Organism : Bacillus cereus ATCC14579 | Module List :
BC1355

Ribonucleoside-diphosphate reductase beta chain (NCBI ptt file)

CircVis
Functional Annotations (7)
Function System
Ribonucleotide reductase, beta subunit cog/ cog
ribonucleoside-diphosphate reductase activity go/ molecular_function
deoxyribonucleoside diphosphate metabolic process go/ biological_process
transition metal ion binding go/ molecular_function
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC1355
(Mouseover regulator name to see its description)

BC1355 is regulated by 25 influences and regulates 0 modules.
Regulators for BC1355 (25)
Regulator Module Operator
BC0116 66 tf
BC0122 66 tf
BC1080 66 tf
BC2410 66 tf
BC2672 66 tf
BC2773 66 tf
BC3982 66 tf
BC4010 66 tf
BC4057 66 tf
BC4356 66 tf
BC5339 66 tf
BC0059 145 tf
BC0122 145 tf
BC1080 145 tf
BC1477 145 tf
BC1889 145 tf
BC2672 145 tf
BC3653 145 tf
BC3814 145 tf
BC3868 145 tf
BC3982 145 tf
BC4356 145 tf
BC4393 145 tf
BC4842 145 tf
BC5339 145 tf

Warning: BC1355 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
4052 2.60e+02 TataAgagGGaG.g
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4053 1.80e+03 cAGAAG
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4206 9.50e+01 GGagGgG
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4207 3.40e+03 GCgGGt.AaG.cG
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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 BC1355

BC1355 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Ribonucleotide reductase, beta subunit cog/ cog
ribonucleoside-diphosphate reductase activity go/ molecular_function
deoxyribonucleoside diphosphate metabolic process go/ biological_process
transition metal ion binding go/ molecular_function
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Module neighborhood information for BC1355

BC1355 has total of 23 gene neighbors in modules 66, 145
Gene neighbors (23)
Gene Common Name Description Module membership
BC0340 BC0340 DNA helicase II (NCBI ptt file) 145, 319
BC0342 BC0342 Sex pheromone staph-cAM373 precursor (NCBI ptt file) 22, 145
BC0350 BC0350 Glutamyl-tRNA(Gln) amidotransferase subunit C (NCBI ptt file) 145, 319
BC0351 BC0351 Glutamyl-tRNA(Gln) amidotransferase subunit A (NCBI ptt file) 22, 145
BC0352 BC0352 Glutamyl-tRNA(Gln) amidotransferase subunit B (NCBI ptt file) 145, 311
BC1354 BC1354 Ribonucleoside-diphosphate reductase alpha chain (NCBI ptt file) 66, 319
BC1355 BC1355 Ribonucleoside-diphosphate reductase beta chain (NCBI ptt file) 66, 145
BC1383 BC1383 Na+ driven multidrug efflux pump (NCBI ptt file) 66, 79
BC1554 BC1554 Recombination protein recU (NCBI ptt file) 145, 319
BC3542 BC3542 Transcriptional regulator (NCBI ptt file) 66, 236
BC3870 BC3870 hypothetical protein (NCBI ptt file) 145, 513
BC3963 BC3963 Transglutaminase (NCBI ptt file) 145, 388
BC4175 BC4175 putative cell adhesion protein (contact hemolysin TlyA-related) (NCBI ptt file) 22, 145
BC4249 BC4249 UDP-N-acetylglucosamine--N-acetylmuramyl-(Pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase (NCBI ptt file) 27, 66
BC4389 BC4389 Exodeoxyribonuclease V alpha chain (NCBI ptt file) 145, 367
BC4411 BC4411 Queuine tRNA-ribosyltransferase (NCBI ptt file) 66, 79
BC4552 BC4552 None 145, 479
BC4704 BC4704 Ribosomal small subunit pseudouridine synthase A (NCBI ptt file) 66, 423
BC4705 BC4705 Export protein for polysaccharides and teichoic acids (NCBI ptt file) 66, 423
BC5393 BC5393 hypothetical protein (NCBI ptt file) 22, 145
BC5430 BC5430 Oligosaccharide translocase (flippase) (NCBI ptt file) 117, 145
BC5433 BC5433 ABC transporter ATP-binding protein uup (NCBI ptt file) 66, 319
BC5454 BC5454 Molybdenum cofactor biosynthesis enzyme and related Fe-S oxidoreductases (NCBI ptt file) 66, 236
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 BC1355
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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