Organism : Bacillus subtilis | Module List :
BSU06730 yefA

putative RNA methyltransferase (RefSeq)

CircVis
Functional Annotations (10)
Function System
SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase cog/ cog
RNA binding go/ molecular_function
RNA processing go/ biological_process
RNA methyltransferase activity go/ molecular_function
Histidine metabolism kegg/ kegg pathway
Tyrosine metabolism kegg/ kegg pathway
Selenocompound metabolism kegg/ kegg pathway
Polycyclic aromatic hydrocarbon degradation kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
rumA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU06730
(Mouseover regulator name to see its description)

BSU06730 is regulated by 16 influences and regulates 0 modules.
Regulators for BSU06730 yefA (16)
Regulator Module Operator
BSU01010 67 tf
BSU02680 67 tf
BSU24250 67 tf
BSU26720 67 tf
BSU27520 67 tf
BSU31410 67 tf
BSU32870 67 tf
BSU33080 67 tf
BSU33740 67 tf
BSU04060 190 tf
BSU15970 190 tf
BSU30020 190 tf
BSU33080 190 tf
BSU33740 190 tf
BSU37620 190 tf
BSU38600 190 tf

Warning: BSU06730 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
5090 8.00e+00 gCCTcTttTtt.Tt...gt.caA
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5091 4.70e+02 Tt.ttT.aa.aata.TtTaa.aag
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5326 3.40e-02 aAGatagaAGggAAacAaa
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5327 2.20e+00 AAgtCcgAtG.GT.gagtgcgaaT
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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 BSU06730

BSU06730 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase cog/ cog
RNA binding go/ molecular_function
RNA processing go/ biological_process
RNA methyltransferase activity go/ molecular_function
Histidine metabolism kegg/ kegg pathway
Tyrosine metabolism kegg/ kegg pathway
Selenocompound metabolism kegg/ kegg pathway
Polycyclic aromatic hydrocarbon degradation kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
rumA tigr/ tigrfam
Module neighborhood information for BSU06730

BSU06730 has total of 46 gene neighbors in modules 67, 190
Gene neighbors (46)
Gene Common Name Description Module membership
BSU06350 yebA hypothetical protein (RefSeq) 67, 271
BSU06370 pbuG hypoxanthine/guanine permease (RefSeq) 190, 294
BSU06730 yefA putative RNA methyltransferase (RefSeq) 67, 190
BSU06760 yeeA putative restriction type II methylase (RefSeq) 67, 142
BSU07340 yfnA metabolite permease (RefSeq) 190, 319
BSU08540 yfhI putative efflux transporter (RefSeq) 67, 293
BSU09120 yhcK putative diguanylate cyclase or phosphodiesterase (RefSeq) 190, 325
BSU09130 tcyP sodium-cystine symporter (RefSeq) 80, 190
BSU09165 BSU09165 None 67, 176
BSU09470 yhdH putative sodium-dependent transporter (RefSeq) 67, 154
BSU09840 hemZ coproporphyrinogen III oxidase (RefSeq) 190, 397
BSU11310 comZ putative late competence gene (RefSeq) 14, 67
BSU13110 purU formyltetrahydrofolate deformylase (RefSeq) 14, 67
BSU16130 gid tRNA (uracil-5-)-methyltransferase Gid (RefSeq) 190, 397
BSU16580 polC DNA polymerase III PolC (RefSeq) 37, 67
BSU18120 alsT amino acid carrier protein (RefSeq) 75, 190
BSU21710 dinF damage inducible, Na+ driven multidrug efflux pump (RefSeq) 67, 170
BSU22160 yptA hypothetical protein (RefSeq) 66, 67
BSU22310 recU Holliday junction-specific endonuclease (RefSeq) 67, 265
BSU22320 ponA peptidoglycan glycosyltransferase (penicillin-binding proteins 1A and 1B) (RefSeq) 67, 292
BSU22330 ypoC hypothetical protein (RefSeq) 67, 199
BSU22340 nth endonuclease III (RefSeq) 67, 293
BSU22350 dnaD DNA-remodelling primosomal protein (RefSeq) 67, 293
BSU23200 ypuI hypothetical protein (RefSeq) 67, 322
BSU23950 yqjA hypothetical protein (RefSeq) 67, 319
BSU26700 azlD branched-chain amino acid transporter (RefSeq) 67, 339
BSU26710 azlC branched-chain amino acid transporter (RefSeq) 67, 339
BSU26720 azlB transcriptional regulator (Lrp/AsnC family) (RefSeq) 67, 339
BSU29730 ytxD flagellar motor protein MotP (RefSeq) 48, 190
BSU30410 ytrF metabolite permease (RefSeq) 125, 190
BSU30420 ytrE ABC transporter (ATP-binding protein) (RefSeq) 125, 190
BSU30430 ytrD ABC transporter, permease component (RefSeq) 190, 339
BSU30440 ytrC ABC transporter, permease component (RefSeq) 190, 339
BSU30450 ytrB ABC transporter (ATP-binding protein) (RefSeq) 190, 339
BSU30460 ytrA transcriptional regulator (GntR family) (RefSeq) 190, 339
BSU31400 alaT hypothetical protein (RefSeq) 67, 132
BSU31410 yugG putative transcriptional regulator (Lrp/AsnC family) (RefSeq) 67, 293
BSU32180 yutK putative Na+(H+)/nucleoside cotransporter (RefSeq) 50, 67
BSU32880 yusP putative multidrug-efflux transporter (RefSeq) 14, 67
BSU33160 yvrA putative vitamin B12 transport system, ATPase component (RefSeq) 48, 190
BSU35690 ggaA poly(glucosyl N-acetylgalactosamine 1-phosphate) glucosyltransferase (RefSeq) 67, 402
BSU36270 ywqB putative replication initiation protein (RefSeq) 190, 397
BSU36280 ywqA putative ATP-binding SNF2 helicase or protein kinase (RefSeq) 190, 271
BSU37150 pyrG CTP synthetase (RefSeq) 190, 319
BSU37490 speB agmatinase (RefSeq) 48, 190
VIMSS38484 VIMSS38484 None 67, 69
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 BSU06730
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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