Organism : Bacillus cereus ATCC14579 | Module List :
BC3008

Catalase (NCBI ptt file)

CircVis
Functional Annotations (10)
Function System
Catalase cog/ cog
catalase activity go/ molecular_function
iron ion binding go/ molecular_function
electron transport go/ biological_process
response to oxidative stress go/ biological_process
heme binding go/ molecular_function
Tryptophan metabolism kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3008
(Mouseover regulator name to see its description)

BC3008 is regulated by 19 influences and regulates 0 modules.
Regulators for BC3008 (19)
Regulator Module Operator
BC0648 239 tf
BC1059 239 tf
BC1335 239 tf
BC1683 239 tf
BC1698 239 tf
BC2517 239 tf
BC2801 239 tf
BC3449 239 tf
BC3522 239 tf
BC3702 239 tf
BC4336 239 tf
BC4603 239 tf
BC5059 239 tf
BC0648 84 tf
BC2811 84 tf
BC3320 84 tf
BC3903 84 tf
BC4336 84 tf
BC5251 84 tf

Warning: BC3008 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
4086 2.20e+03 GGG.GGcG
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4087 1.10e+04 CCGTaAccaCcACaATaaCCGC
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4394 1.40e+04 GGAGcC
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4395 6.70e+03 aTAAatAtttggatg.AGGag
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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 BC3008

BC3008 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Catalase cog/ cog
catalase activity go/ molecular_function
iron ion binding go/ molecular_function
electron transport go/ biological_process
response to oxidative stress go/ biological_process
heme binding go/ molecular_function
Tryptophan metabolism kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
Module neighborhood information for BC3008

BC3008 has total of 30 gene neighbors in modules 84, 239
Gene neighbors (30)
Gene Common Name Description Module membership
BC0199 BC0199 Quinone oxidoreductase (NCBI ptt file) 35, 84
BC0311 BC0311 hypothetical protein (NCBI ptt file) 84, 289
BC0313 BC0313 Methyltransferase (NCBI ptt file) 84, 415
BC0396 BC0396 ATPase (NCBI ptt file) 25, 84
BC1560 BC1560 Spore coat protein D (NCBI ptt file) 84, 241
BC1849 BC1849 Phage protein (NCBI ptt file) 239, 435
BC1908 BC1908 Phage-related protein (NCBI ptt file) 84, 174
BC1943 BC1943 Glycosyltransferase (NCBI ptt file) 239, 453
BC1997 BC1997 Intracellular serine protease (NCBI ptt file) 239, 255
BC2237 BC2237 hypothetical protein (NCBI ptt file) 84, 108
BC2350 BC2350 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 84, 206
BC2640 BC2640 Isochorismatase (NCBI ptt file) 185, 239
BC2646 BC2646 RNA-directed DNA polymerase (NCBI ptt file) 84, 174
BC2696 BC2696 Intein-containing protein (NCBI ptt file) 84, 489
BC2824 BC2824 hypothetical Cytosolic Protein (NCBI ptt file) 239, 376
BC3006 BC3006 hypothetical protein (NCBI ptt file) 239, 424
BC3008 BC3008 Catalase (NCBI ptt file) 84, 239
BC3297 BC3297 hypothetical Cytosolic Protein (NCBI ptt file) 4, 239
BC3517 BC3517 CDP-glucose 4,6-dehydratase (NCBI ptt file) 84, 162
BC3702 BC3702 Antirepressor (NCBI ptt file) 239, 498
BC3959 BC3959 hypothetical protein (NCBI ptt file) 84, 340
BC3997 BC3997 Diguanylate cyclase/phosphodiesterase domain 2 (EAL) (NCBI ptt file) 25, 84
BC4113 BC4113 hypothetical protein (NCBI ptt file) 239, 293
BC4227 BC4227 Superfamily II DNA/RNA helicases, SNF2 family (NCBI ptt file) 84, 255
BC4533 BC4533 Bacitracin transport permease protein BCRB (NCBI ptt file) 155, 239
BC4606 BC4606 hypothetical Membrane Spanning Protein (NCBI ptt file) 84, 407
BC4910 BC4910 Exonuclease KapD (NCBI ptt file) 84, 162
BC4974 BC4974 Cell wall endopeptidase, family M23/M37 (NCBI ptt file) 84, 267
BC5113 BC5113 Zinc finger protein (NCBI ptt file) 4, 84
BC5215 BC5215 PTS system, lichenan oligosaccharide-specific IIA component (NCBI ptt file) 239, 293
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 BC3008
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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