Organism : Bacillus subtilis | Module List :
BSU13720 queC

pre-queuosine 0 synthase (RefSeq)

CircVis
Functional Annotations (9)
Function System
Predicted PP-loop superfamily ATPase cog/ cog
NAD+ synthase (glutamine-hydrolyzing) activity go/ molecular_function
argininosuccinate synthase activity go/ molecular_function
asparagine synthase (glutamine-hydrolyzing) activity go/ molecular_function
ATP binding go/ molecular_function
arginine biosynthetic process go/ biological_process
asparagine biosynthetic process go/ biological_process
NAD biosynthetic process go/ biological_process
TIGR00364 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU13720
(Mouseover regulator name to see its description)

BSU13720 is regulated by 25 influences and regulates 0 modules.
Regulators for BSU13720 queC (25)
Regulator Module Operator
BSU01070 75 tf
BSU06700 75 tf
BSU07820 75 tf
BSU13670 75 tf
BSU13880 75 tf
BSU15470 75 tf
BSU16470 75 tf
BSU21700 75 tf
BSU24020 75 tf
BSU26220 75 tf
BSU26340 75 tf
BSU29690 75 tf
BSU34170 75 tf
BSU35030 75 tf
BSU03890 95 tf
BSU04730 95 tf
BSU05970 95 tf
BSU09480 95 tf
BSU13870 95 tf
BSU17850 95 tf
BSU26220 95 tf
BSU26840 95 tf
BSU35030 95 tf
BSU36600 95 tf
BSU37080 95 tf

Warning: BSU13720 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
5106 1.80e+04 TAaAaaaAaaAGGa
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5107 1.50e+03 AAatGGAAGG
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5144 2.80e+02 aTgcct.tttcaTtTgcAg.gAAa
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5145 8.20e+03 tgAaGagCTTG
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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 BSU13720

BSU13720 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Predicted PP-loop superfamily ATPase cog/ cog
NAD+ synthase (glutamine-hydrolyzing) activity go/ molecular_function
argininosuccinate synthase activity go/ molecular_function
asparagine synthase (glutamine-hydrolyzing) activity go/ molecular_function
ATP binding go/ molecular_function
arginine biosynthetic process go/ biological_process
asparagine biosynthetic process go/ biological_process
NAD biosynthetic process go/ biological_process
TIGR00364 tigr/ tigrfam
Module neighborhood information for BSU13720

BSU13720 has total of 43 gene neighbors in modules 75, 95
Gene neighbors (43)
Gene Common Name Description Module membership
BSU02060 ybxG putative amino acid permease (RefSeq) 95, 199
BSU02290 psd phosphatidylserine decarboxylase (RefSeq) 75, 227
BSU02300 ybfN hypothetical protein (RefSeq) 75, 294
BSU04360 mntH manganese transport protein MntH (RefSeq) 95, 205
BSU04560 ddl D-alanyl-alanine synthetase A (RefSeq) 75, 154
BSU05040 yddN putative alkanal monooxygenase (RefSeq) 44, 95
BSU05510 ydfQ putative thioredoxin or thiol-disulfide isomerase (RefSeq) 95, 294
BSU05910 ydiB putative ATPase or kinase UPF0079 (RefSeq) 75, 312
BSU05940 gcp putative DNA-binding/iron metalloprotein/AP endonuclease (RefSeq) 75, 135
BSU05960 moaC molybdenum cofactor biosynthesis protein MoaC (RefSeq) 95, 201
BSU06630 yerH putative lipoprotein (RefSeq) 75, 227
BSU06700 yerO putative transcriptional regulator (TetR/AcrR family) (RefSeq) 75, 154
BSU06750 yefC putative resolvase (RefSeq) 75, 199
BSU07190 yezD hypothetical protein (RefSeq) 95, 199
BSU07210 yetK putative efflux transporter (RefSeq) 95, 199
BSU07240 yetN hypothetical protein (RefSeq) 75, 154
BSU07260 ltaSA exported glycerol phosphate lipoteichoic acid synthetase and anion-binding protein (RefSeq) 75, 154
BSU07420 yfmM putative ABC efflux transporter (ATP-binding protein) (RefSeq) 75, 154
BSU07650 yflK putative sulfur carrier (RefSeq) 75, 135
BSU07720 yflD hypothetical protein (RefSeq) 95, 294
BSU09090 yhcI putative ABC transporter (permease) (RefSeq) 75, 142
BSU09250 yhcX putative amidohydrolase (RefSeq) 39, 95
BSU09480 yhdI putative PLP-dependent transcriptional regulator (RefSeq) 95, 294
BSU13720 queC pre-queuosine 0 synthase (RefSeq) 75, 95
BSU13870 ykvZ putative transcriptional regulator (LacI family) (RefSeq) 95, 389
BSU17340 hfq RNA-binding protein Hfq (RefSeq) 95, 359
BSU17360 ymzA hypothetical protein (RefSeq) 95, 200
BSU17460 glnA glutamine synthetase (RefSeq) 30, 75
BSU17780 yndG hypothetical protein (RefSeq) 75, 244
BSU17800 yndJ putative integral inner membrane protein (RefSeq) 75, 244
BSU18120 alsT amino acid carrier protein (RefSeq) 75, 190
BSU19420 yojK putative glycosyltransferase (RefSeq) 95, 244
BSU25610 yqeM hypothetical protein (RefSeq) 75, 227
BSU27240 yrhC hypothetical protein (RefSeq) 95, 201
BSU27550 aspS aspartyl-tRNA synthetase (RefSeq) 75, 300
BSU29170 fxsA FxsA (RefSeq) 30, 75
BSU29280 ytnM putative transporter (RefSeq) 95, 333
BSU34110 rsbP serine phosphatase (RefSeq) 75, 132
BSU34400 padC phenolic acid decarboxylase (RefSeq) 95, 294
BSU36250 ptkA protein tyrosine kinase (RefSeq) 75, 395
BSU36740 ywmC hypothetical protein (RefSeq) 95, 364
BSU38780 yxkI putative membrane protease (RefSeq) 10, 95
BSU39530 yxeJ hypothetical protein (RefSeq) 95, 389
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 BSU13720
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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