Organism : Bacillus subtilis | Module List :
BSU23190 dacB

D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5*) (RefSeq)

CircVis
Functional Annotations (3)
Function System
D-alanyl-D-alanine carboxypeptidase cog/ cog
proteolysis go/ biological_process
serine-type D-Ala-D-Ala carboxypeptidase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU23190
(Mouseover regulator name to see its description)

BSU23190 is regulated by 12 influences and regulates 0 modules.
Regulators for BSU23190 dacB (12)
Regulator Module Operator
BSU03750 16 tf
BSU04680 16 tf
BSU05670 16 tf
BSU09830 16 tf
BSU10560 16 tf
BSU25760 16 tf
BSU36420 16 tf
BSU37620 16 tf
BSU04680 396 tf
BSU09830 396 tf
BSU15320 396 tf
BSU37620 396 tf

Warning: BSU23190 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
4994 7.70e-07 AAGGAgG
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4995 3.40e+01 CtcCCtGCCCg
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5702 2.80e+02 GCCaGgaTT.ttctg
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5703 1.60e+01 AAGGAgG
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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 BSU23190

BSU23190 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
D-alanyl-D-alanine carboxypeptidase cog/ cog
proteolysis go/ biological_process
serine-type D-Ala-D-Ala carboxypeptidase activity go/ molecular_function
Module neighborhood information for BSU23190

BSU23190 has total of 32 gene neighbors in modules 16, 396
Gene neighbors (32)
Gene Common Name Description Module membership
BSU01570 ybaN polysaccharide deacetylase involved in sporulation (RefSeq) 16, 304
BSU08920 yhbB hypothetical protein (RefSeq) 16, 126
BSU09830 yhaX putative hydrolase (RefSeq) 126, 396
BSU09940 yhaL sporulation factor (RefSeq) 16, 286
BSU11290 yjaV putative NAD(P) binding enzyme (RefSeq) 16, 224
BSU12110 yjfA hypothetical protein (RefSeq) 16, 224
BSU14810 ylaK putative phosphate starvation inducible protein (RefSeq) 16, 304
BSU15030 ylbJ putative factor required for spore cortex formation (RefSeq) 16, 280
BSU16720 ymxH hypothetical protein (RefSeq) 16, 304
BSU17320 ymaF hypothetical protein (RefSeq) 16, 396
BSU19260 yocM putative spore coat protein (RefSeq) 16, 411
BSU19270 yozN hypothetical protein (RefSeq) 16, 224
BSU19280 yocN hypothetical protein (RefSeq) 16, 224
BSU19320 sqhC squalene-hopene cyclase (RefSeq) 126, 396
BSU23170 spmB spore maturation protein (RefSeq) 286, 396
BSU23180 spmA spore maturation protein (RefSeq) 286, 396
BSU23190 dacB D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5*) (RefSeq) 16, 396
BSU24360 spoIIIAH stage III sporulation ratchet engulfment protein (RefSeq) 16, 396
BSU24370 spoIIIAG stage III sporulation engulfment assembly protein (RefSeq) 224, 396
BSU24380 spoIIIAF stage III sporulation protein (RefSeq) 286, 396
BSU24390 spoIIIAE stage III sporulation protein (RefSeq) 286, 396
BSU24420 spoIIIAB stage III sporulation protein SpoAB (RefSeq) 126, 396
BSU24430 spoIIIAA ATP-binding stage III sporulation protein (RefSeq) 286, 396
BSU25350 yqfD stage IV sporulation protein (RefSeq) 16, 280
BSU27970 spoIVFB membrane metalloprotease (RefSeq) 286, 396
BSU28380 gerM germination (cortex hydrolysis) and sporulation (stage II, multiple polar septa) lytic enzyme (RefSeq) 156, 396
BSU29160 ytvI putative permease (RefSeq) 16, 304
BSU30940 glgP glycogen phosphorylase (RefSeq) 16, 126
BSU31730 yuzC inner spore coat protein (RefSeq) 16, 304
BSU36550 spoIIQ forespore protein required for alternative engulfment (RefSeq) 16, 304
BSU37620 rsfA prespore-specific regulatory gene (RefSeq) 224, 396
BSU40950 yyaC hypothetical protein (RefSeq) 16, 304
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 BSU23190
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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