Organism : Bacillus subtilis | Module List :
BSU15970 ylxM

putative DNA-binding protein (RefSeq)

CircVis
Functional Annotations (5)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU15970
(Mouseover regulator name to see its description)

BSU15970 is regulated by 15 influences and regulates 28 modules.
Regulators for BSU15970 ylxM (15)
Regulator Module Operator
BSU01010 325 tf
BSU15970 325 tf
BSU16600 325 tf
BSU24320 325 tf
BSU33740 325 tf
BSU36020 325 tf
BSU01010 212 tf
BSU01070 212 tf
BSU04650 212 tf
BSU08990 212 tf
BSU15970 212 tf
BSU16170 212 tf
BSU23210 212 tf
BSU24250 212 tf
BSU25200 212 tf

Warning: BSU15970 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
5368 4.40e+03 CctAAAgGGA
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5369 1.90e+04 CGGGGA
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5588 1.60e+01 ta.ATaa.gggGAta
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5589 4.90e+02 CCTTTtTtatt
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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 BSU15970

BSU15970 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
Module neighborhood information for BSU15970

BSU15970 has total of 37 gene neighbors in modules 212, 325
Gene neighbors (37)
Gene Common Name Description Module membership
BSU00500 glmU bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase (RefSeq) 292, 325
BSU00510 prs ribose-phosphate pyrophosphokinase (RefSeq) 292, 325
BSU01010 nusG transcription antitermination protein NusG (RefSeq) 212, 397
BSU02270 pssA phosphatidylserine synthase (RefSeq) 66, 212
BSU02280 ybfM putative membrane phosphatase (RefSeq) 69, 212
BSU04650 endB antitoxin MazF (RefSeq) 212, 266
BSU04660 ndoA endoribonuclease toxin (RefSeq) 212, 266
BSU08450 yfiZ iron(III) siderophore transport permease (RefSeq) 93, 325
BSU08460 yfhA iron(III) siderophore transport permease (RefSeq) 93, 325
BSU09120 yhcK putative diguanylate cyclase or phosphodiesterase (RefSeq) 190, 325
BSU11820 yjcD putative ATP-dependent DNA helicase (RefSeq) 240, 325
BSU14770 bipA GTPase (RefSeq) 212, 374
BSU14780 ylaH hypothetical protein (RefSeq) 212, 397
BSU15970 ylxM putative DNA-binding protein (RefSeq) 212, 325
BSU15980 ffh signal recognition particle-like (SRP) GTPase (RefSeq) 212, 325
BSU15990 rpsP 30S ribosomal protein S16 (RefSeq) 212, 374
BSU16000 ylqC putative RNA binding protein (RefSeq) 116, 212
BSU16530 uppS undecaprenyl pyrophosphate synthase (RefSeq) 325, 343
BSU27990 minD ATPase activator of MinC (RefSeq) 212, 266
BSU28000 minC septum formation inhibitor (RefSeq) 212, 374
BSU30530 ytnA putative amino acid permease (RefSeq) 79, 325
BSU30540 asnB asparagine synthetase (RefSeq) 62, 325
BSU30550 metK S-adenosylmethionine synthetase (RefSeq) 325, 374
BSU30830 menF menaquinone-specific isochorismate synthase (RefSeq) 212, 272
BSU34690 yvcS putative ABC transporter (permease) (RefSeq) 73, 325
BSU34700 yvcR putative ABC transporter (ATP-binding protein) (RefSeq) 325, 339
BSU34710 yvcQ two-component sensor histidine kinase [YvcP] (RefSeq) 202, 325
BSU34720 yvcP two-component response regulator [YvcQ] (RefSeq) 325, 339
BSU35730 tagE UDP-glucose:polyglycerol phosphate alpha-glucosyltransferase (RefSeq) 212, 409
BSU36410 mbl rod shape-determining protein Mbl (RefSeq) 62, 325
BSU36760 murAA UDP-N-acetylglucosamine 1-carboxyvinyltransferase (RefSeq) 170, 325
BSU36770 ywmB hypothetical protein (RefSeq) 172, 325
BSU36780 ywzB hypothetical protein (RefSeq) 172, 325
BSU36880 atpI ATP synthase (subunit i) (RefSeq) 172, 325
BSU36890 upp uracil phosphoribosyltransferase (RefSeq) 292, 325
BSU38520 dltC D-alanine--poly(phosphoribitol) ligase subunit 2 (RefSeq) 172, 325
VIMSS39424 VIMSS39424 None 293, 325
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 BSU15970
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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