Organism : Bacillus subtilis | Module List :
BSU13410 ykoV

ATP-dependent DNA ligase subunit (RefSeq)

CircVis
Functional Annotations (6)
Function System
Uncharacterized conserved protein cog/ cog
DNA binding go/ molecular_function
ATP-dependent DNA helicase activity go/ molecular_function
double-strand break repair via nonhomologous end joining go/ biological_process
Non-homologous end-joining kegg/ kegg pathway
Ku_bact tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU13410
(Mouseover regulator name to see its description)

BSU13410 is regulated by 31 influences and regulates 0 modules.
Regulators for BSU13410 ykoV (31)
Regulator Module Operator
BSU02890 96 tf
BSU03880 96 tf
BSU04680 96 tf
BSU04730 96 tf
BSU05170 96 tf
BSU08340 96 tf
BSU09480 96 tf
BSU12560 96 tf
BSU16900 96 tf
BSU19090 96 tf
BSU25250 96 tf
BSU25760 96 tf
BSU26430 96 tf
BSU27170 96 tf
BSU33030 96 tf
BSU33650 96 tf
BSU33740 96 tf
BSU34060 96 tf
BSU34380 96 tf
BSU40410 96 tf
BSU00980 55 tf
BSU01430 55 tf
BSU16170 55 tf
BSU18760 55 tf
BSU23100 55 tf
BSU25760 55 tf
BSU28410 55 tf
BSU33030 55 tf
BSU36420 55 tf
BSU37160 55 tf
BSU37620 55 tf

Warning: BSU13410 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
5068 8.70e-04 aaaAAAggAGc
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5069 6.70e+00 GAAa.aGC
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5146 2.50e+00 TgaccccctctTgtt
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5147 2.60e+02 ggCttcTTttT
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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 BSU13410

BSU13410 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Uncharacterized conserved protein cog/ cog
DNA binding go/ molecular_function
ATP-dependent DNA helicase activity go/ molecular_function
double-strand break repair via nonhomologous end joining go/ biological_process
Non-homologous end-joining kegg/ kegg pathway
Ku_bact tigr/ tigrfam
Module neighborhood information for BSU13410

BSU13410 has total of 52 gene neighbors in modules 55, 96
Gene neighbors (52)
Gene Common Name Description Module membership
BSU01550 gerD lipoprotein with a role in spores' rapid response to nutrient germinants (RefSeq) 55, 217
BSU02600 cwlJ cell wall hydrolase (RefSeq) 55, 127
BSU02710 yczC putative integral inner membrane protein (RefSeq) 96, 307
BSU03110 ycgH putative amino acid transporter (RefSeq) 96, 156
BSU03400 yckD hypothetical protein (RefSeq) 55, 217
BSU04470 dctP C4-dicarboxylate transporter DctA (RefSeq) 55, 168
BSU08060 acoA acetoin dehydrogenase E1 component (TPP-dependent alpha subunit) (RefSeq) 17, 55
BSU08120 yfjF hypothetical protein (RefSeq) 55, 246
BSU10470 yhjD hypothetical protein (RefSeq) 96, 178
BSU10740 yisJ putative spore coat protein (RefSeq) 55, 356
BSU10900 yisY putative hydrolase (RefSeq) 55, 278
BSU12080 ctaO protoheme IX farnesyltransferase (heme O synthase) (RefSeq) 96, 189
BSU12500 xkdA PBSX phage protein, putative peptidase (RefSeq) 64, 96
BSU13400 ligD ATP-dependent DNA ligase (RefSeq) 87, 96
BSU13410 ykoV ATP-dependent DNA ligase subunit (RefSeq) 55, 96
BSU16110 dprA DNA processing Smf single strand binding protein (RefSeq) 96, 98
BSU17750 yndD putative spore germination protein (RefSeq) 55, 278
BSU18600 yozQ hypothetical protein (RefSeq) 55, 239
BSU18710 yozF putative lipoprotein (RefSeq) 55, 96
BSU18720 yoaR putative factor for cell wall maintenance or synthesis (RefSeq) 96, 127
BSU18770 cyeA cysteine and O-acetyl serine efflux permease (RefSeq) 96, 180
BSU19760 cgeD protein involved in maturation of the outermost layer of the spore (RefSeq) 41, 55
BSU21940 degR activation of degradative enzymes (aprE, nprE, sacB) production or activity (RefSeq) 96, 342
BSU24580 yqhH putative RNA polymerase-associated helicase protein (RefSeq) 55, 411
BSU24910 yqgM putative glycosyltransferase (RefSeq) 71, 96
BSU24920 yqgL hypothetical protein (RefSeq) 71, 96
BSU26120 yqbG conserved hypothetical protein; skin element (RefSeq) 96, 239
BSU28900 ysbB antiholin-like protein LrgB (RefSeq) 96, 405
BSU28910 ysbA murein hydrolase regulator LrgA (RefSeq) 96, 405
BSU29020 gapB glyceraldehyde-3-phosphate dehydrogenase (RefSeq) 55, 241
BSU30330 ytvB putative conserved membrane protein (RefSeq) 55, 323
BSU30560 pckA phosphoenolpyruvate carboxykinase (RefSeq) 55, 241
BSU31270 tgl transglutaminase (RefSeq) 55, 99
BSU31420 yugF putative hydrolase (RefSeq) 55, 96
BSU31430 yugE hypothetical protein (RefSeq) 96, 163
BSU32020 yuiH putative sulfite oxidase (RefSeq) 96, 291
BSU32190 yuzB hypothetical protein (RefSeq) 96, 115
BSU32950 yusW putative lipoprotein (RefSeq) 55, 411
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
BSU33410 yvgO hypothetical protein (RefSeq) 55, 137
BSU33640 yvaM putative hydrolase (RefSeq) 55, 356
BSU33690 yvaQ putative methyl-accepting transducer (RefSeq) 5, 96
BSU34000 cyeB cysteine and O-acetylserine efflux permease (RefSeq) 96, 307
BSU35800 gerBA component of germinant receptor B (RefSeq) 55, 278
BSU35810 gerBB component of germinant receptor B (RefSeq) 55, 278
BSU35820 gerBC lipoprotein component of the germination receptor B (RefSeq) 55, 278
BSU38250 ywbO putative sulfur oxido-reductase (RefSeq) 96, 307
BSU38800 yxkH putative exported polysaccharide deacetylase, lipoprotein (RefSeq) 96, 239
BSU39000 yxjC putative permease (RefSeq) 55, 156
BSU40530 cotF spore coat protein (RefSeq) 96, 174
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 BSU13410
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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