Organism : Bacillus subtilis | Module List :
BSU04340 ydaP

pyruvate oxidase (RefSeq)

CircVis
Functional Annotations (6)
Function System
Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase] cog/ cog
magnesium ion binding go/ molecular_function
transferase activity go/ molecular_function
thiamine pyrophosphate binding go/ molecular_function
Pyruvate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU04340
(Mouseover regulator name to see its description)

BSU04340 is regulated by 6 influences and regulates 0 modules.
Regulators for BSU04340 ydaP (6)
Regulator Module Operator
BSU04730 299 tf
BSU09690 299 tf
BSU24770 299 tf
BSU28400 299 tf
BSU04730 320 tf
BSU24770 320 tf

Warning: BSU04340 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
5536 8.30e-06 aaAGGaGgAt
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5537 9.50e+00 tttt.aA.ttgcaAAAActg
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5578 1.50e+01 AgGAGG
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5579 6.30e+01 AAA.agGTtTA
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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 BSU04340

BSU04340 is enriched for 6 functions in 3 categories.
Module neighborhood information for BSU04340

BSU04340 has total of 37 gene neighbors in modules 299, 320
Gene neighbors (37)
Gene Common Name Description Module membership
BSU00520 ctc 50S ribosomal protein L25/general stress protein Ctc (RefSeq) 320, 391
BSU00530 pth peptidyl-tRNA hydrolase (RefSeq) 320, 391
BSU00540 yabK hypothetical protein (RefSeq) 149, 320
BSU02110 ybyB hypothetical protein (RefSeq) 231, 299
BSU02590 ycbP putative inner integral membrane protein (RefSeq) 137, 299
BSU02830 ycdF putative dehydrogenase (RefSeq) 299, 391
BSU02840 ycdG putative glycosidase (RefSeq) 147, 299
BSU04220 ydaG putative general stress protein (RefSeq) 203, 320
BSU04340 ydaP pyruvate oxidase (RefSeq) 299, 320
BSU04380 ydaT hypothetical protein (RefSeq) 203, 299
BSU04400 gsiB general stress protein (RefSeq) 203, 299
BSU04710 rsbV anti-anti-sigma factor (antagonist of RsbW) (RefSeq) 149, 320
BSU04720 rsbW serine-protein kinase RsbW (RefSeq) 320, 352
BSU04730 sigB RNA polymerase sigma factor SigB (RefSeq) 320, 352
BSU04740 rsbX serine phosphatase (RefSeq) 320, 352
BSU05100 yddT hypothetical protein (RefSeq) 29, 299
BSU07550 yflT heat stress induced protein (RefSeq) 203, 299
BSU07850 yfkM general stress protein 18 (RefSeq) 39, 299
BSU08600 csbB putative glycosyl transferase (RefSeq) 320, 391
BSU09390 ygxB putative integral inner membrane protein (RefSeq) 147, 299
BSU09530 yhdN aldo/keto reductase specific for NADPH (RefSeq) 149, 299
BSU10430 yhxD putative oxidoreductase (RefSeq) 147, 299
BSU13020 ykgA putative aminohydrolase (RefSeq) 320, 352
BSU13160 ohrB organic hydroperoxide resistance reductase B (RefSeq) 203, 299
BSU19240 yocK putative general stress protein (RefSeq) 320, 391
BSU21320 yomL conserved hypothetical protein; phage SPbeta (RefSeq) 29, 299
BSU24770 mgsR transcriptional regulator of stress (RefSeq) 320, 391
BSU28340 ysnF putative stress response protein (RefSeq) 29, 299
BSU29760 ytxJ hypothetical protein (RefSeq) 296, 320
BSU29770 ytxH hypothetical protein (RefSeq) 296, 320
BSU29780 ytxG hypothetical protein (RefSeq) 296, 320
BSU30650 dps DNA-protecting protein, ferritin (RefSeq) 29, 320
BSU33200 yvrE hypothetical protein (RefSeq) 320, 391
BSU33530 yvaA putative oxidoreductase (RefSeq) 147, 320
BSU36670 csbD stress response protein (RefSeq) 203, 299
BSU37210 ywjC hypothetical protein (RefSeq) 320, 391
BSU39050 katE catalase 2 (RefSeq) 147, 299
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 BSU04340
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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