Organism : Bacillus cereus ATCC14579 | Module List :
BC3555

Aldehyde dehydrogenase (NCBI ptt file)

CircVis
Functional Annotations (21)
Function System
NAD-dependent aldehyde dehydrogenases cog/ cog
aldehyde dehydrogenase (NAD) activity go/ molecular_function
metabolic process go/ biological_process
Glycolysis / Gluconeogenesis kegg/ kegg pathway
Pentose and glucuronate interconversions kegg/ kegg pathway
Ascorbate and aldarate metabolism kegg/ kegg pathway
Fatty acid metabolism kegg/ kegg pathway
Valine leucine and isoleucine degradation kegg/ kegg pathway
Lysine degradation kegg/ kegg pathway
Arginine and proline metabolism kegg/ kegg pathway
Histidine metabolism kegg/ kegg pathway
Tryptophan metabolism kegg/ kegg pathway
beta-Alanine metabolism kegg/ kegg pathway
Glycerolipid metabolism kegg/ kegg pathway
Pyruvate metabolism kegg/ kegg pathway
Chloroalkane and chloroalkene degradation kegg/ kegg pathway
Propanoate 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 BC3555
(Mouseover regulator name to see its description)

BC3555 is regulated by 35 influences and regulates 0 modules.
Regulators for BC3555 (35)
Regulator Module Operator
BC0123 146 tf
BC0882 146 tf
BC0950 146 tf
BC0953 146 tf
BC0993 146 tf
BC1915 146 tf
BC2298 146 tf
BC2442 146 tf
BC2558 146 tf
BC2738 146 tf
BC3069 146 tf
BC3244 146 tf
BC3400 146 tf
BC3493 146 tf
BC3497 146 tf
BC3589 146 tf
BC4072 146 tf
BC4474 146 tf
BC0122 294 tf
BC0680 294 tf
BC0806 294 tf
BC0961 294 tf
BC1296 294 tf
BC1789 294 tf
BC1915 294 tf
BC1932 294 tf
BC1998 294 tf
BC2250 294 tf
BC2340 294 tf
BC3062 294 tf
BC3163 294 tf
BC3332 294 tf
BC4474 294 tf
BC4525 294 tf
BC4960 294 tf

Warning: BC3555 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
4208 4.00e+03 gGGAGAg
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4209 2.70e+04 CCCCcTTtTgT
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4504 5.80e-10 AagGaGAggta
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4505 4.70e+04 GGaTGGGGcaG
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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 BC3555

BC3555 is enriched for 21 functions in 3 categories.
Enrichment Table (21)
Function System
NAD-dependent aldehyde dehydrogenases cog/ cog
aldehyde dehydrogenase (NAD) activity go/ molecular_function
metabolic process go/ biological_process
Glycolysis / Gluconeogenesis kegg/ kegg pathway
Pentose and glucuronate interconversions kegg/ kegg pathway
Ascorbate and aldarate metabolism kegg/ kegg pathway
Fatty acid metabolism kegg/ kegg pathway
Valine leucine and isoleucine degradation kegg/ kegg pathway
Lysine degradation kegg/ kegg pathway
Arginine and proline metabolism kegg/ kegg pathway
Histidine metabolism kegg/ kegg pathway
Tryptophan metabolism kegg/ kegg pathway
beta-Alanine metabolism kegg/ kegg pathway
Glycerolipid metabolism kegg/ kegg pathway
Pyruvate metabolism kegg/ kegg pathway
Chloroalkane and chloroalkene degradation kegg/ kegg pathway
Propanoate 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 BC3555

BC3555 has total of 62 gene neighbors in modules 146, 294
Gene neighbors (62)
Gene Common Name Description Module membership
BC0408 BC0408 Arginine/ornithine antiporter (NCBI ptt file) 250, 294
BC0409 BC0409 Carbamate kinase (NCBI ptt file) 250, 294
BC0412 BC0412 FAD-dependent oxidase (NCBI ptt file) 158, 294
BC0413 BC0413 Exo-alpha-1,4-glucosidase (NCBI ptt file) 225, 294
BC0456 BC0456 Signal peptidase I (NCBI ptt file) 146, 163
BC0467 BC0467 Spore coat N-acetylmuramic acid deacetylase (NCBI ptt file) 31, 294
BC0486 BC0486 Glycosyltransferase involved in cell wall biogenesis (NCBI ptt file) 26, 294
BC0681 BC0681 hypothetical protein (NCBI ptt file) 7, 294
BC0890 BC0890 Long-chain-fatty-acid--CoA ligase (NCBI ptt file) 146, 279
BC0950 BC0950 Transcriptional regulator, copG family (NCBI ptt file) 85, 146
BC1040 BC1040 hypothetical protein (NCBI ptt file) 9, 146
BC1229 BC1229 hypothetical protein (NCBI ptt file) 26, 146
BC1468 BC1468 Superoxide dismutase (NCBI ptt file) 158, 294
BC1601 BC1601 hypothetical protein (NCBI ptt file) 7, 146
BC1771 BC1771 Fibronectin-binding protein (NCBI ptt file) 294, 422
BC1789 BC1789 Transcriptional regulatory protein (NCBI ptt file) 220, 294
BC1790 BC1790 Succinyl-CoA:coenzyme A transferase (NCBI ptt file) 294, 400
BC1850 BC1850 Transcriptional regulator (NCBI ptt file) 100, 294
BC1914 BC1914 Phage protein (NCBI ptt file) 63, 146
BC1975 BC1975 hypothetical Exported Protein (NCBI ptt file) 294, 461
BC2040 BC2040 putative spore coat protein (NCBI ptt file) 146, 225
BC2054 BC2054 Glutamyl-tRNA(Gln) amidotransferase subunit A (NCBI ptt file) 146, 427
BC2068 BC2068 Transcriptional regulator, GntR family (NCBI ptt file) 294, 358
BC2176 BC2176 1,3-propanediol dehydrogenase (NCBI ptt file) 294, 389
BC2196 BC2196 Hemolysin III (NCBI ptt file) 294, 478
BC2298 BC2298 Transcriptional repressor (NCBI ptt file) 146, 225
BC2366 BC2366 hypothetical protein (NCBI ptt file) 220, 294
BC2384 BC2384 hypothetical protein (NCBI ptt file) 250, 294
BC2494 BC2494 Aminoglycoside N6'-acetyltransferase (NCBI ptt file) 146, 163
BC2633 BC2633 hypothetical protein (NCBI ptt file) 294, 434
BC2649 BC2649 Transcriptional regulator, MerR family (NCBI ptt file) 26, 294
BC2653 BC2653 hypothetical protein (NCBI ptt file) 294, 415
BC2659 BC2659 Glutamate-rich protein grpB (NCBI ptt file) 7, 294
BC2749 BC2749 Acetyltransferase (NCBI ptt file) 20, 146
BC2776 BC2776 Dihydrolipoamide dehydrogenase (NCBI ptt file) 146, 427
BC2798 BC2798 Chitin binding protein (NCBI ptt file) 190, 294
BC2829 BC2829 putative Metal-dependent phosphohydrolase (NCBI ptt file) 146, 299
BC2854 BC2854 Oxidoreductase (NCBI ptt file) 97, 294
BC2943 BC2943 hypothetical protein (NCBI ptt file) 224, 294
BC2980 BC2980 Arginine permease (NCBI ptt file) 294, 459
BC2981 BC2981 hypothetical protein (NCBI ptt file) 146, 334
BC3062 BC3062 SIR2 family protein (NCBI ptt file) 294, 381
BC3139 BC3139 Oxidoreductase (NCBI ptt file) 220, 294
BC3247 BC3247 None 216, 294
BC3316 BC3316 Regulatory protein (NCBI ptt file) 72, 146
BC3339 BC3339 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 52, 146
BC3341 BC3341 1-deoxy-D-xylulose 5-phosphate reductoisomerase (NCBI ptt file) 220, 294
BC3426 BC3426 RNA polymerase sigma-I factor (NCBI ptt file) 146, 163
BC3492 BC3492 Permease (NCBI ptt file) 248, 294
BC3497 BC3497 Transcriptional regulator, ArsR family (NCBI ptt file) 63, 146
BC3555 BC3555 Aldehyde dehydrogenase (NCBI ptt file) 146, 294
BC3724 BC3724 GABA-specific permease (NCBI ptt file) 146, 163
BC4011 BC4011 Cyclodextrin transport system permease protein (NCBI ptt file) 220, 294
BC4015 BC4015 Oligo-1,6-glucosidase (NCBI ptt file) 294, 303
BC4016 BC4016 Cyclodextrin transport ATP-binding protein (NCBI ptt file) 294, 401
BC4169 BC4169 hypothetical protein (NCBI ptt file) 146, 163
BC4195 BC4195 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 264, 294
BC4424 BC4424 Cysteine desulfhydrase (NCBI ptt file) 294, 475
BC4452 BC4452 hypothetical protein (NCBI ptt file) 220, 294
BC4712 BC4712 hypothetical Cytosolic Protein (NCBI ptt file) 146, 227
BC5049 BC5049 hypothetical Membrane Spanning Protein (NCBI ptt file) 146, 209
BC5448 BC5448 UDP-glucose 4-epimerase (NCBI ptt file) 146, 263
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 BC3555
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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