Organism : Bacillus subtilis | Module List :
BSU30860 ytcA

putative UDP-glucose dehydrogenase (RefSeq)

CircVis
Functional Annotations (11)
Function System
Predicted UDP-glucose 6-dehydrogenase cog/ cog
electron transport go/ biological_process
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor go/ molecular_function
NAD binding go/ molecular_function
Pentose and glucuronate interconversions kegg/ kegg pathway
Ascorbate and aldarate metabolism kegg/ kegg pathway
Starch and sucrose metabolism kegg/ kegg pathway
Amino sugar and nucleotide sugar metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
NDP-sugDHase tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU30860
(Mouseover regulator name to see its description)

BSU30860 is regulated by 33 influences and regulates 0 modules.
Regulators for BSU30860 ytcA (33)
Regulator Module Operator
BSU01730 21 tf
BSU01740 21 tf
BSU02000 21 tf
BSU02160 21 tf
BSU09480 21 tf
BSU13880 21 tf
BSU23100 21 tf
BSU25760 21 tf
BSU26390 21 tf
BSU28410 21 tf
BSU34220 21 tf
BSU34380 21 tf
BSU35080 21 tf
BSU36420 21 tf
BSU38070 21 tf
BSU00980 99 tf
BSU02160 99 tf
BSU02220 99 tf
BSU04820 99 tf
BSU23100 99 tf
BSU25760 99 tf
BSU26390 99 tf
BSU26870 99 tf
BSU28410 99 tf
BSU29270 99 tf
BSU32560 99 tf
BSU33660 99 tf
BSU34220 99 tf
BSU34380 99 tf
BSU35080 99 tf
BSU36110 99 tf
BSU36420 99 tf
BSU38070 99 tf

Warning: BSU30860 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
5004 7.20e-07 cgGatgaAcAaacAtcggG.cccG
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5005 1.40e-03 CCcg.ccTtttTTaAgagcAg
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5152 4.80e-04 AtatCCtataaAaAaaaagctGG
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5153 2.00e+01 cTGaAatTAGGCGgaagC
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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 BSU30860

BSU30860 is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
Predicted UDP-glucose 6-dehydrogenase cog/ cog
electron transport go/ biological_process
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor go/ molecular_function
NAD binding go/ molecular_function
Pentose and glucuronate interconversions kegg/ kegg pathway
Ascorbate and aldarate metabolism kegg/ kegg pathway
Starch and sucrose metabolism kegg/ kegg pathway
Amino sugar and nucleotide sugar metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
NDP-sugDHase tigr/ tigrfam
Module neighborhood information for BSU30860

BSU30860 has total of 30 gene neighbors in modules 21, 99
Gene neighbors (30)
Gene Common Name Description Module membership
BSU05550 cotP spore coat protein (RefSeq) 21, 56
BSU06850 yeeK spore associated protein (RefSeq) 99, 340
BSU10670 gerPF spore germination protein (RefSeq) 21, 56
BSU10910 yisZ putative adenylylsulfate kinase (RefSeq) 21, 99
BSU10920 sat sulfate adenylyltransferase (RefSeq) 21, 99
BSU11740 cotZ spore coat protein (insoluble fraction) (RefSeq) 46, 99
BSU11750 cotY outer spore coat protein (insoluble fraction) (RefSeq) 46, 99
BSU11760 cotX spore coat protein (insoluble fraction) (RefSeq) 46, 99
BSU11770 cotW spore coat protein (insoluble fraction) (RefSeq) 46, 99
BSU11780 cotV spore coat protein (insoluble fraction) (RefSeq) 46, 99
BSU11810 spoVIF sporulation-specific protein needed for heat resistance (RefSeq) 46, 99
BSU14980 ylbE hypothetical protein (RefSeq) 99, 280
BSU16730 spoVFA dipicolinate synthase subunit A (RefSeq) 21, 99
BSU16740 spoVFB dipicolinate synthase subunit B (RefSeq) 21, 99
BSU19490 gerT component of the spore coat (RefSeq) 21, 99
BSU19510 yojB hypothetical protein (RefSeq) 21, 326
BSU22240 ypqA hypothetical protein (RefSeq) 21, 280
BSU25150 yqfQ hypothetical protein (RefSeq) 21, 84
BSU30850 ytdA putative UTP-glucose-1-phosphate uridylyltransferase (RefSeq) 21, 99
BSU30860 ytcA putative UDP-glucose dehydrogenase (RefSeq) 21, 99
BSU30870 ytcB putative UDP-glucose epimerase (RefSeq) 21, 99
BSU30880 ytcC putative glucosyltransferase (RefSeq) 21, 99
BSU30890 ytxO hypothetical protein (RefSeq) 21, 281
BSU30900 cotS spore coat protein (RefSeq) 21, 281
BSU30910 cotSA spore coat protein (RefSeq) 21, 281
BSU30920 cotI spore coat protein (RefSeq) 21, 281
BSU31270 tgl transglutaminase (RefSeq) 55, 99
BSU36050 cotB spore coat protein (outer) (RefSeq) 21, 84
BSU36070 cotG spore morphogenetic protein (RefSeq) 46, 99
BSU39580 yxeE spore coat protein (RefSeq) 46, 99
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 BSU30860
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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