Organism : Bacillus subtilis | Module List :
BSU27000 yraB

putative transcriptional regulator (MerR family) (RefSeq)

CircVis
Functional Annotations (5)
Function System
Predicted transcriptional regulators 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 BSU27000
(Mouseover regulator name to see its description)

BSU27000 is regulated by 20 influences and regulates 11 modules.
Regulators for BSU27000 yraB (20)
Regulator Module Operator
BSU05580 123 tf
BSU05670 123 tf
BSU08410 123 tf
BSU09430 123 tf
BSU10510 123 tf
BSU13150 123 tf
BSU25100 123 tf
BSU27000 123 tf
BSU37550 123 tf
BSU40540 123 tf
BSU05170 200 tf
BSU05290 200 tf
BSU05970 200 tf
BSU08410 200 tf
BSU09380 200 tf
BSU18760 200 tf
BSU19540 200 tf
BSU25100 200 tf
BSU27000 200 tf
BSU40800 200 tf

Warning: BSU27000 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
5198 5.40e-06 AAAGGAGg
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5199 1.30e+03 CCcgGCAaCCGCTgT
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5344 1.70e-04 TttgaTaaAcgtgtTAtgATa
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5345 1.50e-06 gaAacagcAGCcttCCGCTttta
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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 BSU27000

BSU27000 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Predicted transcriptional regulators 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 BSU27000

BSU27000 has total of 56 gene neighbors in modules 123, 200
Gene neighbors (56)
Gene Common Name Description Module membership
BSU00180 tadA tRNA specific adenosine deaminase (RefSeq) 111, 123
BSU00990 rpmG 50S ribosomal protein L33 (RefSeq) 64, 200
BSU02190 ybfF hypothetical protein (RefSeq) 178, 200
BSU02330 ybfQ hypothetical protein (RefSeq) 200, 389
BSU02690 ansZ L-asparaginase (putative lipoprotein) (RefSeq) 130, 200
BSU04550 ydbP putative thioredoxin or thiol-disulfide isomerase (RefSeq) 123, 373
BSU04610 ydcA hypothetical protein (RefSeq) 115, 123
BSU05140 ydzE putative permease (RefSeq) 200, 389
BSU05290 ydeP putative transcriptional regulator (RefSeq) 151, 200
BSU05660 ydgI putative dehydrogenase (RefSeq) 123, 262
BSU05670 ydgJ putative transcriptional regulator (MarR family) (RefSeq) 123, 262
BSU05950 ydiF putative ABC transporter (ATP-binding protein) (RefSeq) 123, 373
BSU07660 yflJ hypothetical protein (RefSeq) 123, 129
BSU07670 yflI hypothetical protein (RefSeq) 123, 151
BSU08210 malQ maltose and maltodextrin ABC transporter subunit (ATP-binding protein) (RefSeq) 123, 296
BSU08410 yfiV putative transcriptional regulator (MarR family) (RefSeq) 200, 378
BSU08880 rpsN 30S ribosomal protein S14 (RefSeq) 123, 200
BSU09210 yhcT putative RNA pseudouridine synthase (RefSeq) 200, 301
BSU09220 yhcU hypothetical protein; orphan (RefSeq) 53, 200
BSU09810 yhaZ hypothetical protein (RefSeq) 178, 200
BSU10480 yhjE putative integral inner membrane protein (RefSeq) 123, 262
BSU10490 sipV type I signal peptidase (RefSeq) 123, 262
BSU11640 yjbQ putative Na+/H+ antiporter (RefSeq) 123, 378
BSU13150 ohrR transcriptional regulator sensing organic peroxides (RefSeq) 111, 123
BSU13810 ykvS hypothetical protein (RefSeq) 39, 200
BSU15060 ylbM hypothetical protein (RefSeq) 111, 123
BSU15110 ylbQ 2-dehydropantoate 2-reductase (RefSeq) 123, 378
BSU17270 ymaC putative phage-related replication protein (RefSeq) 200, 406
BSU17360 ymzA hypothetical protein (RefSeq) 95, 200
BSU17670 cotU spore coat protein (RefSeq) 44, 200
BSU18760 yoaU putative transcriptional regulator (LysR family) (RefSeq) 200, 239
BSU19540 yodB transcriptional repressor (RefSeq) 200, 389
BSU19550 yodC putative oxidoreductase (RefSeq) 200, 378
BSU22000 sspL small acid-soluble spore protein (RefSeq) 200, 239
BSU22940 prsW protease required for RsiW anti-sigma(W) degradation (RefSeq) 123, 311
BSU25060 yqfZ factor involved in motility (RefSeq) 123, 239
BSU25070 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (RefSeq) 151, 200
BSU25110 yqfU putative integral inner membrane protein (RefSeq) 116, 123
BSU27000 yraB putative transcriptional regulator (MerR family) (RefSeq) 123, 200
BSU27880 nifS cysteine desulfurase (RefSeq) 15, 123
BSU28610 yshA cell division protein ZapA (RefSeq) 200, 226
BSU28620 rnhC ribonuclease HIII (RefSeq) 200, 311
BSU33420 nhaK Na+/H+ antiporter (RefSeq) 31, 123
BSU34490 yvdS hypothetical protein (RefSeq) 174, 200
BSU34500 yvdR hypothetical protein (RefSeq) 174, 200
BSU35090 yvmA putative efflux transporter (RefSeq) 123, 378
BSU35609 tuaA 200, 389
BSU37140 ywjG putative oxidoreductase (RefSeq) 123, 378
BSU37550 ywhA putative transcriptional regulator (MarR family) (RefSeq) 111, 123
BSU37680 ywfH carrier protein reductase of bacilysin synthesis (RefSeq) 123, 350
BSU38550 ywaA branched-chain amino acid aminotransferase (RefSeq) 123, 145
BSU38950 yxjH putative methyl-tetrahydrofolate methyltransferase (RefSeq) 28, 123
BSU38960 yxjG putative methyltetrahydrofolate methyltransferase (RefSeq) 28, 123
BSU40740 yyaR putative acetyl-transferase (RefSeq) 200, 231
BSU40800 yyaN putative transcriptional regulator (MerR family) (RefSeq) 200, 238
BSU40810 yyaM putative efflux transporter (RefSeq) 200, 238
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 BSU27000
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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