Organism : Bacillus subtilis | Module List :
BSU38500 dltA

D-alanine--poly(phosphoribitol) ligase subunit 1 (RefSeq)

CircVis
Functional Annotations (6)
Function System
Non-ribosomal peptide synthetase modules and related proteins cog/ cog
AMP binding go/ molecular_function
teichoic acid biosynthetic process go/ biological_process
D-alanine-poly(phosphoribitol) ligase activity go/ molecular_function
D-Alanine metabolism kegg/ kegg pathway
AA-adenyl-dom tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU38500
(Mouseover regulator name to see its description)

BSU38500 is regulated by 22 influences and regulates 0 modules.
Regulators for BSU38500 dltA (22)
Regulator Module Operator
BSU00470 15 tf
BSU01010 15 tf
BSU01070 15 tf
BSU01080 15 tf
BSU01430 15 tf
BSU04650 15 tf
BSU16600 15 tf
BSU19050 15 tf
BSU01810 172 tf
BSU02970 172 tf
BSU13150 172 tf
BSU15690 172 tf
BSU15970 172 tf
BSU16600 172 tf
BSU19200 172 tf
BSU23210 172 tf
BSU24320 172 tf
BSU30020 172 tf
BSU36020 172 tf
BSU37160 172 tf
BSU40670 172 tf
BSU40800 172 tf

Warning: BSU38500 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
4992 1.90e+00 ccATcCtCCtGtTgtTTaCac
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4993 6.20e+01 CGGTCTTCCTCCATCCGTTCTCC
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5292 1.70e+00 AAAAAAaCAgTCAgCCGCAA
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5293 1.50e+01 AACAtGagCcTTTTGgCaG
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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 BSU38500

BSU38500 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Non-ribosomal peptide synthetase modules and related proteins cog/ cog
AMP binding go/ molecular_function
teichoic acid biosynthetic process go/ biological_process
D-alanine-poly(phosphoribitol) ligase activity go/ molecular_function
D-Alanine metabolism kegg/ kegg pathway
AA-adenyl-dom tigr/ tigrfam
Module neighborhood information for BSU38500

BSU38500 has total of 35 gene neighbors in modules 15, 172
Gene neighbors (35)
Gene Common Name Description Module membership
BSU01070 rpoB DNA-directed RNA polymerase subunit beta (RefSeq) 15, 139
BSU01080 rpoC DNA-directed RNA polymerase subunit beta' (RefSeq) 15, 139
BSU02980 opuAA glycine betaine ABC transporter (ATP-binding protein) (RefSeq) 4, 15
BSU02990 opuAB glycine betaine ABC transporter (permease) (RefSeq) 4, 15
BSU03000 opuAC glycine betaine ABC transporter (glycine betaine-binding lipoprotein) (RefSeq) 4, 15
BSU06690 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B (RefSeq) 15, 355
BSU10350 yhfS acetyl-CoA acetyltransferase (RefSeq) 15, 79
BSU10360 yhfT acyl-CoA synthetase (RefSeq) 15, 79
BSU10370 bioY biotin transporter (RefSeq) 15, 79
BSU22740 hepT heptaprenyl diphosphate synthase component II (RefSeq) 15, 289
BSU22760 hepS heptaprenyl diphosphate synthase component I (RefSeq) 15, 187
BSU23070 serA D-3-phosphoglycerate dehydrogenase (RefSeq) 15, 128
BSU27850 nadA quinolinate synthetase (RefSeq) 15, 112
BSU27860 nadC nicotinate-nucleotide pyrophosphorylase (RefSeq) 15, 112
BSU27870 nadB L-aspartate oxidase (RefSeq) 15, 112
BSU27880 nifS cysteine desulfurase (RefSeq) 15, 123
BSU27890 nadR transcriptional repressor of de novo NAD biosynthesis (RefSeq) 15, 199
BSU28920 lytT two-component response regulator [LytS] (RefSeq) 172, 339
BSU28930 lytS two-component sensor histidine kinase [LytT] (RefSeq) 172, 339
BSU28940 ysaA putative phosphatase (RefSeq) 172, 339
BSU36770 ywmB hypothetical protein (RefSeq) 172, 325
BSU36780 ywzB hypothetical protein (RefSeq) 172, 325
BSU36800 atpC F0F1 ATP synthase subunit epsilon (RefSeq) 106, 172
BSU36810 atpD F0F1 ATP synthase subunit beta (RefSeq) 106, 172
BSU36820 atpG F0F1 ATP synthase subunit gamma (RefSeq) 106, 172
BSU36830 atpA F0F1 ATP synthase subunit alpha (RefSeq) 106, 172
BSU36840 atpH F0F1 ATP synthase subunit delta (RefSeq) 106, 172
BSU36860 atpE F0F1 ATP synthase subunit C (RefSeq) 106, 172
BSU36870 atpB F0F1 ATP synthase subunit A (RefSeq) 106, 172
BSU36880 atpI ATP synthase (subunit i) (RefSeq) 172, 325
BSU38500 dltA D-alanine--poly(phosphoribitol) ligase subunit 1 (RefSeq) 15, 172
BSU38510 dltB putative D-alanine esterase for lipoteichoic acid and wall teichoic acid (RefSeq) 15, 172
BSU38520 dltC D-alanine--poly(phosphoribitol) ligase subunit 2 (RefSeq) 172, 325
BSU38530 dltD putative D-alanine esterase for lipoteichoic acid and wall teichoic acid synthesis (RefSeq) 15, 172
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 BSU38500
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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