Organism : Bacillus cereus ATCC14579 | Module List :
BC4857

1,4-dihydroxy-2-naphthoate octaprenyltransferase (NCBI ptt file)

CircVis
Functional Annotations (8)
Function System
1,4-dihydroxy-2-naphthoate octaprenyltransferase cog/ cog
prenyltransferase activity go/ molecular_function
menaquinone biosynthetic process go/ biological_process
integral to membrane go/ cellular_component
Ubiquinone and other terpenoid-quinone biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
menA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4857
(Mouseover regulator name to see its description)

BC4857 is regulated by 26 influences and regulates 0 modules.
Regulators for BC4857 (26)
Regulator Module Operator
BC0607 455 tf
BC0648 455 tf
BC0954 455 tf
BC1302 455 tf
BC1710 455 tf
BC3320 455 tf
BC3332 455 tf
BC3653 455 tf
BC4181 455 tf
BC4294 455 tf
BC5074 455 tf
BC5352 455 tf
BC5368 455 tf
BC5373 455 tf
BC0122 403 tf
BC0123 403 tf
BC0586 403 tf
BC1302 403 tf
BC1818 403 tf
BC3476 403 tf
BC3976 403 tf
BC4057 403 tf
BC4589 403 tf
BC4603 403 tf
BC5339 403 tf
BC5368 403 tf

Warning: BC4857 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
4716 1.10e+01 CacCTCa
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4717 1.10e+02 CGAAAGGCCTGTCAACGTTTAGC
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4820 3.50e-39 ATAAAGTGAAACTTTAATCAGtgG
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4821 1.50e-11 GagTctTACTgCCCataAATgcgg
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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 BC4857

BC4857 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
1,4-dihydroxy-2-naphthoate octaprenyltransferase cog/ cog
prenyltransferase activity go/ molecular_function
menaquinone biosynthetic process go/ biological_process
integral to membrane go/ cellular_component
Ubiquinone and other terpenoid-quinone biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
menA tigr/ tigrfam
Module neighborhood information for BC4857

BC4857 has total of 40 gene neighbors in modules 403, 455
Gene neighbors (40)
Gene Common Name Description Module membership
BC0038 BC0038 Tpl protein (NCBI ptt file) 81, 403
BC0039 BC0039 hypothetical protein (NCBI ptt file) 64, 403
BC0188 BC0188 Phosphoglucosamine mutase (NCBI ptt file) 394, 455
BC0417 BC0417 DNA topoisomerase I (NCBI ptt file) 235, 455
BC0469 BC0469 None 161, 455
BC0510 BC0510 Integral membrane protein (NCBI ptt file) 319, 455
BC0541 BC0541 Monofunctional biosynthetic peptidoglycan transglycosylase (NCBI ptt file) 18, 455
BC0667 BC0667 Bicyclomycin resistance protein (NCBI ptt file) 152, 403
BC1198 BC1198 GTP pyrophosphokinase (NCBI ptt file) 455, 513
BC1200 BC1200 Ribosomal large subunit pseudouridine synthase D (NCBI ptt file) 403, 474
BC1203 BC1203 Cell division protein ftsW (NCBI ptt file) 130, 455
BC1302 BC1302 Transcriptional regulator, GntR family (NCBI ptt file) 439, 455
BC1303 BC1303 (S)-2-hydroxy-acid oxidase, iron-sulfur chain (NCBI ptt file) 235, 455
BC1304 BC1304 iron-sulfur cluster-binding protein (NCBI ptt file) 235, 455
BC1305 BC1305 hypothetical protein (NCBI ptt file) 235, 455
BC2949 BC2949 hypothetical Membrane Spanning Protein (NCBI ptt file) 130, 455
BC3201 BC3201 Two component system histidine kinase (NCBI ptt file) 6, 455
BC3664 BC3664 N-acyl-L-amino acid amidohydrolase (NCBI ptt file) 15, 455
BC3669 BC3669 Murein hydrolase exporter (NCBI ptt file) 298, 403
BC3670 BC3670 Murein hydrolase export regulator (NCBI ptt file) 298, 403
BC3774 BC3774 Pyruvate synthase alpha chain (NCBI ptt file) 371, 455
BC4248 BC4248 hypothetical protein (NCBI ptt file) 235, 455
BC4293 BC4293 hypothetical Cytosolic Protein (NCBI ptt file) 371, 455
BC4294 BC4294 CBS domain containing protein (NCBI ptt file) 371, 455
BC4359 BC4359 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 235, 455
BC4495 BC4495 Germination protein germ (NCBI ptt file) 449, 455
BC4572 BC4572 hypothetical Cytosolic Protein (NCBI ptt file) 263, 455
BC4597 BC4597 hypothetical Membrane Spanning Protein (NCBI ptt file) 235, 455
BC4603 BC4603 Transcriptional regulator, GntR family (NCBI ptt file) 403, 474
BC4604 BC4604 NAD-dependent malic enzyme (NCBI ptt file) 201, 403
BC4798 BC4798 hypothetical protein (NCBI ptt file) 235, 455
BC4799 BC4799 hypothetical protein (NCBI ptt file) 235, 455
BC4800 BC4800 surface protein (NCBI ptt file) 235, 455
BC4855 BC4855 2-oxoglutarate decarboxylase (NCBI ptt file) 403, 467
BC4856 BC4856 Isochorismate synthase (NCBI ptt file) 403, 467
BC4857 BC4857 1,4-dihydroxy-2-naphthoate octaprenyltransferase (NCBI ptt file) 403, 455
BC4902 BC4902 Transcriptional regulator, AsnC family (NCBI ptt file) 175, 455
BC4903 BC4903 Gluconate 2-dehydrogenase (NCBI ptt file) 302, 455
BC5326 BC5326 hypothetical protein (NCBI ptt file) 403, 433
BC5368 BC5368 Transcriptional regulator pfoR (NCBI ptt file) 219, 403
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 BC4857
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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