Organism : Bacillus cereus ATCC14579 | Module List :
BC2967

Fructose-bisphosphate aldolase (NCBI ptt file)

CircVis
Functional Annotations (11)
Function System
DhnA-type fructose-1,6-bisphosphate aldolase and related enzymes cog/ cog
metabolic process go/ biological_process
lyase activity go/ molecular_function
Benzoate degradation kegg/ kegg pathway
Bisphenol degradation kegg/ kegg pathway
Naphthalene degradation kegg/ kegg pathway
Butanoate metabolism kegg/ kegg pathway
Limonene and pinene degradation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2967
(Mouseover regulator name to see its description)

BC2967 is regulated by 23 influences and regulates 0 modules.
Regulators for BC2967 (23)
Regulator Module Operator
BC0566 95 tf
BC0647 95 tf
BC0648 95 tf
BC1059 95 tf
BC1329 95 tf
BC2178 95 tf
BC2410 95 tf
BC2469 95 tf
BC2760 95 tf
BC5251 95 tf
BC5282 95 tf
BC5339 95 tf
BC0649 373 tf
BC1059 373 tf
BC1329 373 tf
BC2410 373 tf
BC2469 373 tf
BC2517 373 tf
BC2964 373 tf
BC3588 373 tf
BC5000 373 tf
BC5024 373 tf
BC5282 373 tf

Warning: BC2967 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
4106 4.00e+03 cGGGGAcTG
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4107 2.90e+03 GGGaGGAg
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4656 2.10e+01 AggGaggAgga
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4657 1.90e+04 AGCGcC
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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 BC2967

BC2967 is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
DhnA-type fructose-1,6-bisphosphate aldolase and related enzymes cog/ cog
metabolic process go/ biological_process
lyase activity go/ molecular_function
Benzoate degradation kegg/ kegg pathway
Bisphenol degradation kegg/ kegg pathway
Naphthalene degradation kegg/ kegg pathway
Butanoate metabolism kegg/ kegg pathway
Limonene and pinene degradation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
Module neighborhood information for BC2967

BC2967 has total of 27 gene neighbors in modules 95, 373
Gene neighbors (27)
Gene Common Name Description Module membership
BC1013 BC1013 hypothetical protein (NCBI ptt file) 95, 418
BC1256 BC1256 hypothetical protein (NCBI ptt file) 35, 95
BC1257 BC1257 hypothetical protein (NCBI ptt file) 95, 278
BC1611 BC1611 hypothetical protein (NCBI ptt file) 183, 373
BC1738 BC1738 Uridylate kinase (NCBI ptt file) 373, 490
BC2254 BC2254 IG hypothetical 18022 (NCBI ptt file) 95, 278
BC2327 BC2327 Oligopeptide transport system permease protein oppC (NCBI ptt file) 200, 373
BC2381 BC2381 Collagen triple helix repeat protein (NCBI ptt file) 95, 174
BC2422 BC2422 Secreted metalloprotease (NCBI ptt file) 95, 278
BC2440 BC2440 hypothetical protein (NCBI ptt file) 95, 336
BC2508 BC2508 Collagen adhesion protein (NCBI ptt file) 195, 373
BC2589 BC2589 Phage protein (NCBI ptt file) 95, 391
BC2591 BC2591 Phage protein (NCBI ptt file) 95, 391
BC2600 BC2600 N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 195, 373
BC2630 BC2630 Molybdopterin biosynthesis MoeB protein (NCBI ptt file) 178, 373
BC2796 BC2796 Ribose 5-phosphate isomerase (NCBI ptt file) 178, 373
BC2856 BC2856 Ankyrin repeat protein (NCBI ptt file) 373, 508
BC2874 BC2874 Spore coat protein X (NCBI ptt file) 373, 494
BC2967 BC2967 Fructose-bisphosphate aldolase (NCBI ptt file) 95, 373
BC3513 BC3513 hypothetical protein (NCBI ptt file) 95, 278
BC3521 BC3521 hypothetical protein (NCBI ptt file) 373, 490
BC3628 BC3628 Long-chain-fatty-acid--CoA ligase (NCBI ptt file) 95, 111
BC3744 BC3744 hypothetical protein (NCBI ptt file) 95, 314
BC3902 BC3902 IG hypothetical 17746 (NCBI ptt file) 183, 373
BC4187 BC4187 Stage III sporulation protein AG (NCBI ptt file) 95, 183
BC4194 BC4194 hypothetical protein (NCBI ptt file) 373, 494
BC5299 BC5299 NADH-quinone oxidoreductase chain C (NCBI ptt file) 93, 373
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 BC2967
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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