Organism : Bacillus subtilis | Module List :
BSU18420 ftsR

transcriptional regulator (LysR family) (RefSeq)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU18420
(Mouseover regulator name to see its description)

BSU18420 is regulated by 20 influences and regulates 7 modules.
Regulators for BSU18420 ftsR (20)
Regulator Module Operator
BSU03960 51 tf
BSU09560 51 tf
BSU18420 51 tf
BSU19200 51 tf
BSU21780 51 tf
BSU24520 51 tf
BSU25100 51 tf
BSU28820 51 tf
BSU36440 51 tf
BSU40350 51 tf
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

Warning: BSU18420 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
5060 9.20e-04 aaaAGGaG
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5061 1.10e+01 AGCtGTTtTcT
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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 BSU18420

BSU18420 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BSU18420

BSU18420 has total of 48 gene neighbors in modules 51, 226
Gene neighbors (48)
Gene Common Name Description Module membership
BSU01000 secE preprotein translocase subunit SecE (RefSeq) 191, 226
BSU02410 mmuM homocysteine methyltransferase (RefSeq) 71, 226
BSU03940 ycnI hypothetical protein (RefSeq) 4, 51
BSU03950 ycnJ putative copper import protein (RefSeq) 4, 51
BSU03960 ycnK putative transcriptional regulator (DeoR family) (RefSeq) 4, 51
BSU03970 ycnL putative reductase or disulfide isomerase (RefSeq) 151, 226
BSU05620 ydgF putative amino acid permease (RefSeq) 226, 258
BSU07380 yfmQ hypothetical protein (RefSeq) 4, 51
BSU12100 yjeA secreted deoxyriboendonuclease (RefSeq) 49, 51
BSU12671 BSU12671 None 51, 176
BSU13370 ykoQ putative metallophosphoesterase (RefSeq) 115, 226
BSU14630 speA arginine decarboxylase (RefSeq) 51, 170
BSU14870 ctaA heme-A synthase (RefSeq) 51, 189
BSU14880 ctaB protoheme IX farnesyltransferase (RefSeq) 51, 379
BSU18420 ftsR transcriptional regulator (LysR family) (RefSeq) 51, 226
BSU18430 yogA putative oxidoreductase (RefSeq) 226, 334
BSU18790 yoaZ putative factor of the oxidative stress response (RefSeq) 115, 226
BSU19140 yozB putative integral inner membrane protein (RefSeq) 51, 379
BSU19170 yocD putative carboxypeptidase (RefSeq) 51, 170
BSU21780 yplP transcriptional enhancer (RefSeq) 159, 226
BSU21790 yplQ putative membrane hydrolase (RefSeq) 51, 191
BSU22010 exoA 5'3'-exonuclease (RefSeq) 216, 226
BSU22970 ypbH adaptor protein (RefSeq) 51, 216
BSU23010 ypbD putative membrane protease (RefSeq) 151, 226
BSU23050 fmnP FMN permease (RefSeq) 51, 54
BSU23230 ypuF hypothetical protein (RefSeq) 94, 226
BSU23650 yqkC hypothetical protein (RefSeq) 51, 82
BSU23870 yqjH DNA polymerase IV (RefSeq) 51, 226
BSU23880 yqzJ hypothetical protein (RefSeq) 51, 226
BSU23890 yqjG OxaA-like protein precursor (RefSeq) 51, 226
BSU25100 zur transcriptional regulator (Fur family) (RefSeq) 51, 226
BSU25160 ispH 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (RefSeq) 226, 266
BSU26550 yrkD hypothetical protein (RefSeq) 51, 216
BSU26620 yrdR putative efflux transporter (RefSeq) 157, 226
BSU26630 yrdQ putative transcriptional regulator (LysR family) (RefSeq) 216, 226
BSU27540 yrvM putative enzyme of sulfur-containing coenzyme synthesis (RefSeq) 51, 161
BSU28600 yshB putative integral inner membrane protein (RefSeq) 216, 226
BSU28610 yshA cell division protein ZapA (RefSeq) 200, 226
BSU30350 yttB putative efflux transporter (RefSeq) 51, 291
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
BSU36440 ywoH putative transcriptional regulator (MarR family) (RefSeq) 51, 216
BSU36450 ywoG putative efflux transporter (RefSeq) 51, 216
BSU36590 clsA cardiolipin synthase (RefSeq) 66, 226
BSU36790 ywmA hypothetical protein (RefSeq) 51, 291
BSU39010 yxjB putative ribosomal RNA methyltransferase (RefSeq) 51, 159
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 BSU18420
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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