Organism : Bacillus subtilis | Module List :
BSU05970 ydiH

redox-sensing transcriptional repressor Rex (RefSeq)

CircVis
Functional Annotations (5)
Function System
AT-rich DNA-binding protein cog/ cog
cytoplasm go/ cellular_component
transcription repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
response to redox state go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU05970
(Mouseover regulator name to see its description)

BSU05970 is regulated by 17 influences and regulates 30 modules.
Regulators for BSU05970 ydiH (17)
Regulator Module Operator
BSU02320 207 tf
BSU05970 207 tf
BSU06540 207 tf
BSU15320 207 tf
BSU17590 207 tf
BSU17850 207 tf
BSU26340 207 tf
BSU35030 207 tf
BSU36600 207 tf
BSU02000 201 tf
BSU02160 201 tf
BSU05970 201 tf
BSU07820 201 tf
BSU09380 201 tf
BSU17590 201 tf
BSU17850 201 tf
BSU30150 201 tf

Warning: BSU05970 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
5346 1.50e+03 TGcaGAAgAcagcttGG
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5347 6.70e+03 CCGGCGGC
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5358 4.30e-03 G.TTaTaAgAaaagtatAtc
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5359 1.90e+00 cCTcCaacAgGaAaGTttGtccG
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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 BSU05970

BSU05970 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
AT-rich DNA-binding protein cog/ cog
cytoplasm go/ cellular_component
transcription repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
response to redox state go/ biological_process
Module neighborhood information for BSU05970

BSU05970 has total of 35 gene neighbors in modules 201, 207
Gene neighbors (35)
Gene Common Name Description Module membership
BSU05960 moaC molybdenum cofactor biosynthesis protein MoaC (RefSeq) 95, 201
BSU05970 ydiH redox-sensing transcriptional repressor Rex (RefSeq) 201, 207
BSU05980 tatAY component of the twin-arginine pre-protein translocation pathway (RefSeq) 207, 310
BSU05990 tatCY component of the twin-arginine pre-protein translocation pathway (RefSeq) 201, 207
BSU06290 yeaA hypothetical protein (RefSeq) 201, 207
BSU06310 gabP gamma-aminobutyrate (GABA) permease (RefSeq) 201, 295
BSU06320 yeaB putative cation efflux transporter (RefSeq) 201, 395
BSU06640 yerI putative kinase (RefSeq) 201, 295
BSU07170 yetI hypothetical protein (RefSeq) 154, 201
BSU09930 yhaM 3'-5' exoribonuclease YhaM (RefSeq) 154, 201
BSU10270 yhfL long-chain-fatty-acid--CoA ligase (RefSeq) 10, 201
BSU10290 yhfN putative membrane metalloprotease (RefSeq) 20, 201
BSU10570 yhjN putative integral inner membrane protein (RefSeq) 201, 207
BSU10710 gerPB spore germination protein (RefSeq) 207, 358
BSU10720 gerPA spore germination protein (RefSeq) 207, 358
BSU17350 ymzC hypothetical protein (RefSeq) 201, 364
BSU17420 spoVK mother cell sporulation ATPase (RefSeq) 207, 358
BSU17470 ynxB hypothetical protein (RefSeq) 201, 295
BSU17490 ynzG hypothetical protein (RefSeq) 39, 207
BSU17530 ynaE hypothetical protein (RefSeq) 207, 364
BSU17550 ynaG hypothetical protein (RefSeq) 207, 364
BSU17590 xylR transcriptional regulator (RefSeq) 201, 295
BSU17850 lexA LexA repressor (RefSeq) 83, 207
BSU17860 yneA cell division suppressor protein YneA (RefSeq) 74, 207
BSU17870 yneB putative cell division protein (RefSeq) 207, 295
BSU17930 ccdA cytochrome c-type biogenesis protein CcdA; thiol-disulfide oxido-reductase (RefSeq) 83, 207
BSU17950 yneJ putative integral inner membrane protein (RefSeq) 83, 201
BSU17970 cotM spore coat protein (outer) (RefSeq) 207, 358
BSU18080 yneT putative CoA-binding protein (RefSeq) 20, 201
BSU18140 ynfE hypothetical protein (RefSeq) 20, 207
BSU18160 xynD endo-1,4-beta-xylanase (xylanase D) (RefSeq) 201, 295
BSU18200 yngD putative ribonuclease (RefSeq) 207, 358
BSU27240 yrhC hypothetical protein (RefSeq) 95, 201
BSU36060 cotH spore coat protein (inner) (RefSeq) 207, 358
BSU37360 sboX putative bacteriocin-like product (RefSeq) 189, 201
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 BSU05970
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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