Organism : Bacillus subtilis | Module List :
BSU25760 spoIVCB

RNA polymerase sporulation-specific sigma factor (sigma-K) (N-terminal half) (RefSeq)

CircVis
Functional Annotations (5)
Function System
sequence-specific DNA binding transcription factor 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
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU25760
(Mouseover regulator name to see its description)

BSU25760 is regulated by 30 influences and regulates 41 modules.
Regulators for BSU25760 spoIVCB (30)
Regulator Module Operator
BSU00330 127 tf
BSU01690 127 tf
BSU01740 127 tf
BSU08340 127 tf
BSU09830 127 tf
BSU13450 127 tf
BSU14240 127 tf
BSU14380 127 tf
BSU24320 127 tf
BSU25760 127 tf
BSU27520 127 tf
BSU29270 127 tf
BSU29400 127 tf
BSU33580 127 tf
BSU35050 127 tf
BSU36420 127 tf
BSU37620 127 tf
BSU40670 127 tf
BSU40970 127 tf
BSU00700 33 tf
BSU04680 33 tf
BSU06140 33 tf
BSU06960 33 tf
BSU09520 33 tf
BSU15320 33 tf
BSU22120 33 tf
BSU25760 33 tf
BSU26320 33 tf
BSU26340 33 tf
BSU36420 33 tf

Warning: BSU25760 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
5026 6.40e-04 Tc.CGa.GGAgg.cggcTtt.ttA
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5027 8.30e-02 CCTccC
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5206 1.60e-04 CCtctCttTTg
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5207 1.50e+02 CCTGTCCC
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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 BSU25760

BSU25760 is enriched for 5 functions in 4 categories.
Enrichment Table (5)
Function System
sequence-specific DNA binding transcription factor 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
Module neighborhood information for BSU25760

BSU25760 has total of 52 gene neighbors in modules 33, 127
Gene neighbors (52)
Gene Common Name Description Module membership
BSU01530 cwlD N-acetylmuramoyl-L-alanine amidase (RefSeq) 33, 304
BSU01910 skfA sporulation killing factor A (RefSeq) 33, 141
BSU01920 skfB synthesis of sporulation killing factor A (RefSeq) 33, 141
BSU01950 skfE sporulation killing factor biosynthesis and export; ABC transporter (binding protein) (RefSeq) 8, 33
BSU01960 skfF sporulation killing factor biosynthesis and export; ABC transporter (permease) (RefSeq) 33, 141
BSU01970 skfG sporulation killing factor biosynthesis and export (RefSeq) 8, 33
BSU02600 cwlJ cell wall hydrolase (RefSeq) 55, 127
BSU06920 yesJ putative acetyltransferase (RefSeq) 33, 156
BSU06930 yesK putative permease (RefSeq) 33, 156
BSU07130 lplD putative glycosidase (RefSeq) 33, 129
BSU07840 yfkN bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase precursor protein (RefSeq) 33, 174
BSU08110 sspH acid-soluble spore protein H (RefSeq) 33, 133
BSU08670 ygaB hypothetical protein (RefSeq) 33, 278
BSU10780 yisN hypothetical protein (RefSeq) 85, 127
BSU10790 asnO asparagine synthetase (RefSeq) 85, 127
BSU11390 appB oligopeptide ABC transporter (permease) (RefSeq) 127, 407
BSU11400 appC oligopeptide ABC transporter (permease) (RefSeq) 127, 407
BSU11410 yjbA putative nucleic acid binding protein (RefSeq) 127, 411
BSU12050 yjdH hypothetical protein (RefSeq) 127, 304
BSU12320 yjmC putative oxidoreductase (RefSeq) 26, 33
BSU12330 yjmD putative oxidoreductase (RefSeq) 26, 33
BSU12340 uxuA mannonate dehydratase (RefSeq) 26, 33
BSU12350 yjmF D-mannonate oxidoreductase (RefSeq) 26, 33
BSU12360 exuT hexuronate transporter (RefSeq) 33, 329
BSU12400 yjnA putative integral inner membrane protein (RefSeq) 127, 302
BSU18720 yoaR putative factor for cell wall maintenance or synthesis (RefSeq) 96, 127
BSU19110 yobW mother cell-specific membrane sporulation protein (RefSeq) 126, 127
BSU22280 yppD hypothetical protein (RefSeq) 25, 33
BSU22570 ypiF hypothetical protein (RefSeq) 33, 340
BSU24510 yqhO hypothetical protein (RefSeq) 33, 86
BSU25600 comER late competence protein ComER (RefSeq) 127, 304
BSU25750 nucB nuclease (RefSeq) 33, 278
BSU25760 spoIVCB RNA polymerase sporulation-specific sigma factor (sigma-K) (N-terminal half) (RefSeq) 33, 127
BSU27670 spoVB putative putative translocase with flippase function for teichoic acid synthesis; involved in spore cortex synthesis (stage V sporulation) (RefSeq) 127, 239
BSU28060 spoIIB spatial and temporal regulator of the dissolution of septal peptidoglycan during engulfment (stage II sporulation) (RefSeq) 33, 277
BSU29910 ytzH hypothetical protein (RefSeq) 127, 239
BSU30710 ythA putative cytochrome d oxidase subunit (RefSeq) 127, 282
BSU32270 yutH spore coat-associated protein (RefSeq) 127, 239
BSU33050 gerAA component of the GerA germination receptor (RefSeq) 96, 127
BSU33060 gerAB component of the germination receptor GerA (RefSeq) 96, 127
BSU33070 gerAC component of the germination receptor GerA (RefSeq) 96, 127
BSU37480 ywhH putative RNA-binding protein (RefSeq) 33, 350
BSU37690 ywfG transaminase (RefSeq) 127, 302
BSU37700 bacE efflux protein for bacilysin excretion, self-protection against bacilysin (RefSeq) 127, 302
BSU37710 bacD alanine-anticapsin ligase (RefSeq) 127, 302
BSU37720 bacC bacilysin biosynthesis oxidoreductase (RefSeq) 127, 302
BSU37730 bacB isomerase component of bacilysin synthetase (RefSeq) 127, 302
BSU38230 ywcB putative phage protein (superinfection immunity) (RefSeq) 33, 411
BSU38240 ywcA putative acetate Na+-dependent symporter (RefSeq) 33, 250
BSU38350 ywbE hypothetical protein (RefSeq) 127, 161
VIMSS37638 VIMSS37638 None 24, 127
VIMSS39549 VIMSS39549 None 117, 127
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 BSU25760
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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