Organism : Bacillus subtilis | Module List :
BSU39360 hutU

urocanate hydratase (RefSeq)

CircVis
Functional Annotations (6)
Function System
Urocanate hydratase cog/ cog
histidine catabolic process go/ biological_process
urocanate hydratase activity go/ molecular_function
Histidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
hutU tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU39360
(Mouseover regulator name to see its description)

BSU39360 is regulated by 25 influences and regulates 0 modules.
Regulators for BSU39360 hutU (25)
Regulator Module Operator
BSU00370 326 tf
BSU02000 326 tf
BSU05370 326 tf
BSU06960 326 tf
BSU07010 326 tf
BSU07590 326 tf
BSU08100 326 tf
BSU09480 326 tf
BSU17590 326 tf
BSU23090 326 tf
BSU23100 326 tf
BSU26320 326 tf
BSU28410 326 tf
BSU39850 326 tf
BSU00470 85 tf
BSU02070 85 tf
BSU15320 85 tf
BSU26870 85 tf
BSU27080 85 tf
BSU27320 85 tf
BSU31530 85 tf
BSU36420 85 tf
BSU37290 85 tf
BSU40410 85 tf
BSU40710 85 tf

Warning: BSU39360 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
5124 6.20e-04 gAAAgAAAcaGga.t.gagC
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5125 7.40e+01 CagCCaATAGa
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5590 3.80e-05 A.aAaaggGAGtTgaag
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5591 9.90e+01 AaGGAg
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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 BSU39360

BSU39360 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Urocanate hydratase cog/ cog
histidine catabolic process go/ biological_process
urocanate hydratase activity go/ molecular_function
Histidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
hutU tigr/ tigrfam
Module neighborhood information for BSU39360

BSU39360 has total of 46 gene neighbors in modules 85, 326
Gene neighbors (46)
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
BSU02510 garD D-galactarate dehydratase (RefSeq) 180, 326
BSU05230 ydeK putative permease (RefSeq) 84, 326
BSU06150 gutB glucitol (sorbitol) dehydrogenase (RefSeq) 180, 326
BSU06160 gutP H+-glucitol symporter (RefSeq) 61, 326
BSU06300 cotA spore copper-dependent laccase (RefSeq) 84, 326
BSU10780 yisN hypothetical protein (RefSeq) 85, 127
BSU10790 asnO asparagine synthetase (RefSeq) 85, 127
BSU10970 yitF putative enolase superfamily enzyme (RefSeq) 175, 326
BSU10980 yitG putative efflux transporter (RefSeq) 152, 326
BSU17110 pksD enzyme involved in polyketide synthesis (RefSeq) 85, 302
BSU17120 pksE enzyme involved in polyketide synthesis (RefSeq) 85, 306
BSU17130 acpK acyl carrier protein (RefSeq) 85, 306
BSU17140 pksF polyketide beta-ketoacyl:acyl carrier protein synthase (RefSeq) 85, 306
BSU17150 pksG acetyl-S-AcpK beta-ketothioester polyketide intermediate transferase (RefSeq) 85, 306
BSU17160 pksH polyketide biosynthesis enoyl-CoA hydratase (RefSeq) 85, 306
BSU17170 pksI polyketide biosynthesis enoyl-CoA hydratase (RefSeq) 85, 306
BSU17180 pksJ polyketide synthase of type I (RefSeq) 85, 306
BSU17190 pksL polyketide synthase of type I (RefSeq) 85, 306
BSU17200 pksM polyketide synthase (RefSeq) 85, 306
BSU17210 pksN polyketide synthase of type I (RefSeq) 85, 306
BSU17220 pksR polyketide synthase (RefSeq) 85, 306
BSU18330 ppsB plipastatin synthetase (RefSeq) 85, 306
BSU18340 ppsA plipastatin synthetase (RefSeq) 85, 306
BSU19510 yojB hypothetical protein (RefSeq) 21, 326
BSU19810 ypqP hypothetical protein (RefSeq) 86, 326
BSU20190 yosA hypothetical protein from phage SPbeta (RefSeq) 180, 326
BSU27030 sacC levanase (RefSeq) 85, 329
BSU27040 levG phosphotransferase system (PTS) fructose-specific enzyme IID component (RefSeq) 85, 117
BSU27050 levF phosphotransferase system (PTS) fructose-specific enzyme IIC component (RefSeq) 85, 117
BSU27060 levE phosphotransferase system (PTS) fructose-specific enzyme IIB component (RefSeq) 85, 117
BSU27070 levD phosphotransferase system (PTS) fructose-specific enzyme IIA component (RefSeq) 85, 329
BSU32470 pucE xanthine dehydrogenase, iron-sulfur subunit (RefSeq) 52, 326
BSU32480 pucD xanthine dehydrogenase, substrate and molybdenum cofactor subunit (RefSeq) 52, 326
BSU32490 pucC xanthine dehydrogenase, FAD-binding subunit (RefSeq) 52, 326
BSU34080 yvfS putative ABC transporter (permease) (RefSeq) 318, 326
BSU34090 yvfR putative ABC efflux transporter (ATP-binding protein) (RefSeq) 318, 326
BSU34530 cotR spore coat protein assembly factor CotR (RefSeq) 281, 326
BSU36030 ywrK putative Na+/H+ antiporter (RefSeq) 281, 326
BSU39350 hutH histidine ammonia-lyase (RefSeq) 85, 326
BSU39360 hutU urocanate hydratase (RefSeq) 85, 326
BSU39370 hutI imidazolonepropionase (RefSeq) 85, 326
BSU39380 hutG formimidoylglutamase (RefSeq) 85, 326
BSU39390 hutM histidine permease (RefSeq) 84, 326
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 BSU39360
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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