Organism : Bacillus subtilis | Module List :
BSU12560 xpf

positive control sigma-like factor (RefSeq)

CircVis
Functional Annotations (11)
Function System
DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
DNA-directed RNA polymerase I activity go/ molecular_function
DNA-directed RNA polymerase II activity go/ molecular_function
DNA-directed RNA polymerase III activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
RNA polymerase kegg/ kegg pathway
sigma70-ECF tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU12560
(Mouseover regulator name to see its description)

BSU12560 is regulated by 24 influences and regulates 17 modules.
Regulators for BSU12560 xpf (24)
Regulator Module Operator
BSU02320 74 tf
BSU03890 74 tf
BSU06540 74 tf
BSU09480 74 tf
BSU09500 74 tf
BSU12560 74 tf
BSU14480 74 tf
BSU18740 74 tf
BSU18760 74 tf
BSU19540 74 tf
BSU27120 74 tf
BSU30150 74 tf
BSU35030 74 tf
BSU36420 74 tf
BSU36600 74 tf
BSU37290 74 tf
BSU04680 9 tf
BSU05170 9 tf
BSU06540 9 tf
BSU12560 9 tf
BSU18760 9 tf
BSU19090 9 tf
BSU26340 9 tf
BSU40990 9 tf

Warning: BSU12560 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
4980 1.00e+03 CCGGCG
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4981 2.50e+03 AGCGCC
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5104 5.60e-01 aAaGGAGg
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5105 6.50e+02 CgGCCTgCcgC
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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 BSU12560

BSU12560 is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
DNA-directed RNA polymerase I activity go/ molecular_function
DNA-directed RNA polymerase II activity go/ molecular_function
DNA-directed RNA polymerase III activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
RNA polymerase kegg/ kegg pathway
sigma70-ECF tigr/ tigrfam
Module neighborhood information for BSU12560

BSU12560 has total of 36 gene neighbors in modules 9, 74
Gene neighbors (36)
Gene Common Name Description Module membership
BSU04540 ydbO putative cation efflux system (RefSeq) 74, 205
BSU04830 sacV transcriptional regulator (RefSeq) 9, 279
BSU04850 ydcP conserved hypothetical protein; mobile element region (RefSeq) 9, 279
BSU04860 ydcQ putative DNA wielding protein; mobile element region (RefSeq) 9, 279
BSU04870 ydcR putative replication protein; mobile element region (RefSeq) 9, 279
BSU04880 ydcS conserved hypothetical protein; mobile element region (RefSeq) 9, 279
BSU04890 ydcT conserved hypothetical protein; mobile element region (RefSeq) 9, 279
BSU04900 yddA conserved hypothetical protein; mobile element region (RefSeq) 9, 279
BSU04910 yddB conserved hypothetical protein; mobile element region (RefSeq) 9, 279
BSU04920 yddC hypothetical protein (RefSeq) 9, 279
BSU04930 yddD hypothetical protein; mobile element region (RefSeq) 9, 279
BSU04940 yddE hypothetical protein (RefSeq) 9, 279
BSU04950 yddF conserved hypothetical protein; mobile element region (RefSeq) 9, 279
BSU04960 yddG conserved hypothetical protein; mobile element region (RefSeq) 9, 279
BSU04970 yddH putative cell wall hydrolase; mobile element region (RefSeq) 9, 279
BSU04980 yddI conserved hypothetical protein; mobile element region (RefSeq) 9, 279
BSU06280 ydjP putative peroxydase (RefSeq) 8, 74
BSU10180 yhfC putative integral membrane protein, putative chaperone (RefSeq) 74, 285
BSU12520 xkdB hypothetical protein (RefSeq) 9, 279
BSU12530 xkdC hypothetical protein (RefSeq) 9, 74
BSU12540 xkdD conserved hypothetical protein; phage protein (RefSeq) 74, 364
BSU12550 xtrA PBSX phage protein, homolog of YqaO of the skin element (RefSeq) 9, 74
BSU12560 xpf positive control sigma-like factor (RefSeq) 9, 74
BSU13060 ykjA hypothetical protein (RefSeq) 74, 88
BSU13330 ykoL hypothetical protein (RefSeq) 74, 205
BSU13520 ykrP putative integral inner membrane protein; putative acyltransferase (RefSeq) 74, 387
BSU17860 yneA cell division suppressor protein YneA (RefSeq) 74, 207
BSU19750 cgeE protein involved in maturation of the outermost layer of the spore (RefSeq) 8, 74
BSU19950 sspC small acid-soluble spore protein (alpha/beta-type SASP); SPbeta phage protein (RefSeq) 74, 367
BSU21350 yomI SPbeta phage protein; lytic transglycosylase (RefSeq) 74, 232
BSU27120 sigV RNA polymerase ECF(extracytoplasmic function)-type sigma factor (sigma(V)) (RefSeq) 74, 174
BSU27130 rsiV anti-sigma(V) factor (RefSeq) 74, 174
BSU30720 ythB putative cytochrome bd ubiquinol oxidase subunit II (RefSeq) 74, 282
BSU32850 fadM oxidoreductase involved in fatty acids degradation (RefSeq) 8, 74
BSU37290 arfM transcriptional regulator (RefSeq) 74, 405
BSU38060 ywcJ formate/nitrite transporter (RefSeq) 74, 206
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 BSU12560
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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