Organism : Bacillus subtilis | Module List :
BSU28250 leuD

isopropylmalate isomerase small subunit (RefSeq)

CircVis
Functional Annotations (10)
Function System
3-isopropylmalate dehydratase small subunit cog/ cog
3-isopropylmalate dehydratase activity go/ molecular_function
leucine biosynthetic process go/ biological_process
3-isopropylmalate dehydratase complex go/ cellular_component
(R)-2-methylmalate dehydratase activity go/ molecular_function
Valine leucine and isoleucine biosynthesis kegg/ kegg pathway
C5-Branched dibasic acid metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
leuD tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU28250
(Mouseover regulator name to see its description)

BSU28250 is regulated by 29 influences and regulates 0 modules.
Regulators for BSU28250 leuD (29)
Regulator Module Operator
BSU04060 192 tf
BSU06540 192 tf
BSU06580 192 tf
BSU08730 192 tf
BSU09060 192 tf
BSU11660 192 tf
BSU19050 192 tf
BSU26430 192 tf
BSU29030 192 tf
BSU33840 192 tf
BSU36420 192 tf
BSU05130 42 tf
BSU06580 42 tf
BSU09060 42 tf
BSU09830 42 tf
BSU11660 42 tf
BSU13150 42 tf
BSU18460 42 tf
BSU19050 42 tf
BSU19100 42 tf
BSU26840 42 tf
BSU29030 42 tf
BSU29740 42 tf
BSU30020 42 tf
BSU33840 42 tf
BSU34200 42 tf
BSU37550 42 tf
BSU38420 42 tf
BSU40010 42 tf

Warning: BSU28250 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
5044 2.40e-02 aAAaaGGggGA
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5045 5.40e+01 AAtCAggGTGGtACCaCGg
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5330 4.50e+01 gctaaTTTaggtGcgAAagGCT
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5331 1.40e+03 GaAAGGggGAG
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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 BSU28250

BSU28250 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
3-isopropylmalate dehydratase small subunit cog/ cog
3-isopropylmalate dehydratase activity go/ molecular_function
leucine biosynthetic process go/ biological_process
3-isopropylmalate dehydratase complex go/ cellular_component
(R)-2-methylmalate dehydratase activity go/ molecular_function
Valine leucine and isoleucine biosynthesis kegg/ kegg pathway
C5-Branched dibasic acid metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
leuD tigr/ tigrfam
Module neighborhood information for BSU28250

BSU28250 has total of 31 gene neighbors in modules 42, 192
Gene neighbors (31)
Gene Common Name Description Module membership
BSU00090 guaB inosine 5'-monophosphate dehydrogenase (RefSeq) 42, 150
BSU00930 cysE serine acetyltransferase (RefSeq) 42, 300
BSU00940 cysS cysteinyl-tRNA synthetase (RefSeq) 42, 300
BSU00950 mrnC ribonuclease for 23S RNA maturation (RefSeq) 42, 300
BSU00960 rlmB 23S rRNA methyltransferase (RefSeq) 42, 300
BSU00970 yacP putative ribonuclease with PIN and NYN domains (RefSeq) 42, 300
BSU11420 trpS tryptophanyl-tRNA synthetase (RefSeq) 42, 158
BSU13120 proB gamma-glutamyl kinase (RefSeq) 42, 158
BSU13130 proA gamma-glutamyl phosphate reductase (RefSeq) 42, 158
BSU14520 adeC adenine deaminase (RefSeq) 42, 255
BSU14860 pycA pyruvate carboxylase (RefSeq) 42, 192
BSU19580 yodF putative Na+/metabolite permease (RefSeq) 28, 42
BSU22750 ubiE ubiquinone/menaquinone biosynthesis methyltransferase (RefSeq) 42, 289
BSU22890 cmk cytidylate kinase (RefSeq) 42, 193
BSU28250 leuD isopropylmalate isomerase small subunit (RefSeq) 42, 192
BSU28260 leuC isopropylmalate isomerase large subunit (RefSeq) 42, 192
BSU28270 leuB 3-isopropylmalate dehydrogenase (RefSeq) 42, 192
BSU28280 leuA 2-isopropylmalate synthase (RefSeq) 42, 192
BSU28290 ilvC ketol-acid reductoisomerase (RefSeq) 42, 192
BSU28300 ilvH acetolactate synthase 3 regulatory subunit (RefSeq) 42, 192
BSU28310 ilvB acetolactate synthase catalytic subunit (RefSeq) 42, 192
BSU30180 ytbQ putative nucleoside-diphosphate-sugar epimerase (RefSeq) 163, 192
BSU30190 bioI cytochrome P450 for pimelic acid formation for biotin biosynthesis (RefSeq) 163, 192
BSU30200 bioB biotin synthase (RefSeq) 146, 192
BSU30210 bioD dithiobiotin synthetase (RefSeq) 146, 192
BSU30220 bioF 8-amino-7-oxononanoate synthase (RefSeq) 146, 192
BSU30230 bioA adenosylmethionine--8-amino-7-oxononanoate transaminase (RefSeq) 146, 192
BSU30240 bioW 6-carboxyhexanoate--CoA ligase (RefSeq) 146, 192
BSU32240 thrB homoserine kinase (RefSeq) 42, 192
BSU32250 thrC threonine synthase (RefSeq) 42, 192
BSU32260 hom homoserine dehydrogenase (RefSeq) 42, 192
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 BSU28250
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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