Organism : Bacillus subtilis | Module List :
BSU26730 yrdF

putative ribonuclease inhibitor (RefSeq)

CircVis
Functional Annotations (1)
Function System
Barstar, RNAse (barnase) inhibitor cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU26730
(Mouseover regulator name to see its description)

BSU26730 is regulated by 17 influences and regulates 7 modules.
Regulators for BSU26730 yrdF (17)
Regulator Module Operator
BSU02370 142 tf
BSU06540 142 tf
BSU06700 142 tf
BSU07010 142 tf
BSU07820 142 tf
BSU09500 142 tf
BSU13670 142 tf
BSU18740 142 tf
BSU26730 142 tf
BSU35030 142 tf
BSU37080 142 tf
BSU02070 295 tf
BSU05970 295 tf
BSU17590 295 tf
BSU17850 295 tf
BSU26730 295 tf
BSU35030 295 tf

Warning: BSU26730 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
5234 2.60e+03 GGAGGaAA
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5235 1.10e+04 AACaCAGCtgGC.G
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5528 1.60e+01 CCTCC.
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5529 3.10e+04 tTttTCtT
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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 BSU26730

BSU26730 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Barstar, RNAse (barnase) inhibitor cog/ cog
Module neighborhood information for BSU26730

BSU26730 has total of 40 gene neighbors in modules 142, 295
Gene neighbors (40)
Gene Common Name Description Module membership
BSU02070 csgA sporulation-specific SASP protein (RefSeq) 295, 358
BSU02200 ybfG putative pepdidoglycan binding protein (RefSeq) 295, 364
BSU02420 glnT glutamine transporter (RefSeq) 295, 305
BSU02790 ycdB putative hydrolase (RefSeq) 135, 142
BSU05780 ydhJ putative metal-dependent phosphohydrolase (RefSeq) 142, 205
BSU05800 pbuE hypoxanthine efflux transporter (RefSeq) 10, 142
BSU06310 gabP gamma-aminobutyrate (GABA) permease (RefSeq) 201, 295
BSU06330 yeaC hypothetical protein (RefSeq) 66, 142
BSU06340 yeaD hypothetical protein (RefSeq) 66, 142
BSU06390 yebD hypothetical protein (RefSeq) 189, 295
BSU06640 yerI putative kinase (RefSeq) 201, 295
BSU06660 opuE proline transporter (RefSeq) 142, 294
BSU06760 yeeA putative restriction type II methylase (RefSeq) 67, 142
BSU08140 yfjD putative integral inner membrane protein (RefSeq) 124, 295
BSU08770 ygzA hypothetical protein (RefSeq) 295, 395
BSU09030 yhcC hypothetical protein (RefSeq) 86, 295
BSU09090 yhcI putative ABC transporter (permease) (RefSeq) 75, 142
BSU09340 yhdA oxidoreductase, NAD(P)H-FMN and ferric iron reductase (RefSeq) 295, 372
BSU09850 yhaU transporter involved in K+ efflux (RefSeq) 295, 395
BSU10220 gltT proton/sodium-glutamate symport protein (RefSeq) 142, 154
BSU10330 yhfQ putative iron(III) dicitrate-binding lipoprotein (RefSeq) 93, 295
BSU14430 ykpA ABC efflux transporter (ATP-binding protein) (RefSeq) 142, 258
BSU15940 smc chromosome condensation and segregation SMC ATPase (RefSeq) 142, 245
BSU17470 ynxB hypothetical protein (RefSeq) 201, 295
BSU17590 xylR transcriptional regulator (RefSeq) 201, 295
BSU17870 yneB putative cell division protein (RefSeq) 207, 295
BSU17910 yneF hypothetical protein (RefSeq) 142, 301
BSU18130 eglS endo-1,4-beta-glucanase (RefSeq) 20, 295
BSU18150 xynC endo-xylanase (RefSeq) 8, 295
BSU18160 xynD endo-1,4-beta-xylanase (xylanase D) (RefSeq) 201, 295
BSU22130 kduI 5-keto-4-deoxyuronate isomerase (RefSeq) 142, 168
BSU22510 ypjC putative integral inner membrane protein (RefSeq) 142, 154
BSU26730 yrdF putative ribonuclease inhibitor (RefSeq) 142, 295
BSU27480 yrrC putative exonuclease with DNA/RNA helicase motif (RefSeq) 135, 142
BSU27680 yrbG hypothetical protein (RefSeq) 295, 395
BSU30630 ytkD nucleoside triphosphate phosphohydrolase (RefSeq) 20, 142
BSU36690 rapB response regulator aspartate phosphatase (RefSeq) 26, 295
BSU37060 tdk thymidine kinase (RefSeq) 89, 142
BSU39570 yxeF hypothetical protein (RefSeq) 142, 233
BSU39970 yxaH putative integral inner membrane protein (RefSeq) 142, 175
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 BSU26730
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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