Organism : Bacillus subtilis | Module List :
BSU38760 cydA

cytochrome bd ubiquinol oxidase (subunit I) (RefSeq)

CircVis
Functional Annotations (7)
Function System
Cytochrome bd-type quinol oxidase, subunit 1 cog/ cog
extracellular region go/ cellular_component
electron transport go/ biological_process
membrane go/ cellular_component
oxidoreductase activity go/ molecular_function
Oxidative phosphorylation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU38760
(Mouseover regulator name to see its description)

BSU38760 is regulated by 17 influences and regulates 0 modules.
Regulators for BSU38760 cydA (17)
Regulator Module Operator
BSU01810 178 tf
BSU03890 178 tf
BSU05060 178 tf
BSU05150 178 tf
BSU05640 178 tf
BSU05970 178 tf
BSU06540 178 tf
BSU09500 178 tf
BSU15690 178 tf
BSU32920 178 tf
BSU35030 178 tf
BSU03960 189 tf
BSU23120 189 tf
BSU33840 189 tf
BSU37290 189 tf
BSU37310 189 tf
BSU40050 189 tf

Warning: BSU38760 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
5304 6.30e+00 GcTgATCggaccgcCgAAggatCT
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5305 2.50e+04 cCCCCC
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5324 2.50e-02 tgacAtttTTgTgAA
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5325 4.10e+03 aAaGGaGg
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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 BSU38760

BSU38760 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Cytochrome bd-type quinol oxidase, subunit 1 cog/ cog
extracellular region go/ cellular_component
electron transport go/ biological_process
membrane go/ cellular_component
oxidoreductase activity go/ molecular_function
Oxidative phosphorylation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Module neighborhood information for BSU38760

BSU38760 has total of 51 gene neighbors in modules 178, 189
Gene neighbors (51)
Gene Common Name Description Module membership
BSU02190 ybfF hypothetical protein (RefSeq) 178, 200
BSU03060 lctP L-lactate permease (RefSeq) 178, 238
BSU03290 nasE assimilatory nitrite reductase subunit (RefSeq) 189, 405
BSU03300 nasD assimilatory nitrite reductase subunit (RefSeq) 189, 405
BSU03350 yciB putative metal uptake system lipoprotein (RefSeq) 178, 406
BSU04240 ydzA hypothetical protein (RefSeq) 22, 189
BSU04510 ydbL hypothetical protein (RefSeq) 189, 233
BSU05480 ydfN putative oxidoreductase (RefSeq) 107, 178
BSU05490 ydfO putative dioxygenase (RefSeq) 52, 178
BSU05500 ydfP putative membrane bound oxidoreductase (RefSeq) 52, 178
BSU05640 ydgG putative transcriptional regulator (MarR family) (RefSeq) 38, 178
BSU05650 ydgH putative membrane component (RefSeq) 38, 178
BSU06390 yebD hypothetical protein (RefSeq) 189, 295
BSU06560 yerA putative amidohydrolase (RefSeq) 131, 189
BSU06740 yefB putative site-specific recombinase / invertase (RefSeq) 178, 199
BSU06790 yeeD hypothetical protein (RefSeq) 129, 178
BSU08230 catD catechol-2,3-dioxygenase membrane subunit (RefSeq) 178, 307
BSU08810 senS transcriptional regulator (activator) (RefSeq) 178, 336
BSU08840 ssuA aliphatic sulfonate ABC transporter (binding lipoprotein) (RefSeq) 178, 336
BSU09810 yhaZ hypothetical protein (RefSeq) 178, 200
BSU10120 hemE uroporphyrinogen decarboxylase (RefSeq) 188, 189
BSU10130 hemH ferrochelatase (RefSeq) 188, 189
BSU10140 hemY protoporphyrinogen oxidase (RefSeq) 188, 189
BSU10160 yhgE putative methyl-accepting protein (RefSeq) 178, 301
BSU10470 yhjD hypothetical protein (RefSeq) 96, 178
BSU12080 ctaO protoheme IX farnesyltransferase (heme O synthase) (RefSeq) 96, 189
BSU13040 hmp nitric oxide dioxygenase (RefSeq) 174, 178
BSU13440 ykoY putative transporter (RefSeq) 178, 294
BSU14870 ctaA heme-A synthase (RefSeq) 51, 189
BSU17260 aprX alkaline serine protease (RefSeq) 129, 178
BSU17840 yndN fosfomycin resistance protein FosB (RefSeq) 178, 379
BSU18170 yngA putative conserved membrane protein (RefSeq) 168, 189
BSU21060 yonK conserved hypothetical protein; phage SPbeta (RefSeq) 18, 178
BSU23110 resE two-component sensor histidine kinase (RefSeq) 189, 340
BSU23120 resD two-component response regulator (RefSeq) 189, 340
BSU25990 yqbS conserved hypothetical protein; skin element (RefSeq) 178, 301
BSU26890 csn chitosanase (RefSeq) 189, 208
BSU35270 cccB cytochrome c551 (RefSeq) 189, 315
BSU37310 fnr transcriptional regulator (FNR/CAP family) (RefSeq) 22, 189
BSU37350 sboA subtilosin A (RefSeq) 26, 189
BSU37360 sboX putative bacteriocin-like product (RefSeq) 189, 201
BSU37370 albA putative antilisterial bacteriocin (subtilosin) production enzyme (RefSeq) 189, 241
BSU37380 albB putative membrane component involved in subtilosin production (RefSeq) 189, 241
BSU38730 cydD ABC membrane transporter (ATP-binding protein) required for cytochrome bd function (RefSeq) 189, 349
BSU38740 cydC ABC membrane transporter (ATP-binding protein) required for cytochrome bd function (RefSeq) 189, 349
BSU38750 cydB cytochrome bd ubiquinol oxidase (subunit II) (RefSeq) 189, 349
BSU38760 cydA cytochrome bd ubiquinol oxidase (subunit I) (RefSeq) 178, 189
BSU39940 yxaL membrane associated protein kinase with beta-propeller domain (RefSeq) 189, 276
BSU40560 yybP putative lipoprotein (RefSeq) 52, 178
VIMSS37650 VIMSS37650 None 164, 189
VIMSS37877 VIMSS37877 None 120, 189
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 BSU38760
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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