Organism : Bacillus subtilis | Module List :
BSU22120 kdgR

Kdg operon transcriptional regulator (LacI family) (RefSeq)

CircVis
Functional Annotations (9)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA ligase (ATP) activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
DNA replication go/ biological_process
DNA repair go/ biological_process
DNA recombination go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU22120
(Mouseover regulator name to see its description)

BSU22120 is regulated by 26 influences and regulates 10 modules.
Regulators for BSU22120 kdgR (26)
Regulator Module Operator
BSU00980 168 tf
BSU02000 168 tf
BSU02550 168 tf
BSU03750 168 tf
BSU03890 168 tf
BSU04250 168 tf
BSU06960 168 tf
BSU07590 168 tf
BSU08100 168 tf
BSU08370 168 tf
BSU22120 168 tf
BSU23100 168 tf
BSU26870 168 tf
BSU01730 223 tf
BSU04820 223 tf
BSU05060 223 tf
BSU05240 223 tf
BSU05970 223 tf
BSU08730 223 tf
BSU09500 223 tf
BSU17850 223 tf
BSU20010 223 tf
BSU20820 223 tf
BSU21020 223 tf
BSU22120 223 tf
BSU36600 223 tf

Warning: BSU22120 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
5284 2.60e+00 atcctcA.atAaaaGgAgGT
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5285 1.60e+02 aTtAataaAagcccTtcCaa
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5390 3.30e-01 aAAagAGttga
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5391 1.70e+03 gGaaaggGGAt
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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 BSU22120

BSU22120 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA ligase (ATP) activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
DNA replication go/ biological_process
DNA repair go/ biological_process
DNA recombination go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BSU22120

BSU22120 has total of 48 gene neighbors in modules 168, 223
Gene neighbors (48)
Gene Common Name Description Module membership
BSU02460 ycbC 5-dehydro-4-deoxyglucarate dehydratase (RefSeq) 168, 326
BSU02470 ycbD 2,5-dioxovalerate dehydrogenase (alpha-ketoglutaric semialdehyde dehydrogenase) (RefSeq) 168, 326
BSU02490 gudD glucarate dehydratase (RefSeq) 86, 168
BSU02530 rtpA anti-TRAP regulator (RefSeq) 102, 168
BSU02550 ycbL two-component response regulator [YcbM] (RefSeq) 168, 219
BSU03530 ycxA putative permease (RefSeq) 71, 168
BSU04000 ycsA tartrate dehydrogenase (RefSeq) 168, 411
BSU04470 dctP C4-dicarboxylate transporter DctA (RefSeq) 55, 168
BSU04800 ydcL putative phage integrase (RefSeq) 47, 223
BSU04810 immA immunity anti-repressor conserved in prophages (RefSeq) 47, 223
BSU04820 immR phage element (ICEBs1)transcriptional regulator (Xre family) (RefSeq) 47, 223
BSU04840 ydcO hypothetical protein; mobile element region (RefSeq) 223, 279
BSU05190 ydeG putative permease (RefSeq) 168, 290
BSU08010 yfjP putative DNA-modified purine glycosidase (RefSeq) 114, 168
BSU08170 yfjA hypothetical protein (RefSeq) 92, 168
BSU10500 yhjG hypothetical protein (RefSeq) 168, 285
BSU12010 manP phosphotransferase system (PTS) mannose-specific enzyme IIBCA component (RefSeq) 61, 168
BSU17580 xynB xylan beta-1,4-xylosidase (RefSeq) 168, 321
BSU18170 yngA putative conserved membrane protein (RefSeq) 168, 189
BSU19520 yojA putative H+/anion permease (RefSeq) 61, 168
BSU19840 yotL conserved hypothetical protein; phage SPbeta (RefSeq) 223, 242
BSU19970 yosX conserved hypothetical protein; phage SPbeta (RefSeq) 110, 223
BSU19990 yosV conserved hypothetical protein; phage SPbeta (RefSeq) 223, 400
BSU20010 yosT conserved hypothetical protein; phage SPbeta (RefSeq) 118, 223
BSU20050 yosQ SPbeta phage endodeoxyribonuclease (homing endonuclease, responsible for intron mobility) (RefSeq) 223, 376
BSU20470 yoqY hypothetical protein; phage SPbeta (RefSeq) 58, 223
BSU20530 yoqS hypothetical protein; phage SPbeta (RefSeq) 223, 303
BSU20540 yoqR hypothetical protein; phage SPbeta (RefSeq) 223, 376
BSU20600 yoqK hypothetical protein; phage SPbeta (RefSeq) 223, 400
BSU20610 yoqJ conserved hypothetical protein; phage SPbeta (RefSeq) 223, 400
BSU20640 yoqG hypothetical protein; phage SPbeta (RefSeq) 223, 400
BSU20680 yoqC putative nucleotide-binding protein; phage SPbeta (RefSeq) 223, 297
BSU20950 yopB putative transcriptional regulator; phage SPbeta (RefSeq) 223, 376
BSU21740 ypmR putative exported lipase/acylhydrolase (lipoprotein) (RefSeq) 47, 223
BSU22090 kdgT 2-keto-3-deoxygluconate permease (RefSeq) 152, 168
BSU22100 kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase (RefSeq) 152, 168
BSU22110 kdgK 2-keto-3-deoxygluconate kinase (RefSeq) 152, 168
BSU22120 kdgR Kdg operon transcriptional regulator (LacI family) (RefSeq) 168, 223
BSU22130 kduI 5-keto-4-deoxyuronate isomerase (RefSeq) 142, 168
BSU22140 kduD 2-deoxy-D-gluconate 3-dehydrogenase (RefSeq) 150, 168
BSU22210 yprB putative nucleic acid binding enzyme (RefSeq) 30, 223
BSU22220 yprA putative ATP-dependent helicase (RefSeq) 47, 223
BSU22230 ypqE putative phosphotransferase system enzyme IIA component (RefSeq) 47, 223
BSU22260 yppF putative site-specific integrase (RefSeq) 47, 223
BSU26040 yqbN hypothetical protein (RefSeq) 47, 223
BSU26860 yraO putative citrate transporter (RefSeq) 152, 168
BSU26870 yraN putative transcriptional regulator (LysR family) (RefSeq) 152, 168
BSU39420 deoC deoxyribose-phosphate aldolase (RefSeq) 168, 285
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 BSU22120
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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