Organism : Bacillus subtilis | Module List :
BSU13610 mtnB

methylthioribulose-1-phosphate dehydratase (RefSeq)

CircVis
Functional Annotations (6)
Function System
Ribulose-5-phosphate 4-epimerase and related epimerases and aldolases cog/ cog
methylthioribulose 1-phosphate dehydratase activity go/ molecular_function
metal ion binding go/ molecular_function
Cysteine and methionine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
salvage_mtnB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU13610
(Mouseover regulator name to see its description)

BSU13610 is regulated by 25 influences and regulates 0 modules.
Regulators for BSU13610 mtnB (25)
Regulator Module Operator
BSU04060 28 tf
BSU04100 28 tf
BSU05330 28 tf
BSU06580 28 tf
BSU07220 28 tf
BSU08520 28 tf
BSU09270 28 tf
BSU10830 28 tf
BSU13150 28 tf
BSU19050 28 tf
BSU33840 28 tf
BSU37550 28 tf
BSU04060 386 tf
BSU05150 386 tf
BSU05700 386 tf
BSU07220 386 tf
BSU08520 386 tf
BSU11660 386 tf
BSU19050 386 tf
BSU19100 386 tf
BSU27170 386 tf
BSU33840 386 tf
BSU34480 386 tf
BSU37550 386 tf
BSU39850 386 tf

Warning: BSU13610 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
5016 6.40e-12 agaA.gGTGCtAAaTCcatcAag
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5017 2.80e-02 tcTggaAGATaAGa
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5684 4.20e-02 AagGTGCtAAaTCcaGCAagc
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5685 1.80e-01 GctTGaaAGATAAGA
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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 BSU13610

BSU13610 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Ribulose-5-phosphate 4-epimerase and related epimerases and aldolases cog/ cog
methylthioribulose 1-phosphate dehydratase activity go/ molecular_function
metal ion binding go/ molecular_function
Cysteine and methionine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
salvage_mtnB tigr/ tigrfam
Module neighborhood information for BSU13610

BSU13610 has total of 36 gene neighbors in modules 28, 386
Gene neighbors (36)
Gene Common Name Description Module membership
BSU06040 ydiM hypothetical protein (RefSeq) 28, 81
BSU10340 phoE phosphatase (RefSeq) 28, 240
BSU11010 yitJ bifunctional homocysteine S-methyltransferase/5,10-methylenetetrahydrofolate reductase protein (RefSeq) 28, 386
BSU11190 argC N-acetyl-gamma-glutamyl-phosphate reductase (RefSeq) 275, 386
BSU11200 argJ bifunctional ornithine acetyltransferase/N-acetylglutamate synthase protein (RefSeq) 275, 386
BSU11210 argB acetylglutamate kinase (RefSeq) 28, 275
BSU11220 argD acetylornithine aminotransferase (RefSeq) 28, 275
BSU11230 carA carbamoyl phosphate synthase small subunit (RefSeq) 28, 275
BSU11240 carB carbamoyl phosphate synthase large subunit (RefSeq) 28, 275
BSU11250 argF ornithine carbamoyltransferase (RefSeq) 28, 275
BSU11870 yjcI cystathionine gamma-synthase (RefSeq) 28, 386
BSU11880 yjcJ cystathionine beta-lyase (RefSeq) 28, 386
BSU13180 metE 5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltransferase (RefSeq) 28, 386
BSU13550 mtnA methylthioribose-1-phosphate isomerase (RefSeq) 28, 125
BSU13560 mtnK methylthioribose kinase (RefSeq) 28, 125
BSU13580 ykrV transaminase (RefSeq) 28, 199
BSU13590 mtnW 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (RefSeq) 28, 386
BSU13600 mtnX 2-hydroxy-3-keto-5-methylthiopentenyl-1- phosphate phosphatase (RefSeq) 28, 386
BSU13610 mtnB methylthioribulose-1-phosphate dehydratase (RefSeq) 28, 386
BSU13620 mtnD acireductone dioxygenase (Ni2+ or Fe2+-requiring) (RefSeq) 28, 386
BSU18540 yoaB negatively charged metabolite transporter (RefSeq) 28, 386
BSU18550 yoaC hydroxylated metabolite kinase (RefSeq) 28, 386
BSU18560 yoaD putative 2-hydroxyacid dehydrogenase (RefSeq) 28, 386
BSU18570 yoaE molybdopterin cofactor oxido-reductase (RefSeq) 28, 386
BSU18580 yoaF hypothetical protein (RefSeq) 28, 386
BSU19580 yodF putative Na+/metabolite permease (RefSeq) 28, 42
BSU21870 ilvD dihydroxy-acid dehydratase (RefSeq) 28, 111
BSU23960 artR High affinity arginine ABC transporter (ATP-binding protein) (RefSeq) 275, 386
BSU23970 artQ High affinity arginine ABC transporter (permease) (RefSeq) 275, 386
BSU23980 artP High affinity arginine ABC transporter binding lipoprotein (RefSeq) 275, 386
BSU26760 yrdC putative hydrolase (RefSeq) 28, 36
BSU29430 ytzD hypothetical protein (RefSeq) 275, 386
BSU29440 argH argininosuccinate lyase (RefSeq) 275, 386
BSU29450 argG argininosuccinate synthase (RefSeq) 275, 386
BSU38950 yxjH putative methyl-tetrahydrofolate methyltransferase (RefSeq) 28, 123
BSU38960 yxjG putative methyltetrahydrofolate methyltransferase (RefSeq) 28, 123
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 BSU13610
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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