Organism : Bacillus subtilis | Module List :
BSU13000 ykfD

putative cell wall oligopeptide ABC transporter (ATP binding protein) (RefSeq)

CircVis
Functional Annotations (7)
Function System
ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component cog/ cog
ATP binding go/ molecular_function
peptide transporter activity go/ molecular_function
peptide transport go/ biological_process
ATPase activity go/ molecular_function
ABC transporters kegg/ kegg pathway
oligo_HPY tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU13000
(Mouseover regulator name to see its description)

BSU13000 is regulated by 25 influences and regulates 0 modules.
Regulators for BSU13000 ykfD (25)
Regulator Module Operator
BSU00700 134 tf
BSU03850 134 tf
BSU08190 134 tf
BSU09510 134 tf
BSU09990 134 tf
BSU10150 134 tf
BSU19030 134 tf
BSU28550 134 tf
BSU29110 134 tf
BSU05050 136 tf
BSU05640 136 tf
BSU07590 136 tf
BSU09330 136 tf
BSU09510 136 tf
BSU09650 136 tf
BSU09990 136 tf
BSU10150 136 tf
BSU10860 136 tf
BSU15330 136 tf
BSU19030 136 tf
BSU23450 136 tf
BSU28550 136 tf
BSU29690 136 tf
BSU29740 136 tf
BSU33740 136 tf

Warning: BSU13000 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
5220 2.60e+01 AAAagGcGGaG
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5221 4.50e+03 GGtGCTG
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5224 5.90e-01 AaAAAggagagGcgt
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5225 1.00e+03 gcgGaAaGgcgtT
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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 BSU13000

BSU13000 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component cog/ cog
ATP binding go/ molecular_function
peptide transporter activity go/ molecular_function
peptide transport go/ biological_process
ATPase activity go/ molecular_function
ABC transporters kegg/ kegg pathway
oligo_HPY tigr/ tigrfam
Module neighborhood information for BSU13000

BSU13000 has total of 30 gene neighbors in modules 134, 136
Gene neighbors (30)
Gene Common Name Description Module membership
BSU03010 amhX amidohydrolase (RefSeq) 101, 136
BSU09670 dat D-alanine aminotransferase (RefSeq) 101, 136
BSU12920 dppA D-alanyl-aminopeptidase (RefSeq) 134, 136
BSU12930 dppB dipeptide ABC transporter (permease) (RefSeq) 134, 136
BSU12940 dppC dipeptide ABC transporter (permease) (RefSeq) 134, 136
BSU12950 dppD dipeptide ABC transporter (ATP-binding protein) (RefSeq) 134, 136
BSU12960 dppE dipeptide ABC transporter (dipeptide-binding lipoprotein) (RefSeq) 134, 136
BSU12970 ykfA putative L,D-carboxypeptidase (RefSeq) 134, 136
BSU12980 ykfB L-Ala-D/L-Glu epimerase (RefSeq) 134, 136
BSU12990 ykfC cell wall endopeptidase (RefSeq) 134, 136
BSU13000 ykfD putative cell wall oligopeptide ABC transporter (ATP binding protein) (RefSeq) 134, 136
BSU18350 dacC D-alanyl-D-alanine carboxypeptidase (RefSeq) 136, 287
BSU18360 yoxA putative epimerase (RefSeq) 136, 287
BSU24030 bkdB branched-chain alpha-keto acid dehydrogenase subunit E2 (RefSeq) 134, 340
BSU24040 bkdAB branched-chain alpha-keto acid dehydrogenase E1 subunit (RefSeq) 134, 340
BSU24050 bkdAA branched-chain alpha-keto acid dehydrogenase E1 subunit (RefSeq) 134, 340
BSU24060 lpdV dihydrolipoamide dehydrogenase (RefSeq) 134, 340
BSU24070 buk butyrate kinase (RefSeq) 134, 340
BSU24080 bcd branched-chain amino acid dehydrogenase (RefSeq) 134, 340
BSU24090 ptb phosphate butyryltransferase (RefSeq) 134, 340
BSU29680 acsA acetyl-CoA synthetase (RefSeq) 134, 321
BSU31330 yugN hypothetical protein (RefSeq) 134, 136
BSU31340 yugM putative transporter (RefSeq) 134, 136
BSU35980 ywsA hypothetical protein (RefSeq) 134, 136
BSU36640 ureC urease subunit alpha (RefSeq) 101, 136
BSU36650 ureB urease (beta subunit) (RefSeq) 101, 136
BSU36660 ureA urease subunit gamma (RefSeq) 101, 136
BSU39330 abnB arabinan endo-1,5-alpha-L-arabinosidase (RefSeq) 136, 323
BSU40250 yycR putative dehydrogenase (RefSeq) 136, 287
VIMSS37491 VIMSS37491 None 101, 136
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 BSU13000
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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