Organism : Bacillus subtilis | Module List :
BSU20040 nrdF

ribonucleotide-diphosphate reductase subunit beta (NCBI)

CircVis
Functional Annotations (7)
Function System
Ribonucleotide reductase, beta subunit cog/ cog
ribonucleoside-diphosphate reductase activity go/ molecular_function
deoxyribonucleoside diphosphate metabolic process go/ biological_process
transition metal ion binding go/ molecular_function
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU20040
(Mouseover regulator name to see its description)

BSU20040 is regulated by 25 influences and regulates 0 modules.
Regulators for BSU20040 nrdF (25)
Regulator Module Operator
BSU03080 102 tf
BSU08990 102 tf
BSU09060 102 tf
BSU09330 102 tf
BSU11500 102 tf
BSU18460 102 tf
BSU29740 102 tf
BSU30020 102 tf
BSU30260 102 tf
BSU33080 102 tf
BSU33840 102 tf
BSU36630 102 tf
BSU38220 102 tf
BSU40710 102 tf
BSU02680 66 tf
BSU05330 66 tf
BSU05670 66 tf
BSU08990 66 tf
BSU09510 66 tf
BSU13880 66 tf
BSU18420 66 tf
BSU24770 66 tf
BSU33990 66 tf
BSU34170 66 tf
BSU35050 66 tf

Warning: BSU20040 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
5088 1.20e+03 GaAAGGaaTGA
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5089 2.30e+02 AAaaaaaCaGCtT.C
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5158 8.40e+00 C.aCCTTTttc
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5159 2.40e+03 gGAaAggAg
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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 BSU20040

BSU20040 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Ribonucleotide reductase, beta subunit cog/ cog
ribonucleoside-diphosphate reductase activity go/ molecular_function
deoxyribonucleoside diphosphate metabolic process go/ biological_process
transition metal ion binding go/ molecular_function
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Module neighborhood information for BSU20040

BSU20040 has total of 51 gene neighbors in modules 66, 102
Gene neighbors (51)
Gene Common Name Description Module membership
BSU00570 yabM putative exporter (RefSeq) 66, 409
BSU00580 yabN putative fusion methylase and nucleotide pyrophosphohydrolase (RefSeq) 66, 193
BSU02270 pssA phosphatidylserine synthase (RefSeq) 66, 212
BSU02530 rtpA anti-TRAP regulator (RefSeq) 102, 168
BSU05250 ydeM putative dehydratase (RefSeq) 23, 102
BSU05680 ydgK putative efflux transporter (RefSeq) 14, 66
BSU06330 yeaC hypothetical protein (RefSeq) 66, 142
BSU06340 yeaD hypothetical protein (RefSeq) 66, 142
BSU06380 yebC putative integral inner membrane protein (RefSeq) 14, 66
BSU07500 yfmE iron-dicitrate ABC transporter (permease) (RefSeq) 66, 151
BSU07980 pdaA exported N-acetylmuramic acid deacetylase (RefSeq) 66, 293
BSU08040 yfjM hypothetical protein (RefSeq) 102, 361
BSU08050 yfjL hypothetical protein (RefSeq) 102, 255
BSU09000 yhbJ putative integral inner membrane protein; putative exporter subunit (RefSeq) 66, 225
BSU09020 yhcB putative oxidoreductase associated to oxygen stress (RefSeq) 14, 66
BSU09060 yhcF putative transcriptional regulator (GntR family) (RefSeq) 11, 102
BSU09440 citA citrate synthase I (RefSeq) 102, 411
BSU13090 ykkC efflux transporter (RefSeq) 37, 66
BSU13100 ykkD efflux transporter (RefSeq) 66, 293
BSU13880 glcT transcriptional antiterminator (BglG family) (RefSeq) 66, 283
BSU16825 BSU16825 None 66, 120
BSU19220 yocI putative ATP-dependent nucleic acid helicase (RefSeq) 102, 334
BSU19230 yocJ azoreductase (RefSeq) 66, 164
BSU19480 yojE putative integral inner membrane protein (RefSeq) 102, 255
BSU19530 yodA putative tautomerase (RefSeq) 66, 322
BSU19590 ctpA carboxy-terminal processing protease (RefSeq) 102, 309
BSU20040 nrdF ribonucleotide-diphosphate reductase subunit beta (NCBI) 66, 102
BSU21730 ypmS hypothetical protein (RefSeq) 66, 370
BSU21770 ilvA threonine dehydratase (RefSeq) 102, 155
BSU22030 ypbR putative GTP-binding protein (RefSeq) 102, 179
BSU22160 yptA hypothetical protein (RefSeq) 66, 67
BSU22720 cheR methyl-accepting chemotaxis proteins (MCPs) methyltransferase (RefSeq) 102, 334
BSU23600 yqxK hypothetical protein (RefSeq) 66, 292
BSU23750 yqjT putative lyase (RefSeq) 102, 334
BSU23800 proI pyrroline-5-carboxylate reductase (RefSeq) 66, 409
BSU23840 yqjK ribonuclease Z (RefSeq) 102, 233
BSU27090 aapA d-Serine/d-alanine/glycine permease (RefSeq) 38, 66
BSU27200 yrhG putative formate/nitrite transporter (RefSeq) 80, 102
BSU27210 yrhF hypothetical protein (RefSeq) 14, 66
BSU29970 ytkP putative cysteine synthase-like protein (RefSeq) 66, 151
BSU31130 yubD putative efflux transporter (RefSeq) 66, 216
BSU31490 pbpD penicillin-binding protein 4 (RefSeq) 102, 402
BSU32630 yurR putative oxidoreductase (RefSeq) 102, 327
BSU33100 liaF integral inner membrane protein (RefSeq) 66, 319
BSU33990 yvbU putative transcriptional regulator (LysR family) (RefSeq) 14, 66
BSU34820 bmrA efflux transporter (ATP-binding and permease protein) (RefSeq) 102, 339
BSU35660 mnaA UDP-N-acetylmannosamine 2-epimerase (RefSeq) 102, 402
BSU36590 clsA cardiolipin synthase (RefSeq) 66, 226
BSU36990 ywkF hypothetical protein (RefSeq) 14, 66
BSU37330 argS arginyl-tRNA synthetase (RefSeq) 102, 155
BSU38220 ywcC putative transcriptional regulator (RefSeq) 102, 116
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 BSU20040
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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