Organism : Bacillus cereus ATCC14579 | Module List :
BC5339

DNA-directed RNA polymerase delta chain (NCBI ptt file)

CircVis
Functional Annotations (11)
Function System
DNA-directed RNA polymerase, delta subunit cog/ cog
DNA binding go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
DNA-directed RNA polymerase I activity go/ molecular_function
DNA-directed RNA polymerase II activity go/ molecular_function
DNA-directed RNA polymerase III activity go/ molecular_function
transcription, DNA-dependent go/ biological_process
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC5339
(Mouseover regulator name to see its description)

BC5339 is regulated by 21 influences and regulates 61 modules.
Regulators for BC5339 (21)
Regulator Module Operator
BC0051 226 tf
BC0880 226 tf
BC1603 226 tf
BC3522 226 tf
BC3868 226 tf
BC4256 226 tf
BC4672 226 tf
BC5010 226 tf
BC5339 226 tf
BC0116 423 tf
BC0122 423 tf
BC1337 423 tf
BC1603 423 tf
BC3826 423 tf
BC3868 423 tf
BC4057 423 tf
BC4356 423 tf
BC4859 423 tf
BC5024 423 tf
BC5339 423 tf
BC5402 423 tf

Warning: BC5339 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
4368 2.70e+01 aAAaGgaaGtg
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4369 2.10e+02 aatAaGGAgAGgT
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4756 6.10e+01 GatGaa.gGaa
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4757 5.90e+03 CgTTtTgT
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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 BC5339

BC5339 is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
DNA-directed RNA polymerase, delta subunit cog/ cog
DNA binding go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
DNA-directed RNA polymerase I activity go/ molecular_function
DNA-directed RNA polymerase II activity go/ molecular_function
DNA-directed RNA polymerase III activity go/ molecular_function
transcription, DNA-dependent go/ biological_process
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
Module neighborhood information for BC5339

BC5339 has total of 27 gene neighbors in modules 226, 423
Gene neighbors (27)
Gene Common Name Description Module membership
BC0880 BC0880 putative transcriptional regulator (NCBI ptt file) 226, 350
BC1048 BC1048 IG hypothetical 17707 (NCBI ptt file) 226, 350
BC1049 BC1049 Bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) (NCBI ptt file) 15, 226
BC1159 BC1159 nucleotide-binding protein (RefSeq) 226, 406
BC1169 BC1169 hypothetical protein (NCBI ptt file) 226, 296
BC1472 BC1472 Ribosomal large subunit pseudouridine synthase B (NCBI ptt file) 147, 423
BC1497 BC1497 Cytidylate kinase (NCBI ptt file) 231, 423
BC2200 BC2200 DegV family protein (NCBI ptt file) 226, 300
BC2933 BC2933 ABC transporter ATP-binding protein (NCBI ptt file) 236, 423
BC3680 BC3680 hypothetical Exported Protein (NCBI ptt file) 226, 350
BC3946 BC3946 Heme O monooxygenase (NCBI ptt file) 198, 423
BC3977 BC3977 Zn-dependent hydrolase (NCBI ptt file) 226, 474
BC4057 BC4057 Transcriptional regulator, LuxR family (NCBI ptt file) 147, 423
BC4274 BC4274 hypothetical protein (NCBI ptt file) 226, 270
BC4410 BC4410 Protein translocase subunit YajC (NCBI ptt file) 226, 251
BC4480 BC4480 Trigger factor, ppiase (NCBI ptt file) 270, 423
BC4649 BC4649 Septation ring formation regulator (NCBI ptt file) 226, 296
BC4657 BC4657 Tyrosyl-tRNA synthetase (NCBI ptt file) 236, 423
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
BC4735 BC4735 hypothetical protein (NCBI ptt file) 226, 300
BC4925 BC4925 NADH dehydrogenase (NCBI ptt file) 231, 423
BC4962 BC4962 Fructose-1,6-bisphosphatase (NCBI ptt file) 231, 423
BC4963 BC4963 hypothetical Cytosolic Protein (NCBI ptt file) 231, 423
BC5088 BC5088 putative lantibiotic precursor peptide (NCBI ptt file) 226, 513
BC5338 BC5338 CTP synthase (NCBI ptt file) 236, 423
BC5339 BC5339 DNA-directed RNA polymerase delta chain (NCBI ptt file) 226, 423
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 BC5339
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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