Organism : Bacillus subtilis | Module List :
BSU15470 pyrR

bifunctional pyrimidine regulatory protein PyrR uracil phosphoribosyltransferase (RefSeq)

CircVis
Functional Annotations (5)
Function System
Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase cog/ cog
uracil phosphoribosyltransferase activity go/ molecular_function
nucleoside metabolic process go/ biological_process
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU15470
(Mouseover regulator name to see its description)

BSU15470 is regulated by 19 influences and regulates 11 modules.
Regulators for BSU15470 pyrR (19)
Regulator Module Operator
BSU01430 267 tf
BSU04100 267 tf
BSU05130 267 tf
BSU13450 267 tf
BSU15470 267 tf
BSU16600 267 tf
BSU24320 267 tf
BSU33230 267 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: BSU15470 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
Loader icon
5081 3.20e+02 aaagagaAaAaAgG
Loader icon
5474 2.40e+02 agGaGGagcAcag
Loader icon
5475 1.60e+03 GAAgCGaACG
Loader icon
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 BSU15470

BSU15470 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase cog/ cog
uracil phosphoribosyltransferase activity go/ molecular_function
nucleoside metabolic process go/ biological_process
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Module neighborhood information for BSU15470

BSU15470 has total of 33 gene neighbors in modules 62, 267
Gene neighbors (33)
Gene Common Name Description Module membership
BSU00110 yaaD pyridoxal biosynthesis lyase PdxS (RefSeq) 144, 267
BSU00120 yaaE glutamine amidotransferase subunit PdxT (RefSeq) 144, 267
BSU01050 rplL 50S ribosomal protein L7/L12 (RefSeq) 62, 104
BSU01060 ybxB ribosomal RNA methyltransferase (RefSeq) 62, 234
BSU06420 purE phosphoribosylaminoimidazole carboxylase I (RefSeq) 267, 383
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
BSU15510 pyrAA carbamoyl phosphate synthase small subunit (RefSeq) 57, 267
BSU15520 carB carbamoyl phosphate synthase large subunit (RefSeq) 241, 267
BSU15530 pyrK dihydroorotate dehydrogenase electron transfer subunit (RefSeq) 57, 267
BSU15540 pyrD dihydroorotate dehydrogenase 1B (RefSeq) 57, 267
BSU15550 pyrF orotidine 5'-phosphate decarboxylase (RefSeq) 57, 267
BSU15560 pyrE orotate phosphoribosyltransferase (RefSeq) 57, 267
BSU16510 pyrH uridylate kinase (RefSeq) 62, 104
BSU16520 frr ribosome recycling factor (RefSeq) 62, 104
BSU22060 pbuX xanthine permease (RefSeq) 267, 383
BSU22070 xpt xanthine phosphoribosyltransferase (RefSeq) 267, 383
BSU24310 folD bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase (RefSeq) 234, 267
BSU24320 nusB transcription antitermination protein NusB (RefSeq) 234, 267
BSU29470 ackA acetate kinase (RefSeq) 62, 79
BSU30540 asnB asparagine synthetase (RefSeq) 62, 325
BSU36410 mbl rod shape-determining protein Mbl (RefSeq) 62, 325
BSU37500 speE spermidine synthase (RefSeq) 62, 193
BSU40420 purA adenylosuccinate synthetase (RefSeq) 267, 383
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 BSU15470
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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