Organism : Bacillus subtilis | Module List :
BSU21780 yplP

transcriptional enhancer (RefSeq)

CircVis
Functional Annotations (6)
Function System
Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain cog/ cog
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU21780
(Mouseover regulator name to see its description)

BSU21780 is regulated by 20 influences and regulates 10 modules.
Regulators for BSU21780 yplP (20)
Regulator Module Operator
BSU02680 226 tf
BSU05180 226 tf
BSU08340 226 tf
BSU18420 226 tf
BSU19200 226 tf
BSU21780 226 tf
BSU25100 226 tf
BSU26630 226 tf
BSU28400 226 tf
BSU36440 226 tf
BSU01730 159 tf
BSU05120 159 tf
BSU11300 159 tf
BSU11930 159 tf
BSU13310 159 tf
BSU21780 159 tf
BSU23090 159 tf
BSU23100 159 tf
BSU35840 159 tf
BSU36440 159 tf

Warning: BSU21780 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
5266 2.50e+03 C..TTtTttgT
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5267 4.60e+04 GaaGAaGgg.cTTT
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5396 1.00e-04 atcactttt.TtcATTtTAct.ta
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5397 8.60e-02 CTCCTTTTCttTaAattgACA
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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 BSU21780

BSU21780 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain cog/ cog
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
Module neighborhood information for BSU21780

BSU21780 has total of 57 gene neighbors in modules 159, 226
Gene neighbors (57)
Gene Common Name Description Module membership
BSU01000 secE preprotein translocase subunit SecE (RefSeq) 191, 226
BSU01730 sigW RNA polymerase sigma factor SigW (RefSeq) 159, 166
BSU01740 rsiW anti-sigma(W) factor (RefSeq) 159, 166
BSU02410 mmuM homocysteine methyltransferase (RefSeq) 71, 226
BSU03970 ycnL putative reductase or disulfide isomerase (RefSeq) 151, 226
BSU05120 cspC cold-shock protein (RefSeq) 151, 159
BSU05200 ydeH putative integral inner membrane protein (RefSeq) 115, 159
BSU05620 ydgF putative amino acid permease (RefSeq) 226, 258
BSU06270 ydjO hypothetical protein (RefSeq) 159, 266
BSU11300 med positive regulator of comK (RefSeq) 14, 159
BSU11920 yjcN hypothetical protein (RefSeq) 36, 159
BSU11930 yjcO putative DNA binding protein (RefSeq) 36, 159
BSU12040 yjdG putative acetyltransferase (RefSeq) 49, 159
BSU13320 ykzB hypothetical protein (RefSeq) 159, 216
BSU13370 ykoQ putative metallophosphoesterase (RefSeq) 115, 226
BSU14990 ylbF putative regulatory protein (RefSeq) 159, 170
BSU17060 ymzD putative integral inner membrane protein (RefSeq) 115, 159
BSU17230 pksS cytochrome P450 of bacillaene metabolism (RefSeq) 36, 159
BSU18420 ftsR transcriptional regulator (LysR family) (RefSeq) 51, 226
BSU18430 yogA putative oxidoreductase (RefSeq) 226, 334
BSU18650 pelB pectin lyase (RefSeq) 159, 179
BSU18790 yoaZ putative factor of the oxidative stress response (RefSeq) 115, 226
BSU18980 yobJ hypothetical protein (RefSeq) 159, 166
BSU21670 BSU21670 None 25, 159
BSU21780 yplP transcriptional enhancer (RefSeq) 159, 226
BSU22010 exoA 5'3'-exonuclease (RefSeq) 216, 226
BSU23010 ypbD putative membrane protease (RefSeq) 151, 226
BSU23090 rsiX negative regulator of sigma(X) activity (RefSeq) 145, 159
BSU23100 sigX RNA polymerase sigma factor SigX (RefSeq) 145, 159
BSU23230 ypuF hypothetical protein (RefSeq) 94, 226
BSU23310 sipS type I signal peptidase (RefSeq) 94, 159
BSU23720 yqzH hypothetical protein (RefSeq) 159, 270
BSU23730 yqjV putative efflux transporter (RefSeq) 36, 159
BSU23870 yqjH DNA polymerase IV (RefSeq) 51, 226
BSU23880 yqzJ hypothetical protein (RefSeq) 51, 226
BSU23890 yqjG OxaA-like protein precursor (RefSeq) 51, 226
BSU25090 yqfW putative nucleotidase (RefSeq) 151, 159
BSU25100 zur transcriptional regulator (Fur family) (RefSeq) 51, 226
BSU25160 ispH 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (RefSeq) 226, 266
BSU25560 holA DNA polymerase III subunit delta (RefSeq) 151, 159
BSU25690 sda check point factor coupling initiation of sporulation and replication initiation (RefSeq) 36, 159
BSU25700 yqeF putative lipoprotein; putative esterase (RefSeq) 121, 159
BSU26610 yrkA putative membrane associated protein (RefSeq) 159, 170
BSU26620 yrdR putative efflux transporter (RefSeq) 157, 226
BSU26630 yrdQ putative transcriptional regulator (LysR family) (RefSeq) 216, 226
BSU28600 yshB putative integral inner membrane protein (RefSeq) 216, 226
BSU28610 yshA cell division protein ZapA (RefSeq) 200, 226
BSU35530 tagO UDP-N-acetylglucosamine:undecaprenyl-P N-acetylglucosaminyl-1-P transferase (RefSeq) 151, 226
BSU35740 tagD glycerol-3-phosphate cytidylyltransferase (RefSeq) 216, 226
BSU35750 tagA N-acetylmannosamine (ManNAc) C4 hydroxyl of a membrane-anchored N-acetylglucosaminyl diphospholipid (GlcNAc-pp-undecaprenyl, lipid I) glycosyltransferase (RefSeq) 51, 226
BSU35760 tagB teichoic acid primase, CDP-glycerol:N-acetyl-beta-d-mannosaminyl-1, 4-N-acetyl-d-glucosaminyldiphosphoundecaprenyl glycerophosphotransferase (RefSeq) 226, 266
BSU35840 ywtF putative transcriptional regulator (RefSeq) 159, 170
BSU36590 clsA cardiolipin synthase (RefSeq) 66, 226
BSU39010 yxjB putative ribosomal RNA methyltransferase (RefSeq) 51, 159
BSU39240 yxxF putative transporter (RefSeq) 159, 350
BSU40470 yycC hypothetical protein (RefSeq) 159, 191
BSU40480 yycB putative anion ABC transporter (permease) (RefSeq) 159, 191
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 BSU21780
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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