Organism : Bacillus subtilis | Module List :
BSU13010 ykgB

putative 6-phosphogluconolactonase (RefSeq)

CircVis
Functional Annotations (5)
Function System
3-carboxymuconate cyclase cog/ cog
Pentose phosphate pathway kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU13010
(Mouseover regulator name to see its description)

BSU13010 is regulated by 22 influences and regulates 0 modules.
Regulators for BSU13010 ykgB (22)
Regulator Module Operator
BSU04680 29 tf
BSU04730 29 tf
BSU05700 29 tf
BSU09380 29 tf
BSU12510 29 tf
BSU26670 29 tf
BSU28400 29 tf
BSU28410 29 tf
BSU28820 29 tf
BSU31410 29 tf
BSU34200 29 tf
BSU36440 29 tf
BSU38220 29 tf
BSU40350 29 tf
BSU01010 113 tf
BSU02680 113 tf
BSU04680 113 tf
BSU15640 113 tf
BSU19120 113 tf
BSU24770 113 tf
BSU28820 113 tf
BSU38220 113 tf

Warning: BSU13010 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
5018 5.20e-12 aaaAAGGaGGA
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5019 2.00e+00 ag.gAaAaAatTgaAAAaAAC
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5180 7.60e-08 gAAgGAG.
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5181 7.90e+03 cACaaTaCCGC
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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 BSU13010

BSU13010 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
3-carboxymuconate cyclase cog/ cog
Pentose phosphate pathway kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
Module neighborhood information for BSU13010

BSU13010 has total of 45 gene neighbors in modules 29, 113
Gene neighbors (45)
Gene Common Name Description Module membership
BSU00910 ispF 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (RefSeq) 70, 113
BSU01540 salA Mrp family regulator (RefSeq) 113, 296
BSU03130 nadE NAD synthetase (RefSeq) 29, 169
BSU04410 ydbB putative enzyme ; cupin family (RefSeq) 29, 353
BSU04420 ydbC hypothetical protein (RefSeq) 29, 353
BSU05100 yddT hypothetical protein (RefSeq) 29, 299
BSU08220 yfiC putative ABC transporter (ATP-binding protein) (RefSeq) 113, 296
BSU09240 yhcW putative phosphoglycolate phosphatase (RefSeq) 113, 252
BSU09310 pgcA alpha-phosphoglucomutase (RefSeq) 113, 252
BSU10100 yhgC hypothetical protein (RefSeq) 113, 412
BSU10240 yhfI putative metal-dependent hydrolase (RefSeq) 113, 252
BSU10250 yhfJ putative lipoate-protein ligase (RefSeq) 113, 252
BSU10320 yhfP putative oxidoreductase (RefSeq) 29, 252
BSU11150 yitV putative hydrolase (RefSeq) 113, 254
BSU13010 ykgB putative 6-phosphogluconolactonase (RefSeq) 29, 113
BSU14450 ampS aminopeptidase (RefSeq) 113, 252
BSU15040 ylbK putative hydrolase (RefSeq) 113, 252
BSU15120 yllA putative nucleoid associated protein (RefSeq) 78, 113
BSU18990 yobK hypothetical protein (RefSeq) 113, 116
BSU19000 yobL putative phage DNA manipulating enzyme (RefSeq) 113, 116
BSU21320 yomL conserved hypothetical protein; phage SPbeta (RefSeq) 29, 299
BSU23620 yqkF NADPH-dependent aldo-keto reductase (RefSeq) 113, 398
BSU24470 yqhS 3-dehydroquinate dehydratase (RefSeq) 29, 256
BSU28340 ysnF putative stress response protein (RefSeq) 29, 299
BSU28410 gerE transcriptional regulator (RefSeq) 29, 248
BSU30650 dps DNA-protecting protein, ferritin (RefSeq) 29, 320
BSU32100 yumB putative NAD-disulfide oxidoreductase (RefSeq) 29, 391
BSU32450 pucL urate oxidase with peroxide reductase N-terminal domain (RefSeq) 29, 231
BSU32500 pucB enzyme for molybdopterin cofactor synthesis required for xanthine dehydrogenase (RefSeq) 29, 231
BSU32810 yusI putative oxidoreductase with thioredoxin domain (RefSeq) 113, 252
BSU33620 yvaK carboxylesterase (RefSeq) 29, 149
BSU34680 yvcT putative 2-hydroxyacid dehydrogenase (RefSeq) 29, 169
BSU35970 ywsB hypothetical protein (RefSeq) 29, 149
BSU37130 spo0F two-component response regulator (RefSeq) 70, 113
BSU37300 ywiC putative integral inner membrane protein (RefSeq) 29, 238
BSU37940 ywdJ putative purine/pyrimidine permease (RefSeq) 29, 243
BSU37950 ywdI hypothetical protein (RefSeq) 29, 243
BSU38190 galT galactose-1-phosphate uridylyltransferase (RefSeq) 29, 149
BSU38200 galK galactokinase (RefSeq) 29, 183
BSU38620 yxlJ 3-methyladenine DNA glycosylase (RefSeq) 29, 59
BSU38920 pepT peptidase T (RefSeq) 113, 222
BSU38980 scoB succinyl CoA:3-oxoacid CoA-transferase (subunit B) (RefSeq) 29, 231
BSU39560 yxeG putative integral inner membrane protein (RefSeq) 29, 233
BSU40030 yxaB putative exopolysaccharide pyruvyl transferase (RefSeq) 113, 403
VIMSS39609 VIMSS39609 None 2, 29
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 BSU13010
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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