Organism : Bacillus subtilis | Module List :
BSU02220 ybfI

putative transcriptional regulator (AraC/XylS family, cupin family) (RefSeq)

CircVis
Functional Annotations (6)
Function System
Adenosine deaminase cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU02220
(Mouseover regulator name to see its description)

BSU02220 is regulated by 17 influences and regulates 15 modules.
Regulators for BSU02220 ybfI (17)
Regulator Module Operator
BSU00700 141 tf
BSU02220 141 tf
BSU15320 141 tf
BSU15330 141 tf
BSU23450 141 tf
BSU29630 141 tf
BSU36420 141 tf
BSU03890 86 tf
BSU05970 86 tf
BSU06540 86 tf
BSU09480 86 tf
BSU18760 86 tf
BSU26320 86 tf
BSU26340 86 tf
BSU26430 86 tf
BSU30150 86 tf
BSU36600 86 tf

Warning: BSU02220 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
5126 2.60e+03 AGGAGG
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5127 4.00e+03 CaGGctGaCGC
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5232 4.20e+00 aGg.GGgAgc
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5233 3.50e+03 aA.atctT.CagGAa
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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 BSU02220

BSU02220 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Adenosine deaminase cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for BSU02220

BSU02220 has total of 44 gene neighbors in modules 86, 141
Gene neighbors (44)
Gene Common Name Description Module membership
BSU00640 spoIIE serine phosphatase (RefSeq) 131, 141
BSU00650 yabS hypothetical protein (RefSeq) 131, 141
BSU00660 yabT putative serine/threonine-protein kinase (RefSeq) 137, 141
BSU01590 ybaS putative sodium dependent transporter (RefSeq) 86, 231
BSU01910 skfA sporulation killing factor A (RefSeq) 33, 141
BSU01920 skfB synthesis of sporulation killing factor A (RefSeq) 33, 141
BSU01960 skfF sporulation killing factor biosynthesis and export; ABC transporter (permease) (RefSeq) 33, 141
BSU01980 skfH sibling killing effect ; sporulation killing factor biosynthesis and export (RefSeq) 141, 304
BSU02040 ybdN hypothetical protein (RefSeq) 25, 141
BSU02220 ybfI putative transcriptional regulator (AraC/XylS family, cupin family) (RefSeq) 86, 141
BSU02490 gudD glucarate dehydratase (RefSeq) 86, 168
BSU05730 ydhF putative lipoprotein (RefSeq) 86, 358
BSU05740 phoB alkaline phosphatase III (RefSeq) 86, 411
BSU07320 yfnC putative efflux transporter (RefSeq) 86, 311
BSU09030 yhcC hypothetical protein (RefSeq) 86, 295
BSU09040 yhcD hypothetical protein (RefSeq) 86, 285
BSU15330 sigG sporulation sigma factor SigG (RefSeq) 131, 141
BSU18930 yobH putative DNA repair protein (RefSeq) 86, 181
BSU19690 kamA lysine 2,3-aminomutase (RefSeq) 141, 399
BSU19720 yodR putative acyloate-acetoacetate CoA-transferase (RefSeq) 141, 399
BSU19730 yodS putative aminoacyloate CoA-transferase (RefSeq) 141, 399
BSU19810 ypqP hypothetical protein (RefSeq) 86, 326
BSU19930 yotC hypothetical protein; phage SPbeta (RefSeq) 86, 242
BSU20220 yorX hypothetical protein; phage SPbeta (RefSeq) 86, 376
BSU22540 qcrC menaquinol:cytochrome c oxidoreductase (cytochrome cc subunit) (RefSeq) 141, 210
BSU24510 yqhO hypothetical protein (RefSeq) 33, 86
BSU25420 yqeW putative Na+/anion cotransporter (RefSeq) 86, 150
BSU25940 yqcD conserved hypothetical protein; skin element (RefSeq) 86, 222
BSU26570 yrkB hypothetical protein (RefSeq) 86, 222
BSU26940 yraH putative lyase (RefSeq) 86, 239
BSU29630 yttP putative transcriptional regulator (RefSeq) 12, 141
BSU30640 ytkC putative autolytic amidase (RefSeq) 86, 387
BSU30960 glgD glucose-1-phosphate adenylyltransferase (ADP-glucose pyrophosphorylase) beta subunit (RefSeq) 126, 141
BSU30980 glgB glycogen branching enzyme (RefSeq) 141, 304
BSU32510 pucA xanthine dehydrogenase molybdopterin recruitment factor (RefSeq) 86, 231
BSU33140 yvqJ putative efflux protein (RefSeq) 91, 141
BSU37750 ywfA putative efflux transporter (RefSeq) 86, 310
BSU39060 citH secondary transporter of divalent metal ions/citrate complexes (RefSeq) 141, 278
BSU39260 bglH aryl-phospho-beta-d-glucosidase (RefSeq) 141, 330
BSU39270 bglP phosphotransferase system (PTS) beta-glucoside-specific enzyme IIBCA component (RefSeq) 141, 330
BSU39890 yxbB putative S-adenosylmethionine-dependent methyltransferase (RefSeq) 19, 141
BSU39910 yxnB hypothetical protein (RefSeq) 19, 141
BSU39920 asnH asparagine synthetase (glutamine-hydrolyzing) (RefSeq) 141, 407
BSU39930 yxaM putative efflux transporter (RefSeq) 85, 141
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 BSU02220
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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