Organism : Bacillus cereus ATCC14579 | Module List :
BC3092

Glutathione-dependent formaldehyde dehydrogenase (NCBI ptt file)

CircVis
Functional Annotations (14)
Function System
Threonine dehydrogenase and related Zn-dependent dehydrogenases cog/ cog
alcohol dehydrogenase activity, metal ion-independent go/ molecular_function
alcohol dehydrogenase activity, zinc-dependent go/ molecular_function
alcohol dehydrogenase activity, iron-dependent go/ molecular_function
zinc ion binding go/ molecular_function
Glycolysis / Gluconeogenesis kegg/ kegg pathway
Fatty acid metabolism kegg/ kegg pathway
Tyrosine metabolism kegg/ kegg pathway
Chloroalkane and chloroalkene degradation kegg/ kegg pathway
Naphthalene degradation kegg/ kegg pathway
Methane metabolism 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 BC3092
(Mouseover regulator name to see its description)

BC3092 is regulated by 17 influences and regulates 0 modules.
Regulators for BC3092 (17)
Regulator Module Operator
BC1059 131 tf
BC2517 131 tf
BC2680 131 tf
BC2837 131 tf
BC3589 131 tf
BC3903 131 tf
BC5251 131 tf
BC0477 128 tf
BC1814 128 tf
BC2680 128 tf
BC2811 128 tf
BC3039 128 tf
BC3320 128 tf
BC3332 128 tf
BC3982 128 tf
BC4181 128 tf
BC5250 128 tf

Warning: BC3092 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
4172 1.60e-01 cCCTcC
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4173 8.40e+03 TTCcaTaCtAAaCAcccAcC
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4178 1.20e+02 taagGgGaGAa
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4179 1.80e+03 gt.caaCcA.a.G..G.aGtTgT
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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 BC3092

BC3092 is enriched for 14 functions in 3 categories.
Enrichment Table (14)
Function System
Threonine dehydrogenase and related Zn-dependent dehydrogenases cog/ cog
alcohol dehydrogenase activity, metal ion-independent go/ molecular_function
alcohol dehydrogenase activity, zinc-dependent go/ molecular_function
alcohol dehydrogenase activity, iron-dependent go/ molecular_function
zinc ion binding go/ molecular_function
Glycolysis / Gluconeogenesis kegg/ kegg pathway
Fatty acid metabolism kegg/ kegg pathway
Tyrosine metabolism kegg/ kegg pathway
Chloroalkane and chloroalkene degradation kegg/ kegg pathway
Naphthalene degradation kegg/ kegg pathway
Methane metabolism 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 BC3092

BC3092 has total of 45 gene neighbors in modules 128, 131
Gene neighbors (45)
Gene Common Name Description Module membership
BC0212 BC0212 hypothetical protein (NCBI ptt file) 9, 128
BC0255 BC0255 Amino acid permease (NCBI ptt file) 131, 384
BC0489 BC0489 Glycosyltransferase involved in cell wall biogenesis (NCBI ptt file) 131, 376
BC0490 BC0490 hypothetical protein (NCBI ptt file) 131, 376
BC0701 BC0701 N-acyl-L-amino acid amidohydrolase (NCBI ptt file) 131, 135
BC0783 BC0783 Spore germination protein, gerC family (NCBI ptt file) 25, 131
BC0784 BC0784 Spore germination protein, gerA family (NCBI ptt file) 131, 162
BC0891 BC0891 hypothetical protein (NCBI ptt file) 128, 415
BC0987 BC0987 hypothetical protein (NCBI ptt file) 128, 415
BC1084 BC1084 hypothetical protein (NCBI ptt file) 128, 284
BC1221 BC1221 hypothetical Membrane Spanning Protein (NCBI ptt file) 128, 185
BC1274 BC1274 hypothetical protein (NCBI ptt file) 25, 128
BC1280 BC1280 hypothetical protein (NCBI ptt file) 128, 138
BC1418 BC1418 hypothetical protein (NCBI ptt file) 128, 354
BC1429 BC1429 hypothetical protein (NCBI ptt file) 128, 334
BC1538 BC1538 hypothetical protein (NCBI ptt file) 131, 521
BC1555 BC1555 hypothetical protein (NCBI ptt file) 131, 376
BC1831 BC1831 hypothetical protein (NCBI ptt file) 128, 158
BC1942 BC1942 hypothetical protein (NCBI ptt file) 128, 131
BC2138 BC2138 hypothetical protein (NCBI ptt file) 128, 317
BC2325 BC2325 Macrolide-efflux protein (NCBI ptt file) 131, 280
BC2355 BC2355 hypothetical protein (NCBI ptt file) 128, 280
BC2590 BC2590 Phage protein (NCBI ptt file) 25, 131
BC2680 BC2680 Transcriptional regulator, GntR family (NCBI ptt file) 131, 397
BC2694 BC2694 hypothetical protein (NCBI ptt file) 128, 189
BC2752 BC2752 hypothetical Membrane Spanning Protein (NCBI ptt file) 128, 459
BC3059 BC3059 putative cephalosporin hydroxylase CmcI (NCBI ptt file) 131, 463
BC3092 BC3092 Glutathione-dependent formaldehyde dehydrogenase (NCBI ptt file) 128, 131
BC3327 BC3327 3-oxoacyl-[acyl-carrier protein] reductase (NCBI ptt file) 131, 301
BC3403 BC3403 hypothetical protein (NCBI ptt file) 131, 459
BC3444 BC3444 hypothetical protein (NCBI ptt file) 128, 498
BC3508 BC3508 hypothetical protein (NCBI ptt file) 128, 337
BC3752 BC3752 None 128, 303
BC3928 BC3928 hypothetical Membrane Spanning Protein (NCBI ptt file) 131, 339
BC4047 BC4047 hypothetical protein (NCBI ptt file) 128, 358
BC4070 BC4070 Stage V sporulation protein AA (NCBI ptt file) 131, 334
BC4185 BC4185 hypothetical protein (NCBI ptt file) 128, 317
BC4191 BC4191 Stage III sporulation protein AC (NCBI ptt file) 131, 162
BC4228 BC4228 hypothetical protein (NCBI ptt file) 25, 128
BC4409 BC4409 hypothetical protein (NCBI ptt file) 128, 272
BC4418 BC4418 hypothetical protein (NCBI ptt file) 128, 227
BC4527 BC4527 hypothetical Membrane Spanning Protein (NCBI ptt file) 25, 131
BC4635 BC4635 hypothetical protein (NCBI ptt file) 128, 334
BC4943 BC4943 hypothetical protein (NCBI ptt file) 131, 509
BC5480 BC5480 hypothetical protein (NCBI ptt file) 131, 272
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 BC3092
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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