Organism : Bacillus subtilis | Module List :
BSU16990 tdh

L-threonine 3-dehydrogenase (RefSeq)

CircVis
Functional Annotations (6)
Function System
Threonine dehydrogenase and related Zn-dependent dehydrogenases cog/ cog
threonine catabolic process go/ biological_process
zinc ion binding go/ molecular_function
L-threonine 3-dehydrogenase activity go/ molecular_function
Glycine serine and threonine metabolism kegg/ kegg pathway
tdh tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU16990
(Mouseover regulator name to see its description)

BSU16990 is regulated by 19 influences and regulates 0 modules.
Regulators for BSU16990 tdh (19)
Regulator Module Operator
BSU08190 186 tf
BSU13340 186 tf
BSU15320 186 tf
BSU19030 186 tf
BSU23450 186 tf
BSU28550 186 tf
BSU33740 186 tf
BSU35910 186 tf
BSU36630 186 tf
BSU00800 217 tf
BSU10560 217 tf
BSU15880 217 tf
BSU15970 217 tf
BSU18760 217 tf
BSU26390 217 tf
BSU29630 217 tf
BSU30460 217 tf
BSU37620 217 tf
BSU38070 217 tf

Warning: BSU16990 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
5318 8.30e+01 CgttTaCAaaAACaaggagGg
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5319 3.90e+03 gAAAAatgg.tGg
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5378 2.30e-01 tttaT.aAaaggAAAT.gAG
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5379 2.30e+02 aGaGG.GATg
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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 BSU16990

BSU16990 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Threonine dehydrogenase and related Zn-dependent dehydrogenases cog/ cog
threonine catabolic process go/ biological_process
zinc ion binding go/ molecular_function
L-threonine 3-dehydrogenase activity go/ molecular_function
Glycine serine and threonine metabolism kegg/ kegg pathway
tdh tigr/ tigrfam
Module neighborhood information for BSU16990

BSU16990 has total of 34 gene neighbors in modules 186, 217
Gene neighbors (34)
Gene Common Name Description Module membership
BSU01550 gerD lipoprotein with a role in spores' rapid response to nutrient germinants (RefSeq) 55, 217
BSU03400 yckD hypothetical protein (RefSeq) 55, 217
BSU03410 bglC aryl-phospho-beta-d-glucosidase (RefSeq) 90, 217
BSU11040 yitM hypothetical protein (RefSeq) 217, 307
BSU16990 tdh L-threonine 3-dehydrogenase (RefSeq) 186, 217
BSU17000 kbl 2-amino-3-ketobutyrate coenzyme A ligase (RefSeq) 12, 186
BSU18820 yobB putative transcriptional regulator from bacteriophage (RefSeq) 217, 238
BSU18900 yozJ hypothetical protein (RefSeq) 217, 332
BSU19010 yobM hypothetical protein (RefSeq) 217, 337
BSU19310 dhaS putative aldehyde dehydrogenase (RefSeq) 217, 323
BSU20580 yoqM putative membrane bound protein; phage SPbeta (RefSeq) 18, 217
BSU21330 yomK hypothetical protein; phage SPbeta (RefSeq) 217, 337
BSU23830 yqjL putative hydrolase (RefSeq) 94, 217
BSU24650 yqzG hypothetical protein (RefSeq) 217, 278
BSU25770 spoIVCA site-specific DNA recombinase (RefSeq) 49, 217
BSU26400 yrkS hypothetical protein (RefSeq) 181, 217
BSU28710 cstA carbon starvation-induced membrane protein (RefSeq) 133, 186
BSU31080 yuaB hypothetical protein (RefSeq) 217, 238
BSU32350 yunB putative protein involved in spore formation (RefSeq) 213, 217
BSU35910 rbsR transcriptional regulator (LacI family) (RefSeq) 133, 186
BSU35920 rbsK ribokinase (RefSeq) 133, 186
BSU35930 rbsD D-ribose pyranase (RefSeq) 133, 186
BSU35940 rbsA ribose ABC transporter (ATP-binding protein) (RefSeq) 133, 186
BSU35950 rbsC ribose ABC transporter (permease) (RefSeq) 133, 186
BSU35960 rbsB ribose ABC transporter (ribose-binding lipoprotein) (RefSeq) 133, 186
BSU36530 bcrC undecaprenyl pyrophosphate phosphatase (RefSeq) 177, 217
BSU37740 bacA bacilysin biosynthesis protein, dehydratase (RefSeq) 157, 217
BSU38130 ywcE protein required for proper spore morphogenesis and germination (RefSeq) 12, 217
BSU38560 licH 6-phospho-beta-glucosidase (RefSeq) 186, 321
BSU38570 licA phosphotransferase system (PTS) lichenan-specific enzyme IIA component (RefSeq) 186, 321
BSU38580 licC phosphotransferase system (PTS) lichenan-specific enzyme IIC component (RefSeq) 186, 321
BSU38590 licB phosphotransferase system (PTS) lichenan-specific enzyme IIB component (RefSeq) 186, 321
BSU38810 msmX multiple sugar-binding transporter ATP-binding protein (RefSeq) 133, 186
BSU38930 yxjJ hypothetical protein (RefSeq) 217, 342
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 BSU16990
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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