Organism : Bacillus subtilis | Module List :
BSU08300 yfiK

two-component response regulator [YfiJ] (RefSeq)

CircVis
Functional Annotations (7)
Function System
Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU08300
(Mouseover regulator name to see its description)

BSU08300 is regulated by 21 influences and regulates 9 modules.
Regulators for BSU08300 yfiK (21)
Regulator Module Operator
BSU01010 48 tf
BSU08300 48 tf
BSU15970 48 tf
BSU23210 48 tf
BSU24250 48 tf
BSU29740 48 tf
BSU30020 48 tf
BSU30460 48 tf
BSU33080 48 tf
BSU33990 48 tf
BSU35050 48 tf
BSU39990 48 tf
BSU04730 307 tf
BSU08300 307 tf
BSU12560 307 tf
BSU18760 307 tf
BSU26320 307 tf
BSU26340 307 tf
BSU34220 307 tf
BSU38070 307 tf
BSU40990 307 tf

Warning: BSU08300 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
5054 2.10e+03 AAagaGCCGGg
Loader icon
5055 5.00e+01 ataAaAAAAGc
Loader icon
5552 1.70e+01 aAGGaG
Loader icon
5553 1.10e+05 GCGcGG
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 BSU08300

BSU08300 is enriched for 7 functions in 3 categories.
Module neighborhood information for BSU08300

BSU08300 has total of 45 gene neighbors in modules 48, 307
Gene neighbors (45)
Gene Common Name Description Module membership
BSU00410 rnmV ribonuclease M5 (RefSeq) 48, 397
BSU00420 ksgA dimethyladenosine transferase (RefSeq) 48, 397
BSU01580 ybaR putative permease (RefSeq) 48, 397
BSU02710 yczC putative integral inner membrane protein (RefSeq) 96, 307
BSU03340 yciA putative GTP cyclohydrolase (RefSeq) 307, 406
BSU04110 lipC lysophopholipase (RefSeq) 11, 307
BSU05930 rimI ribosomal protein S18 alanine N-acetyltransferase (RefSeq) 1, 48
BSU06870 yesE hypothetical protein (RefSeq) 307, 361
BSU08230 catD catechol-2,3-dioxygenase membrane subunit (RefSeq) 178, 307
BSU08240 catE catechol-2,3-dioxygenase subunit (RefSeq) 238, 307
BSU08290 yfiJ two-component sensor histidine kinase [YfiK] (RefSeq) 132, 307
BSU08300 yfiK two-component response regulator [YfiJ] (RefSeq) 48, 307
BSU10170 fabHB 3-oxoacyl-(acyl carrier protein) synthase III (RefSeq) 307, 411
BSU11040 yitM hypothetical protein (RefSeq) 217, 307
BSU11320 yjzB hypothetical protein (RefSeq) 307, 411
BSU16920 pgsA CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase (RefSeq) 48, 245
BSU16930 cinA competence damage-inducible protein A (RefSeq) 48, 245
BSU19650 yodM putative phospholipid phosphatase (RefSeq) 48, 319
BSU21310 yozP hypothetical protein; phage SPbeta (RefSeq) 174, 307
BSU21530 yolB conserved hypothetical protein; phage SPbeta (RefSeq) 298, 307
BSU21540 yolA exported protein of unknown function; phage SPbeta (RefSeq) 298, 307
BSU25670 yqeH GTP-binding protein YqeH (RefSeq) 48, 314
BSU25680 yqeG putative hydrolase (RefSeq) 48, 314
BSU26740 cypA cytochrome P450 (RefSeq) 280, 307
BSU29720 ytxE flagellar motor protein MotS (RefSeq) 48, 202
BSU29730 ytxD flagellar motor protein MotP (RefSeq) 48, 190
BSU31090 ktrA potassium uptake protein (RefSeq) 48, 397
BSU32070 yuiC hypothetical protein (RefSeq) 291, 307
BSU32650 yurS hypothetical protein (RefSeq) 280, 307
BSU33080 liaR two-component response regulator [YvqE] responding to cell wall stress (RefSeq) 48, 319
BSU33090 liaS two-component sensor histidine kinase [YvqC] sensing cell wall stress (RefSeq) 48, 319
BSU33150 yvqK ATP:cob(I)alamin adenosyltransferase (RefSeq) 1, 48
BSU33160 yvrA putative vitamin B12 transport system, ATPase component (RefSeq) 48, 190
BSU33170 yvrB putative vitamin B12 permease (RefSeq) 1, 48
BSU33180 yvrC putative lipoprotein binding vitamin B12 (RefSeq) 48, 63
BSU34000 cyeB cysteine and O-acetylserine efflux permease (RefSeq) 96, 307
BSU35280 yvjA putative integral inner membrane protein (RefSeq) 307, 411
BSU35770 tagC putative polyglycerol phosphate assembly and export protein (teichoic acid biosynthesis) (RefSeq) 239, 307
BSU36480 ywoD putative efflux transporter (RefSeq) 50, 307
BSU36490 ywoC putative hydrolase (RefSeq) 50, 307
BSU36500 ywoB putative integral inner membrane protein (RefSeq) 130, 307
BSU37490 speB agmatinase (RefSeq) 48, 190
BSU37590 ywgA hypothetical protein (RefSeq) 48, 322
BSU37600 ywfO putative metal-dependent phosphohydrolase (RefSeq) 48, 322
BSU38250 ywbO putative sulfur oxido-reductase (RefSeq) 96, 307
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 BSU08300
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