Organism : Bacillus subtilis | Module List :
BSU08370 yfiR

transcriptional regulator (TetR/AcrR family) (RefSeq)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU08370
(Mouseover regulator name to see its description)

BSU08370 is regulated by 20 influences and regulates 7 modules.
Regulators for BSU08370 yfiR (20)
Regulator Module Operator
BSU00700 114 tf
BSU01430 114 tf
BSU01810 114 tf
BSU08250 114 tf
BSU08370 114 tf
BSU09330 114 tf
BSU09650 114 tf
BSU10560 114 tf
BSU15690 114 tf
BSU16600 114 tf
BSU24320 114 tf
BSU29630 114 tf
BSU38600 114 tf
BSU06960 152 tf
BSU07010 152 tf
BSU07590 152 tf
BSU08370 152 tf
BSU26870 152 tf
BSU28410 152 tf
BSU29690 152 tf

Warning: BSU08370 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
5182 2.80e+03 CCtCCT
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5183 9.30e+02 gCAcaCccCtT
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5254 3.00e+01 cGttTTTaATTgTATgggAAAaaG
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5255 1.10e+00 caaaaaAAaGAtTG
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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 BSU08370

BSU08370 is enriched for 5 functions in 3 categories.
Module neighborhood information for BSU08370

BSU08370 has total of 46 gene neighbors in modules 114, 152
Gene neighbors (46)
Gene Common Name Description Module membership
BSU03780 phrC secreted regulator of the activity of phosphatase RapC and competence and sporulation stimulating factor (CSF) (RefSeq) 114, 208
BSU05630 dinB nuclease inhibitor (RefSeq) 49, 114
BSU07580 citS two-component sensor histidine kinase (RefSeq) 152, 156
BSU07590 citT two-component response regulator (RefSeq) 152, 156
BSU07600 yflP hypothetical protein (RefSeq) 152, 156
BSU08010 yfjP putative DNA-modified purine glycosidase (RefSeq) 114, 168
BSU08250 yfiF putative transcriptional regulator (AraC/XylS family; cupin family) (RefSeq) 114, 171
BSU08370 yfiR transcriptional regulator (TetR/AcrR family) (RefSeq) 114, 152
BSU08380 yfiS putative efflux transporter (RefSeq) 152, 318
BSU08390 yfiT metal-dependent hydrolase (RefSeq) 145, 152
BSU08870 ygaN putative sulfur oxidoreductase (RefSeq) 46, 114
BSU09200 yhcS putative secreted enzyme; sortase (RefSeq) 114, 208
BSU09320 yhcY two-component sensor histidine kinase [YhcZ] (RefSeq) 114, 318
BSU09330 yhcZ two-component response regulator [YhcY] (RefSeq) 114, 318
BSU10300 aprE serine alkaline protease (subtilisin E) (RefSeq) 114, 287
BSU10980 yitG putative efflux transporter (RefSeq) 152, 326
BSU12210 yjiB putative monooxygenase (cytochrome P450) (RefSeq) 101, 114
BSU12220 yjiC putative glycosyltransferase (RefSeq) 101, 114
BSU12300 uxaC glucuronate isomerase (RefSeq) 152, 180
BSU12310 exuM putative Na+:altronate/mannonate symporter (RefSeq) 152, 180
BSU17250 ymaE putative hydrolase (RefSeq) 114, 359
BSU18780 yoaW biofilm forming exported protein (RefSeq) 25, 114
BSU19020 yobN putative amine oxidase (RefSeq) 114, 157
BSU22090 kdgT 2-keto-3-deoxygluconate permease (RefSeq) 152, 168
BSU22100 kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase (RefSeq) 152, 168
BSU22110 kdgK 2-keto-3-deoxygluconate kinase (RefSeq) 152, 168
BSU25840 phrE regulator of the activity of phosphatase RapE (RefSeq) 25, 114
BSU25880 yqxJ hypothetical protein; skin element (RefSeq) 114, 208
BSU25890 yqxI hypothetical protein; skin element (RefSeq) 114, 208
BSU26860 yraO putative citrate transporter (RefSeq) 152, 168
BSU26870 yraN putative transcriptional regulator (LysR family) (RefSeq) 152, 168
BSU28720 abfA alpha-L-arabinofuranosidase (RefSeq) 152, 250
BSU28770 araL putative phosphatase (RefSeq) 152, 250
BSU28790 araB ribulokinase (RefSeq) 152, 250
BSU28800 araA L-arabinose isomerase (RefSeq) 152, 250
BSU32540 bsn extracellular ribonuclease (RefSeq) 114, 208
BSU34120 ganB secreted arabinogalactan oligomer endo-hydrolase (RefSeq) 152, 156
BSU34130 ganA arabinogalactan type I oligomer exo-hydrolase (beta-galactosidase, lactase) (RefSeq) 10, 152
BSU34140 ganQ arabinogalactan oligomer permease (RefSeq) 152, 156
BSU34150 ganP arabinogalactan oligomer permease (RefSeq) 152, 156
BSU34160 cycB cyclodextrin-binding lipoprotein (RefSeq) 152, 156
BSU37030 racA polar chromosome segregation protein (RefSeq) 25, 114
BSU38600 licR transcriptional activator of the lichenan operon (RefSeq) 114, 208
BSU40180 yydF peptide controlling LiaRS (RefSeq) 114, 359
BSU40290 yycN putative N-acetyltransferase (RefSeq) 114, 287
BSU40630 yybI inner spore coat protein (RefSeq) 114, 287
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 BSU08370
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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