Organism : Bacillus cereus ATCC14579 | Module List :
BC0695

Cytochrome aa3 quinol oxidase polypeptide IV (NCBI ptt file)

CircVis
Functional Annotations (7)
Function System
Heme/copper-type cytochrome/quinol oxidase, subunit 4 cog/ cog
integral to membrane go/ cellular_component
oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor go/ molecular_function
ATP synthesis coupled electron transport go/ biological_process
Oxidative phosphorylation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
QoxD tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0695
(Mouseover regulator name to see its description)

BC0695 is regulated by 28 influences and regulates 0 modules.
Regulators for BC0695 (28)
Regulator Module Operator
BC0042 188 tf
BC0122 188 tf
BC0158 188 tf
BC0265 188 tf
BC0806 188 tf
BC1075 188 tf
BC1387 188 tf
BC1841 188 tf
BC3128 188 tf
BC3253 188 tf
BC3706 188 tf
BC3976 188 tf
BC4708 188 tf
BC4842 188 tf
BC5141 188 tf
BC0806 380 tf
BC1282 380 tf
BC1387 380 tf
BC3922 380 tf
BC3976 380 tf
BC4170 380 tf
BC4174 380 tf
BC4240 380 tf
BC4256 380 tf
BC4425 380 tf
BC4826 380 tf
BC5409 380 tf
BC5483 380 tf

Warning: BC0695 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
4292 2.00e+00 gCcaa.gAAAGcG
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4293 2.60e+02 ggaCatacagacAtg
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4670 1.90e-01 AAgaaaAG.Gg
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4671 4.50e+04 GcaGGAcG
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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 BC0695

BC0695 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Heme/copper-type cytochrome/quinol oxidase, subunit 4 cog/ cog
integral to membrane go/ cellular_component
oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor go/ molecular_function
ATP synthesis coupled electron transport go/ biological_process
Oxidative phosphorylation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
QoxD tigr/ tigrfam
Module neighborhood information for BC0695

BC0695 has total of 35 gene neighbors in modules 188, 380
Gene neighbors (35)
Gene Common Name Description Module membership
BC0128 BC0128 Protein Translation Elongation Factor G (EF-G) (NCBI ptt file) 188, 292
BC0129 BC0129 Protein Translation Elongation Factor Tu (EF-TU) (NCBI ptt file) 188, 430
BC0220 BC0220 Molybdenum transport system permease protein modB (NCBI ptt file) 28, 380
BC0221 BC0221 Molybdate-binding protein (NCBI ptt file) 296, 380
BC0546 BC0546 23S rRNA methyltransferase (NCBI ptt file) 90, 380
BC0695 BC0695 Cytochrome aa3 quinol oxidase polypeptide IV (NCBI ptt file) 188, 380
BC0696 BC0696 Cytochrome aa3 quinol oxidase polypeptide III (NCBI ptt file) 14, 188
BC0697 BC0697 Cytochrome aa3 quinol oxidase polypeptide I (NCBI ptt file) 14, 188
BC0698 BC0698 Cytochrome aa3 quinol oxidase polypeptide II (NCBI ptt file) 14, 188
BC0738 BC0738 hypothetical protein (NCBI ptt file) 296, 380
BC0805 BC0805 outer surface protein (NCBI ptt file) 7, 380
BC1021 BC1021 CMP-binding factor (NCBI ptt file) 350, 380
BC1282 BC1282 SinR protein (NCBI ptt file) 350, 380
BC1387 BC1387 Transcriptional regulator, MarR family (NCBI ptt file) 28, 380
BC1562 BC1562 Cell division protein DIVIVA (NCBI ptt file) 166, 380
BC2844 BC2844 None 129, 380
BC3970 BC3970 Dihydrolipoamide dehydrogenase (NCBI ptt file) 70, 188
BC3971 BC3971 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex (NCBI ptt file) 70, 188
BC3972 BC3972 Pyruvate dehydrogenase E1 component beta subunit (NCBI ptt file) 70, 188
BC3973 BC3973 Pyruvate dehydrogenase E1 component alpha subunit (NCBI ptt file) 70, 188
BC4048 BC4048 Phosphoenolpyruvate-protein phosphotransferase (NCBI ptt file) 188, 471
BC4049 BC4049 Phosphocarrier protein HPr (NCBI ptt file) 70, 188
BC4050 BC4050 PTS system, glucose-specific IIABC component (NCBI ptt file) 188, 311
BC4170 BC4170 Stage 0 sporulation protein A (NCBI ptt file) 350, 380
BC4174 BC4174 Arginine repressor, argR (NCBI ptt file) 350, 380
BC4861 BC4861 hypothetical protein (NCBI ptt file) 90, 380
BC5135 BC5135 Enolase (NCBI ptt file) 28, 188
BC5136 BC5136 Phosphoglycerate mutase (NCBI ptt file) 70, 188
BC5137 BC5137 None 70, 188
BC5140 BC5140 Glyceraldehyde 3-phosphate dehydrogenase (NCBI ptt file) 70, 188
BC5141 BC5141 Central glycolytic genes regulator (NCBI ptt file) 70, 188
BC5201 BC5201 UDP-N-acetylglucosamine 2-epimerase (NCBI ptt file) 372, 380
BC5356 BC5356 methionine aminopeptidase (RefSeq) 350, 380
BC5409 BC5409 Catabolite gene activator (NCBI ptt file) 187, 380
VIMSS12791523 VIMSS12791523 None 70, 188
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 BC0695
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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