Organism : Bacillus subtilis | Module List :
BSU10390 yhfW

putative Rieske [2Fe-2S] oxygenase (RefSeq)

CircVis
Functional Annotations (7)
Function System
Glycine/D-amino acid oxidases (deaminating) cog/ cog
monooxygenase activity go/ molecular_function
electron transport go/ biological_process
cellular aromatic compound metabolic process go/ biological_process
ubiquinol-cytochrome-c reductase activity go/ molecular_function
thiamine biosynthetic process go/ biological_process
membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU10390
(Mouseover regulator name to see its description)

BSU10390 is regulated by 18 influences and regulates 0 modules.
Regulators for BSU10390 yhfW (18)
Regulator Module Operator
BSU00560 350 tf
BSU01430 350 tf
BSU01690 350 tf
BSU08250 350 tf
BSU10860 350 tf
BSU15970 350 tf
BSU16170 350 tf
BSU16600 350 tf
BSU24320 350 tf
BSU30150 350 tf
BSU35050 350 tf
BSU09830 304 tf
BSU10560 304 tf
BSU25760 304 tf
BSU35050 304 tf
BSU35520 304 tf
BSU36420 304 tf
BSU37620 304 tf

Warning: BSU10390 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
5546 5.80e-07 cCTCCTTt
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5547 1.60e+02 TGaAaAaaaAaAataatGaAA
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5626 1.40e-02 aAAAcaGGgGGcga
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5627 7.20e+01 gGGcTgcCcT
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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 BSU10390

BSU10390 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Glycine/D-amino acid oxidases (deaminating) cog/ cog
monooxygenase activity go/ molecular_function
electron transport go/ biological_process
cellular aromatic compound metabolic process go/ biological_process
ubiquinol-cytochrome-c reductase activity go/ molecular_function
thiamine biosynthetic process go/ biological_process
membrane go/ cellular_component
Module neighborhood information for BSU10390

BSU10390 has total of 50 gene neighbors in modules 304, 350
Gene neighbors (50)
Gene Common Name Description Module membership
BSU01530 cwlD N-acetylmuramoyl-L-alanine amidase (RefSeq) 33, 304
BSU01570 ybaN polysaccharide deacetylase involved in sporulation (RefSeq) 16, 304
BSU01650 ybbC hypothetical protein (RefSeq) 350, 407
BSU01660 ybbD putative beta-hexosaminidase, putative lipoprotein (RefSeq) 350, 407
BSU01670 ybbE hypothetical protein (RefSeq) 350, 407
BSU01690 ybbH putative transcriptional regulator (RefSeq) 302, 350
BSU01700 murQ N-acetylmuramic acid-6-phosphate etherase (RefSeq) 302, 350
BSU01710 ybbJ putative acyltransferase (RefSeq) 171, 350
BSU01720 ybbK hypothetical protein (RefSeq) 171, 350
BSU01980 skfH sibling killing effect ; sporulation killing factor biosynthesis and export (RefSeq) 141, 304
BSU02240 mpr extracellular metalloprotease (RefSeq) 257, 304
BSU02770 yccK putative ion channel associated enzyme (RefSeq) 219, 350
BSU03640 ubiD putative 3-polyprenyl-4-hydroxybenzoate decarboxylase (RefSeq) 329, 350
BSU05710 ydhD spore cortex lytic enzyme (RefSeq) 180, 304
BSU07140 yetF hypothetical protein (RefSeq) 129, 304
BSU08980 yhbH hypothetical protein (RefSeq) 126, 304
BSU10390 yhfW putative Rieske [2Fe-2S] oxygenase (RefSeq) 304, 350
BSU11350 yjaZ hypothetical protein (RefSeq) 350, 407
BSU11360 appD oligopeptide ABC transporter (ATP-binding protein) (RefSeq) 350, 407
BSU11370 appF oligopeptide ABC transporter (ATP-binding protein) (RefSeq) 350, 407
BSU11480 yjbB putative exporter (RefSeq) 64, 350
BSU12030 yjdF hypothetical protein (RefSeq) 330, 350
BSU12050 yjdH hypothetical protein (RefSeq) 127, 304
BSU13530 kinE two-component sensor histidine kinase (RefSeq) 219, 350
BSU14120 ykzF hypothetical protein (RefSeq) 25, 350
BSU14320 yknU putative ABC transporter (ATP-binding protein) (RefSeq) 257, 304
BSU14810 ylaK putative phosphate starvation inducible protein (RefSeq) 16, 304
BSU15170 spoVD penicillin-binding protein (RefSeq) 126, 304
BSU16720 ymxH hypothetical protein (RefSeq) 16, 304
BSU16980 spoVS regulator required for dehydratation of the spore core and assembly of the coat (stage V sporulation) (RefSeq) 304, 340
BSU17720 yndA hypothetical protein (RefSeq) 286, 304
BSU25600 comER late competence protein ComER (RefSeq) 127, 304
BSU25830 rapE response regulator aspartate phosphatase (RefSeq) 350, 407
BSU26780 yrdA hypothetical protein (RefSeq) 304, 404
BSU27310 pbpI penicillin-binding protein PBP4B (RefSeq) 304, 411
BSU27810 yrbD sodium/proton-dependent alanine transporter (RefSeq) 64, 304
BSU29160 ytvI putative permease (RefSeq) 16, 304
BSU29260 ytpI hypothetical protein (RefSeq) 91, 304
BSU30950 glgA glycogen synthase (RefSeq) 126, 304
BSU30980 glgB glycogen branching enzyme (RefSeq) 141, 304
BSU31010 yuaG putative flotillin-like protein (RefSeq) 350, 407
BSU31020 yuaF putative membreane integrity integral inner membrane protein (RefSeq) 350, 407
BSU31540 yufN putative lipoprotein (RefSeq) 329, 350
BSU31730 yuzC inner spore coat protein (RefSeq) 16, 304
BSU36550 spoIIQ forespore protein required for alternative engulfment (RefSeq) 16, 304
BSU36750 spoIID autolysin required for complete dissolution of the asymmetric septum (stage II sporulation) (RefSeq) 220, 304
BSU37480 ywhH putative RNA-binding protein (RefSeq) 33, 350
BSU37680 ywfH carrier protein reductase of bacilysin synthesis (RefSeq) 123, 350
BSU39240 yxxF putative transporter (RefSeq) 159, 350
BSU40950 yyaC hypothetical protein (RefSeq) 16, 304
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 BSU10390
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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