Organism : Bacillus subtilis | Module List :
BSU15460 rluD

pseudouridylate synthase (RefSeq)

CircVis
Functional Annotations (5)
Function System
Pseudouridylate synthases, 23S RNA-specific cog/ cog
pseudouridine synthesis go/ biological_process
RNA binding go/ molecular_function
pseudouridine synthase activity go/ molecular_function
rluA_subfam tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU15460
(Mouseover regulator name to see its description)

BSU15460 is regulated by 15 influences and regulates 0 modules.
Regulators for BSU15460 rluD (15)
Regulator Module Operator
BSU05420 89 tf
BSU26730 89 tf
BSU37080 89 tf
BSU39990 89 tf
BSU01010 62 tf
BSU01070 62 tf
BSU05270 62 tf
BSU13760 62 tf
BSU15470 62 tf
BSU16600 62 tf
BSU23210 62 tf
BSU24020 62 tf
BSU24320 62 tf
BSU36020 62 tf
BSU38600 62 tf

Warning: BSU15460 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
5080 4.20e+02 AtAgaGgcTG
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5081 3.20e+02 aaagagaAaAaAgG
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5132 3.40e-03 CaGt.AaaCaGcaG
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5133 1.90e-01 ccTCCtcc
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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 BSU15460

BSU15460 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Pseudouridylate synthases, 23S RNA-specific cog/ cog
pseudouridine synthesis go/ biological_process
RNA binding go/ molecular_function
pseudouridine synthase activity go/ molecular_function
rluA_subfam tigr/ tigrfam
Module neighborhood information for BSU15460

BSU15460 has total of 47 gene neighbors in modules 62, 89
Gene neighbors (47)
Gene Common Name Description Module membership
BSU01050 rplL 50S ribosomal protein L7/L12 (RefSeq) 62, 104
BSU01060 ybxB ribosomal RNA methyltransferase (RefSeq) 62, 234
BSU01990 ybdG putative hydrolase/transferase (RefSeq) 89, 360
BSU02950 yceI putative transporter (RefSeq) 89, 365
BSU03250 ycgR putative permease (RefSeq) 89, 233
BSU04500 ydbK putative efflux ABC-transporter (permease component) (RefSeq) 89, 240
BSU09890 natA Na+-efflux ABC transporter (ATP-binding protein) (RefSeq) 89, 313
BSU09900 natB Na+ exporter (ABC permease) (RefSeq) 89, 313
BSU11180 yitZ putative transport protein (RefSeq) 89, 313
BSU12480 yjqB putative PBSX phage-related replication protein (RefSeq) 89, 202
BSU13430 ykoX putative integral inner membrane protein (RefSeq) 38, 89
BSU13890 ptsG phosphotransferase system (PTS) glucose-specific enzyme IICBA component (RefSeq) 89, 138
BSU14710 ylaA hypothetical protein (RefSeq) 89, 361
BSU14720 ylaB hypothetical protein (RefSeq) 89, 231
BSU15180 murE UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase (RefSeq) 62, 234
BSU15190 mraY phospho-N-acetylmuramoyl-pentapeptide- transferase (RefSeq) 62, 234
BSU15200 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase (RefSeq) 62, 234
BSU15210 spoVE factor for spore cortex peptidoglycan synthesis (stage V sporulation) (RefSeq) 62, 234
BSU15450 lspA lipoprotein signal peptidase (RefSeq) 62, 385
BSU15460 rluD pseudouridylate synthase (RefSeq) 62, 89
BSU15470 pyrR bifunctional pyrimidine regulatory protein PyrR uracil phosphoribosyltransferase (RefSeq) 62, 267
BSU15480 pyrP uracil permease (RefSeq) 62, 267
BSU15490 pyrB aspartate carbamoyltransferase catalytic subunit (RefSeq) 62, 267
BSU15500 pyrC dihydroorotase (RefSeq) 62, 267
BSU16510 pyrH uridylate kinase (RefSeq) 62, 104
BSU16520 frr ribosome recycling factor (RefSeq) 62, 104
BSU24880 yqgO hypothetical protein (RefSeq) 89, 202
BSU24890 yqgN 5-formyltetrahydrofolate cyclo-ligase (RefSeq) 89, 385
BSU26680 yrdK hypothetical protein (RefSeq) 89, 270
BSU26748 yrdD 89, 199
BSU29470 ackA acetate kinase (RefSeq) 62, 79
BSU30540 asnB asparagine synthetase (RefSeq) 62, 325
BSU32530 yurH allantoate amidohydrolase (RefSeq) 89, 318
BSU34450 sacB levansucrase (RefSeq) 40, 89
BSU36410 mbl rod shape-determining protein Mbl (RefSeq) 62, 325
BSU36470 pucI allantoin permease (RefSeq) 84, 89
BSU37060 tdk thymidine kinase (RefSeq) 89, 142
BSU37500 speE spermidine synthase (RefSeq) 62, 193
BSU38710 yxlA putative purine-cytosine permease (RefSeq) 89, 177
BSU38900 yxjM two-component sensor histidine kinase [YxjL] (RefSeq) 89, 233
BSU39620 yxeA hypothetical protein (RefSeq) 89, 208
BSU39630 yxdM ABC transporter (permease); efflux of cationic peptides (RefSeq) 84, 89
BSU39640 yxdL ABC transporter (ATP-binding protein); efflux of cationic peptides (RefSeq) 84, 89
BSU39650 yxdK two-component sensor histidine kinase [YxdJ] (RefSeq) 89, 361
BSU39660 yxdJ two-component response regulator [YxdK] (RefSeq) 89, 361
BSU40880 exoAA apurinic/apyrimidinic endonuclease (RefSeq) 89, 301
BSU41050 rnpA ribonuclease P (RefSeq) 15, 62
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 BSU15460
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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