (RefSeq) 171, 287
VIMSS37404 VIMSS37404 None 70, 287
VIMSS37491 VIMSS37491 None 101, 136
VIMSS38706 VIMSS38706 None 117, 287
VIMSS39865 VIMSS39865 None 158, 287
VIMSS40339 VIMSS40339 None 70, 287
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 BSU40250
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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