Organism : Bacillus subtilis | Module List :
BSU17670 cotU

spore coat protein (RefSeq)

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU17670
(Mouseover regulator name to see its description)

BSU17670 is regulated by 23 influences and regulates 0 modules.
Regulators for BSU17670 cotU (23)
Regulator Module Operator
BSU02160 44 tf
BSU05850 44 tf
BSU09500 44 tf
BSU15690 44 tf
BSU18740 44 tf
BSU19100 44 tf
BSU26220 44 tf
BSU26320 44 tf
BSU26430 44 tf
BSU26840 44 tf
BSU36600 44 tf
BSU40010 44 tf
BSU40800 44 tf
BSU05170 200 tf
BSU05290 200 tf
BSU05970 200 tf
BSU08410 200 tf
BSU09380 200 tf
BSU18760 200 tf
BSU19540 200 tf
BSU25100 200 tf
BSU27000 200 tf
BSU40800 200 tf

Warning: BSU17670 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
5048 4.90e+00 AtGcTC.CCACaAAT
Loader icon
5049 2.10e+02 aaatccCtCcttT.taatt..t.t
Loader icon
5344 1.70e-04 TttgaTaaAcgtgtTAtgATa
Loader icon
5345 1.50e-06 gaAacagcAGCcttCCGCTttta
Loader icon
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 BSU17670

Warning: No Functional annotations were found!

Module neighborhood information for BSU17670

BSU17670 has total of 58 gene neighbors in modules 44, 200
Gene neighbors (58)
Gene Common Name Description Module membership
BSU00990 rpmG 50S ribosomal protein L33 (RefSeq) 64, 200
BSU02190 ybfF hypothetical protein (RefSeq) 178, 200
BSU02330 ybfQ hypothetical protein (RefSeq) 200, 389
BSU02690 ansZ L-asparaginase (putative lipoprotein) (RefSeq) 130, 200
BSU04290 ydaL hypothetical protein (RefSeq) 44, 213
BSU04310 ydaN putative regulator (RefSeq) 44, 213
BSU05040 yddN putative alkanal monooxygenase (RefSeq) 44, 95
BSU05140 ydzE putative permease (RefSeq) 200, 389
BSU05290 ydeP putative transcriptional regulator (RefSeq) 151, 200
BSU08410 yfiV putative transcriptional regulator (MarR family) (RefSeq) 200, 378
BSU08880 rpsN 30S ribosomal protein S14 (RefSeq) 123, 200
BSU09210 yhcT putative RNA pseudouridine synthase (RefSeq) 200, 301
BSU09220 yhcU hypothetical protein; orphan (RefSeq) 53, 200
BSU09500 yhdK negative regulator of the activity of sigma-M (RefSeq) 38, 44
BSU09810 yhaZ hypothetical protein (RefSeq) 178, 200
BSU13770 ykvO putative oxidoreductase (RefSeq) 44, 216
BSU13790 ykvQ putative sporulation-specific glycosylase (RefSeq) 44, 291
BSU13810 ykvS hypothetical protein (RefSeq) 39, 200
BSU17270 ymaC putative phage-related replication protein (RefSeq) 200, 406
BSU17300 ebrA small multidrug resistance efflux transporter (RefSeq) 38, 44
BSU17360 ymzA hypothetical protein (RefSeq) 95, 200
BSU17410 cwlC N-acetylmuramoyl-L-alanine amidase (RefSeq) 44, 283
BSU17670 cotU spore coat protein (RefSeq) 44, 200
BSU17770 yndF putative spore germination lipoprotein (RefSeq) 44, 301
BSU18110 ynfC hypothetical protein (RefSeq) 44, 94
BSU18180 yngB putative UTP-sugar-phosphate uridylyltransferase (RefSeq) 44, 52
BSU18740 yozG putative transcriptional regulator (RefSeq) 44, 47
BSU18760 yoaU putative transcriptional regulator (LysR family) (RefSeq) 200, 239
BSU19540 yodB transcriptional repressor (RefSeq) 200, 389
BSU19550 yodC putative oxidoreductase (RefSeq) 200, 378
BSU20710 yopZ conserved hypothetical protein; phage SPbeta (RefSeq) 44, 52
BSU22000 sspL small acid-soluble spore protein (RefSeq) 200, 239
BSU24200 yqiH putative lipoprotein (RefSeq) 44, 52
BSU25070 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (RefSeq) 151, 200
BSU25900 cwlA N-acetylmuramoyl-L-alanine amidase; skin element (RefSeq) 44, 206
BSU25910 yqxH putative holin; skin element (RefSeq) 44, 206
BSU26410 yrkR phosphate-starvation-inducible protein PsiE (RefSeq) 44, 129
BSU26430 yrkP two-component response regulator [YrkQ] (RefSeq) 44, 129
BSU26440 yrkO putative integral inner membrane protein (RefSeq) 44, 129
BSU26490 yrkJ putative integral inner membrane protein (RefSeq) 44, 71
BSU26500 yrkI hypothetical protein (RefSeq) 44, 71
BSU26510 yrkH putative hydrolase (RefSeq) 44, 71
BSU26530 yrkF putative rhodanese-related sulfur transferase (RefSeq) 44, 71
BSU26840 sigZ RNA polymerase sigma factor SigZ (RefSeq) 44, 206
BSU27000 yraB putative transcriptional regulator (MerR family) (RefSeq) 123, 200
BSU27150 yrhK hypothetical protein (RefSeq) 44, 387
BSU28610 yshA cell division protein ZapA (RefSeq) 200, 226
BSU28620 rnhC ribonuclease HIII (RefSeq) 200, 311
BSU34490 yvdS hypothetical protein (RefSeq) 174, 200
BSU34500 yvdR hypothetical protein (RefSeq) 174, 200
BSU35040 yvnB putative exported phosphohydrolase (RefSeq) 44, 238
BSU35609 tuaA 200, 389
BSU35870 pgsE factor required for polyglutamate synthesis (RefSeq) 44, 61
BSU38390 ywbA putative phosphotransferase system enzyme IIC permease component (RefSeq) 44, 130
BSU40240 yycS putative integrase/transposase (RefSeq) 44, 285
BSU40740 yyaR putative acetyl-transferase (RefSeq) 200, 231
BSU40800 yyaN putative transcriptional regulator (MerR family) (RefSeq) 200, 238
BSU40810 yyaM putative efflux transporter (RefSeq) 200, 238
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 BSU17670
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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