Organism : Bacillus subtilis | Module List :
BSU29560 ytcI

putative acyl-coenzyme A synthetase (RefSeq)

CircVis
Functional Annotations (11)
Function System
Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases cog/ cog
catalytic activity go/ molecular_function
metabolic process go/ biological_process
Glycolysis / Gluconeogenesis kegg/ kegg pathway
Pyruvate metabolism kegg/ kegg pathway
Propanoate metabolism kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Carbon fixation pathways in prokaryotes kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU29560
(Mouseover regulator name to see its description)

BSU29560 is regulated by 19 influences and regulates 0 modules.
Regulators for BSU29560 ytcI (19)
Regulator Module Operator
BSU04160 261 tf
BSU04680 261 tf
BSU13450 261 tf
BSU19050 261 tf
BSU24100 261 tf
BSU30020 261 tf
BSU30260 261 tf
BSU33840 261 tf
BSU02220 243 tf
BSU04680 243 tf
BSU04730 243 tf
BSU05170 243 tf
BSU09830 243 tf
BSU10830 243 tf
BSU24250 243 tf
BSU25760 243 tf
BSU28820 243 tf
BSU29630 243 tf
BSU29740 243 tf

Warning: BSU29560 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
5428 3.90e-04 atcCct.ctGAaaaaGcatataT
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5429 9.60e+01 cgCgcgAggTTtgTc
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5462 3.10e-04 ccctttcCgcCtttaT.ttaacAa
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5463 2.70e+02 AttgaAaagGA
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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 BSU29560

BSU29560 is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases cog/ cog
catalytic activity go/ molecular_function
metabolic process go/ biological_process
Glycolysis / Gluconeogenesis kegg/ kegg pathway
Pyruvate metabolism kegg/ kegg pathway
Propanoate metabolism kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Carbon fixation pathways in prokaryotes kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
Module neighborhood information for BSU29560

BSU29560 has total of 44 gene neighbors in modules 243, 261
Gene neighbors (44)
Gene Common Name Description Module membership
BSU00380 metS methionyl-tRNA synthetase (RefSeq) 7, 243
BSU00390 yabD metal-dependent DNase (RefSeq) 1, 243
BSU00690 ftsH cell-division protein and general stress protein (class III heat-shock) (RefSeq) 160, 243
BSU00920 gltX glutamyl-tRNA synthetase (RefSeq) 160, 243
BSU03180 cah S-deacylase (RefSeq) 80, 261
BSU03220 ycgO putative proline/ornithine permease (RefSeq) 11, 261
BSU04670 rsbRA component of the piezosome (stressosome); positive regulation of sigma(B) activity in response to salt and heat stress (RefSeq) 160, 243
BSU04680 rsbS antagonist of RsbT (RefSeq) 160, 243
BSU04690 rsbT switch protein/serine-threonine kinase; controls the activity of the piezosome (stressosome) (RefSeq) 160, 243
BSU04700 rsbU serine phosphatase; controls the activity of the piezosome (stressosome) (RefSeq) 160, 243
BSU09790 yheB hypothetical protein (RefSeq) 63, 243
BSU11430 oppA oligopeptide ABC transporter (binding lipoprotein) (RefSeq) 36, 261
BSU11440 oppB oligopeptide ABC transporter (permease) (RefSeq) 144, 261
BSU11450 oppC oligopeptide ABC transporter (permease) (RefSeq) 144, 261
BSU11460 oppD oligopeptide ABC transporter (ATP-binding protein) (RefSeq) 144, 261
BSU11470 oppF oligopeptide ABC transporter (ATP-binding protein) (RefSeq) 144, 261
BSU14260 mobA molybdopterin-guanine dinucleotide biosynthesis protein A (RefSeq) 128, 243
BSU14270 moeB thiamine/molybdopterin biosynthesis MoeB-like protein (RefSeq) 243, 261
BSU14280 moeA molybdene to molybdopterin ligation enzyme (RefSeq) 243, 261
BSU14290 mobB molybdopterin-guanine dinucleotide biosynthesis protein B (RefSeq) 243, 261
BSU14300 moaE molybdopterin synthase (large subunit) (RefSeq) 243, 261
BSU19040 csaA molecular chaperone (RefSeq) 261, 302
BSU19050 yobQ putative transcriptional regulator (AraC/XylS family) (RefSeq) 11, 261
BSU19060 yobR putative acetyltransferase (RefSeq) 11, 261
BSU23680 yqjZ putative degradation enzyme (oxygenase) (RefSeq) 79, 261
BSU24100 bkdR transcriptional regulator (RefSeq) 11, 261
BSU28200 lonA class III heat-shock ATP-dependent LonA protease (RefSeq) 63, 243
BSU28350 ysnB phosphoesterase (RefSeq) 187, 243
BSU28360 ysnA nucleoside-triphosphatase (RefSeq) 187, 243
BSU29460 moaB molybdopterin GTP-binding precursor Z biosynthesis component (RefSeq) 187, 243
BSU29550 ytcJ putative metal-dependent hydrolase (RefSeq) 243, 261
BSU29560 ytcI putative acyl-coenzyme A synthetase (RefSeq) 243, 261
BSU32360 yunC putative RNA binding protein (RefSeq) 243, 252
BSU33730 opuBA choline ABC transporter (ATP-binding protein) (RefSeq) 24, 261
BSU33800 opuCD glycine betaine/carnitine/choline/choline sulfate ABC transporter (permease) (RefSeq) 24, 261
BSU33810 opuCC glycine betaine/carnitine/choline/choline sulfate ABC transporter (osmoprotectant-binding lipoprotein) (RefSeq) 24, 261
BSU33820 opuCB glycine betaine/carnitine/choline/choline sulfate ABC transporter (permease) (RefSeq) 24, 261
BSU33830 opuCA glycine betaine/carnitine/choline/choline sulfate ABC transporter (ATP-binding protein) (RefSeq) 24, 261
BSU33840 yvbF putative transcriptional regulator (RefSeq) 24, 261
BSU37940 ywdJ putative purine/pyrimidine permease (RefSeq) 29, 243
BSU37950 ywdI hypothetical protein (RefSeq) 29, 243
BSU37960 ywdH putative aldehyde dehydrogenase (RefSeq) 111, 243
BSU37980 ywdF putative glycosyltransferase (RefSeq) 1, 243
BSU40520 yybS putative integral inner membrane protein (RefSeq) 1, 243
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 BSU29560
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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