Organism : Bacillus subtilis | Module List :
BSU00560 spoVT

transcriptional regulator (RefSeq)

CircVis
Functional Annotations (2)
Function System
Regulators of stationary/sporulation gene expression cog/ cog
lp_hng_hel_AbrB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU00560
(Mouseover regulator name to see its description)

BSU00560 is regulated by 12 influences and regulates 11 modules.
Regulators for BSU00560 spoVT (12)
Regulator Module Operator
BSU00560 284 tf
BSU10830 284 tf
BSU16170 284 tf
BSU00560 149 tf
BSU01730 149 tf
BSU04650 149 tf
BSU04730 149 tf
BSU09380 149 tf
BSU09690 149 tf
BSU10830 149 tf
BSU13870 149 tf
BSU24770 149 tf

Warning: BSU00560 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
5248 1.80e-01 ggGAGG
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5249 1.30e+02 cctTtTttccgTTatcgCagG
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5506 1.70e+03 G.aGCGccTG
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5507 3.60e+03 GAGAGGAGG
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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 BSU00560

BSU00560 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Regulators of stationary/sporulation gene expression cog/ cog
lp_hng_hel_AbrB tigr/ tigrfam
Module neighborhood information for BSU00560

BSU00560 has total of 33 gene neighbors in modules 149, 284
Gene neighbors (33)
Gene Common Name Description Module membership
BSU00540 yabK hypothetical protein (RefSeq) 149, 320
BSU00550 mfd transcription-repair coupling factor (RefSeq) 149, 391
BSU00560 spoVT transcriptional regulator (RefSeq) 149, 284
BSU04710 rsbV anti-anti-sigma factor (antagonist of RsbW) (RefSeq) 149, 320
BSU07880 yfkJ protein-tyrosine-phosphatase (RefSeq) 149, 352
BSU07890 yfkI hypothetical protein (RefSeq) 149, 391
BSU09530 yhdN aldo/keto reductase specific for NADPH (RefSeq) 149, 299
BSU09910 yhaO putative exonuclease (RefSeq) 213, 284
BSU11120 yitT putative integral inner membrane protein (RefSeq) 149, 264
BSU11130 ipi intracellular proteinase inhibitor BsuPI (RefSeq) 149, 180
BSU12130 yjfC hypothetical protein (RefSeq) 137, 149
BSU12270 yjlB conserved hypothetical protein ; cupin family (RefSeq) 149, 391
BSU23160 rluB pseudouridine synthase (RefSeq) 173, 284
BSU23329 ypuC 149, 257
BSU23340 ypuB hypothetical protein (RefSeq) 149, 387
BSU24130 prpD 2-methylcitrate dehydratase (RefSeq) 284, 292
BSU27750 bofC Bypass of forespore C, intercompartmental signaling factor (RefSeq) 149, 391
BSU27760 csbX putative permease (RefSeq) 149, 391
BSU29150 ytwI putative integral inner membrane protein (RefSeq) 202, 284
BSU29880 malS malate dehydrogenase (RefSeq) 149, 169
BSU30780 menC O-succinylbenzoate-CoA synthase (RefSeq) 149, 341
BSU30930 ytaB putative receptor (RefSeq) 59, 149
BSU33610 rnr ribonuclease R (RefSeq) 149, 264
BSU33620 yvaK carboxylesterase (RefSeq) 29, 149
BSU35970 ywsB hypothetical protein (RefSeq) 29, 149
BSU36680 ywmF putative integral inner membrane protein (RefSeq) 59, 149
BSU38190 galT galactose-1-phosphate uridylyltransferase (RefSeq) 29, 149
BSU38720 yxkO putative carbohydrate kinase (RefSeq) 59, 149
BSU40000 yxnA short chain dehydrogenase (RefSeq) 137, 149
BSU40070 gntP gluconate permease (RefSeq) 73, 284
BSU40080 gntZ 6-phosphogluconate dehydrogenase (RefSeq) 13, 284
BSU40450 yycD hypothetical protein (RefSeq) 137, 149
BSU40860 yyaH putative lyase (RefSeq) 149, 257
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 BSU00560
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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