Organism : Bacillus subtilis | Module List :
BSU23590 ansR

transcriptional regulator of ansAB (Xre family) (RefSeq)

CircVis
Functional Annotations (1)
Function System
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU23590
(Mouseover regulator name to see its description)

BSU23590 is regulated by 22 influences and regulates 4 modules.
Regulators for BSU23590 ansR (22)
Regulator Module Operator
BSU08340 258 tf
BSU08520 258 tf
BSU12370 258 tf
BSU12510 258 tf
BSU13310 258 tf
BSU17080 258 tf
BSU21780 258 tf
BSU23590 258 tf
BSU32140 258 tf
BSU32420 258 tf
BSU33660 258 tf
BSU33670 258 tf
BSU33790 258 tf
BSU08520 151 tf
BSU13880 151 tf
BSU14990 151 tf
BSU19100 151 tf
BSU19200 151 tf
BSU23590 151 tf
BSU24520 151 tf
BSU25100 151 tf
BSU33740 151 tf

Warning: BSU23590 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
5252 7.70e-05 Tgagaat.aTTataA.ATaAg
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5253 9.00e+01 AGaAAggaA.G
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5456 2.90e-07 gtTgtgttacAataA.aGA.a.gG
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5457 4.90e+00 AGcGAATaacTTCTCtcaaCC
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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 BSU23590

BSU23590 is enriched for 1 functions in 2 categories.
Enrichment Table (1)
Function System
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for BSU23590

BSU23590 has total of 61 gene neighbors in modules 151, 258
Gene neighbors (61)
Gene Common Name Description Module membership
BSU03670 dtpT di-tripeptide-proton ABC symporter (RefSeq) 258, 315
BSU03750 yclJ two-component response regulator [YclK] (RefSeq) 37, 258
BSU03760 yclK two-component sensor histidine kinase [YclJ] (RefSeq) 37, 258
BSU03970 ycnL putative reductase or disulfide isomerase (RefSeq) 151, 226
BSU04770 ydcH putative transcriptional regulator (RefSeq) 151, 258
BSU05120 cspC cold-shock protein (RefSeq) 151, 159
BSU05290 ydeP putative transcriptional regulator (RefSeq) 151, 200
BSU05300 ydeQ putative NAD(P)H oxidoreductase (RefSeq) 151, 161
BSU05620 ydgF putative amino acid permease (RefSeq) 226, 258
BSU07330 yfnB putative hydrolase (RefSeq) 215, 258
BSU07390 yfmP transcriptional regulator (MerR family) of metal efflux transporter expression (RefSeq) 161, 258
BSU07490 yfmF iron-dicitrate ABC transporter (ATP-binding protein) (RefSeq) 31, 151
BSU07500 yfmE iron-dicitrate ABC transporter (permease) (RefSeq) 66, 151
BSU07670 yflI hypothetical protein (RefSeq) 123, 151
BSU08340 padR transcriptional regulator (RefSeq) 216, 258
BSU08520 recX recombination regulator RecX (RefSeq) 94, 258
BSU09610 yhdV integral membrane protein possibly involved in chromosome condensation (RefSeq) 94, 258
BSU09620 yhdW putative glycerophosphodiester phosphodiesterase (RefSeq) 23, 258
BSU12510 xre Phage PBSX transcriptional regulator (RefSeq) 191, 258
BSU13310 tnrA nitrogen sensing transcriptional regulator (RefSeq) 216, 258
BSU13450 sigI putative RNA polymerase sigma factor SigI (RefSeq) 151, 379
BSU14080 ykuH hypothetical protein (RefSeq) 151, 157
BSU14420 ykoA hypothetical protein (RefSeq) 219, 258
BSU14430 ykpA ABC efflux transporter (ATP-binding protein) (RefSeq) 142, 258
BSU14830 ylaM glutaminase (RefSeq) 258, 323
BSU17080 pksA putative transcriptional regulator (RefSeq) 191, 258
BSU17620 yncB DNA nuclease, lipoprotein (RefSeq) 151, 379
BSU17730 yndB hypothetical protein (RefSeq) 258, 323
BSU22980 ypbG putative phosphoesterase (RefSeq) 94, 258
BSU23000 ypbE hypothetical protein (RefSeq) 151, 311
BSU23010 ypbD putative membrane protease (RefSeq) 151, 226
BSU23020 recQ ATP-dependent DNA helicase (RefSeq) 151, 311
BSU23030 ypbB hypothetical protein (RefSeq) 151, 311
BSU23040 fer ferredoxin (RefSeq) 94, 151
BSU23570 aspA aspartate ammonia-lyase (RefSeq) 258, 293
BSU23580 ansA exported L-asparaginase (RefSeq) 258, 293
BSU23590 ansR transcriptional regulator of ansAB (Xre family) (RefSeq) 151, 258
BSU25070 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (RefSeq) 151, 200
BSU25090 yqfW putative nucleotidase (RefSeq) 151, 159
BSU25560 holA DNA polymerase III subunit delta (RefSeq) 151, 159
BSU27800 yrzH hypothetical protein (RefSeq) 64, 258
BSU28180 ysxD putative integral inner membrane protein (RefSeq) 151, 270
BSU29920 ytmP putative kinase/phosphotransferase (RefSeq) 14, 151
BSU29970 ytkP putative cysteine synthase-like protein (RefSeq) 66, 151
BSU30070 opuD glycine betaine transporter (RefSeq) 14, 151
BSU30310 ytwF putative sulfur transferase (RefSeq) 258, 323
BSU32170 dapF diaminopimelate epimerase (RefSeq) 164, 258
BSU32420 pucR transcriptional regulator of the purine degradation operon (RefSeq) 257, 258
BSU33030 yuxN putative transcriptional regulator (RefSeq) 151, 216
BSU33370 yvgK putative molybdate binding regulator (RefSeq) 164, 258
BSU33660 rghRA transcriptional repressor (RefSeq) 49, 258
BSU33670 rghRB putative transcriptional repressor (RefSeq) 49, 258
BSU33680 yvaP putative transcriptional regulator (RefSeq) 49, 258
BSU33780 sdpI integral inner membrane regulator of autophagy (RefSeq) 191, 258
BSU33790 sdpR transcriptional regulator (ArsR family) (RefSeq) 191, 258
BSU34420 yveF hypothetical protein (RefSeq) 174, 258
BSU35530 tagO UDP-N-acetylglucosamine:undecaprenyl-P N-acetylglucosaminyl-1-P transferase (RefSeq) 151, 226
BSU37610 ywzC hypothetical protein (RefSeq) 151, 397
BSU38490 menA 1,4-dihydroxy-2-naphthoate octaprenyltransferase (RefSeq) 14, 151
BSU40720 yyaT putative acetyltransferase (RefSeq) 151, 270
BSU40730 yyaS putative integral inner membrane protein (RefSeq) 151, 270
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 BSU23590
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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