Organism : Bacillus subtilis | Module List :
BSU36020 alsR

transcriptional regulator (LysR family) (RefSeq)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU36020
(Mouseover regulator name to see its description)

BSU36020 is regulated by 32 influences and regulates 33 modules.
Regulators for BSU36020 alsR (32)
Regulator Module Operator
BSU01010 412 tf
BSU04680 412 tf
BSU05270 412 tf
BSU10510 412 tf
BSU11500 412 tf
BSU13150 412 tf
BSU13760 412 tf
BSU15970 412 tf
BSU21020 412 tf
BSU33080 412 tf
BSU33740 412 tf
BSU36020 412 tf
BSU38070 412 tf
BSU39850 412 tf
BSU40350 412 tf
BSU40540 412 tf
BSU00230 68 tf
BSU00830 68 tf
BSU02890 68 tf
BSU04160 68 tf
BSU04680 68 tf
BSU04730 68 tf
BSU05120 68 tf
BSU05580 68 tf
BSU25490 68 tf
BSU27170 68 tf
BSU31530 68 tf
BSU36020 68 tf
BSU37650 68 tf
BSU38600 68 tf
BSU39990 68 tf
BSU40050 68 tf

Warning: BSU36020 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
5092 5.00e-03 AaGGAggg
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5093 1.90e+03 ccTtcTTTcca
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5728 2.30e+00 CCtCCtcc
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5729 8.40e+02 CGGGCAGct.TctTtAAAACg
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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 BSU36020

BSU36020 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BSU36020

BSU36020 has total of 47 gene neighbors in modules 68, 412
Gene neighbors (47)
Gene Common Name Description Module membership
BSU00250 xpaC putative phosphatase (RefSeq) 54, 68
BSU00830 ctsR transcriptional regulator (RefSeq) 68, 388
BSU00840 mcsA activator of protein kinase McsB (RefSeq) 68, 388
BSU00850 mcsB ATP:guanido phosphotransferase (RefSeq) 68, 388
BSU00860 clpC class III stress response-related ATPase, AAA+ superfamily (RefSeq) 68, 388
BSU00870 radA DNA repair protein RadA (RefSeq) 68, 388
BSU00880 yacK DNA integrity scanning protein DisA (RefSeq) 68, 388
BSU03030 ycgB putative integral inner membrane protein (RefSeq) 262, 412
BSU03040 amyE alpha-amylase (RefSeq) 68, 341
BSU03860 ycnD NADPH-FMN oxidoreductase (nitroreductase) (RefSeq) 68, 77
BSU03870 ycnE hypothetical protein (RefSeq) 68, 77
BSU03910 gabD succinate-semialdehyde dehydrogenase (RefSeq) 259, 412
BSU04210 ydaF putative ribosomal protein N-acetyltransferase (RefSeq) 68, 101
BSU10100 yhgC hypothetical protein (RefSeq) 113, 412
BSU10260 yhfK putative epimerase (RefSeq) 252, 412
BSU11160 yitW hypothetical protein (RefSeq) 398, 412
BSU11540 pepF oligoendopeptidase F (RefSeq) 90, 412
BSU12870 mhqA putative hydroquinone-specific extradiol dioxygenase (RefSeq) 50, 412
BSU16860 ymfH putative processing protease (RefSeq) 68, 252
BSU24210 yqiG putative NADH-dependent flavin oxidoreductase (RefSeq) 259, 412
BSU25470 dnaK molecular chaperone DnaK (RefSeq) 68, 388
BSU25480 grpE heat shock protein GrpE (RefSeq) 68, 388
BSU25490 hrcA heat-inducible transcription repressor (RefSeq) 68, 388
BSU27020 yraA general stress protein (RefSeq) 259, 412
BSU29410 ytkL metal-dependent hydrolase (RefSeq) 68, 296
BSU29850 ytoQ putative enzyme with sugar binding fold (RefSeq) 68, 398
BSU29870 ytzB hypothetical protein (RefSeq) 398, 412
BSU30510 ytpA phospholipase component of bacilysocin synthesis or export (RefSeq) 68, 398
BSU30580 ytmA putative hydrolase (RefSeq) 77, 412
BSU32370 yunD putative nuclease/nucleotidase/phosphoesterase (RefSeq) 68, 252
BSU32380 yunE putative integral inner membrane protein (RefSeq) 68, 252
BSU32390 yunF hypothetical protein (RefSeq) 68, 252
BSU32400 yunG hypothetical protein (RefSeq) 68, 252
BSU33400 yvgN glyoxal/methylglyoxal reductase (RefSeq) 259, 412
BSU34540 clpP ATP-dependent Clp protease proteolytic subunit (RefSeq) 68, 70
BSU35160 uvrA excinuclease ABC subunit A (RefSeq) 54, 68
BSU35170 uvrB excinuclease ABC subunit B (RefSeq) 54, 68
BSU36020 alsR transcriptional regulator (LysR family) (RefSeq) 68, 412
BSU36080 ywrF hypothetical protein (RefSeq) 109, 412
BSU36520 glnK nitrogen-regulated PII-like regulator protein (RefSeq) 68, 101
BSU36580 ywnF hypothetical protein (RefSeq) 381, 412
BSU37670 ywfI putative heme peroxidase (RefSeq) 381, 412
BSU38100 ywcH putative monooxygenase (RefSeq) 259, 412
BSU38110 nfrA FMN-containing NADPH-linked nitro/flavin reductase (RefSeq) 381, 412
BSU39080 licT transcriptional antiterminator (BglG family) (RefSeq) 68, 91
BSU39540 yxeI putative hydrolase (RefSeq) 259, 412
BSU40040 glxK glycerate kinase (RefSeq) 68, 296
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 BSU36020
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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