Organism : Bacillus cereus ATCC14579 | Module List :
BC5301

NADH-quinone oxidoreductase chain A (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
NADH:ubiquinone oxidoreductase subunit 3 (chain A) cog/ cog
mitochondrial electron transport, NADH to ubiquinone go/ biological_process
NADH dehydrogenase (ubiquinone) activity go/ molecular_function
Oxidative phosphorylation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC5301
(Mouseover regulator name to see its description)

BC5301 is regulated by 29 influences and regulates 0 modules.
Regulators for BC5301 (29)
Regulator Module Operator
BC1059 490 tf
BC1329 490 tf
BC1603 490 tf
BC2401 490 tf
BC2469 490 tf
BC2517 490 tf
BC2837 490 tf
BC2964 490 tf
BC2988 490 tf
BC3588 490 tf
BC0042 321 tf
BC0613 321 tf
BC0848 321 tf
BC0958 321 tf
BC1059 321 tf
BC1731 321 tf
BC1884 321 tf
BC2250 321 tf
BC2386 321 tf
BC2444 321 tf
BC2517 321 tf
BC2837 321 tf
BC2903 321 tf
BC3320 321 tf
BC3690 321 tf
BC4240 321 tf
BC4395 321 tf
BC5176 321 tf
BC5363 321 tf

Warning: BC5301 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
4556 1.50e-02 gtGggGAatga
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4557 3.90e+03 GCAAACTTCAAATTCCTATGTCG
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4890 3.30e+00 AGgGgG
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4891 1.20e+04 GcAGaGGATG
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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 BC5301

BC5301 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
NADH:ubiquinone oxidoreductase subunit 3 (chain A) cog/ cog
mitochondrial electron transport, NADH to ubiquinone go/ biological_process
NADH dehydrogenase (ubiquinone) activity go/ molecular_function
Oxidative phosphorylation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Module neighborhood information for BC5301

BC5301 has total of 34 gene neighbors in modules 321, 490
Gene neighbors (34)
Gene Common Name Description Module membership
BC0602 BC0602 Bacillolysin (NCBI ptt file) 104, 321
BC0639 BC0639 Glutamine transport ATP-binding protein glnQ (NCBI ptt file) 418, 490
BC0948 BC0948 hypothetical protein (NCBI ptt file) 24, 321
BC1738 BC1738 Uridylate kinase (NCBI ptt file) 373, 490
BC1895 BC1895 Phage protein (NCBI ptt file) 186, 321
BC1968 BC1968 hypothetical protein (NCBI ptt file) 5, 490
BC2167 BC2167 Bacillolysin (NCBI ptt file) 321, 393
BC2395 BC2395 hypothetical protein (NCBI ptt file) 218, 321
BC2453 BC2453 Peptide synthetase (NCBI ptt file) 484, 490
BC2550 BC2550 D-alanine--D-alanine ligase (NCBI ptt file) 244, 490
BC2645 BC2645 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 490, 522
BC2810 BC2810 hypothetical protein (NCBI ptt file) 321, 453
BC3112 BC3112 None 232, 321
BC3192 BC3192 Protein ydhR precursor (NCBI ptt file) 179, 321
BC3436 BC3436 Daunorubicin resistance ATP-binding protein drrA (NCBI ptt file) 38, 490
BC3521 BC3521 hypothetical protein (NCBI ptt file) 373, 490
BC3630 BC3630 Medium-chain-fatty-acid--CoA ligase (NCBI ptt file) 168, 490
BC4066 BC4066 Stage V sporulation protein AE (NCBI ptt file) 321, 355
BC4071 BC4071 Sodium/proline symporter (NCBI ptt file) 321, 405
BC4190 BC4190 Stage III sporulation protein AD (NCBI ptt file) 130, 321
BC4236 BC4236 ComG operon protein 4 (NCBI ptt file) 263, 321
BC4237 BC4237 ComG operon protein 3 (NCBI ptt file) 205, 321
BC5283 BC5283 Stage II sporulation protein Q (NCBI ptt file) 13, 321
BC5291 BC5291 NADH-quinone oxidoreductase chain N (NCBI ptt file) 321, 490
BC5292 BC5292 NADH-quinone oxidoreductase chain M (NCBI ptt file) 229, 490
BC5293 BC5293 NADH-quinone oxidoreductase chain L (NCBI ptt file) 393, 490
BC5294 BC5294 NADH-quinone oxidoreductase chain K (NCBI ptt file) 321, 484
BC5295 BC5295 NADH-quinone oxidoreductase chain J (NCBI ptt file) 321, 490
BC5296 BC5296 NADH-quinone oxidoreductase chain I (NCBI ptt file) 321, 393
BC5297 BC5297 NADH-quinone oxidoreductase chain H (NCBI ptt file) 229, 490
BC5300 BC5300 NADH-quinone oxidoreductase chain B (NCBI ptt file) 321, 490
BC5301 BC5301 NADH-quinone oxidoreductase chain A (NCBI ptt file) 321, 490
BC5302 BC5302 Sensory box/GGDEF family protein (NCBI ptt file) 139, 321
BC5327 BC5327 Stage II sporulation protein R (NCBI ptt file) 108, 321
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 BC5301
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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