Organism : Bacillus cereus ATCC14579 | Module List :
BC0122

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

CircVis
Functional Annotations (12)
Function System
DNA-directed RNA polymerase, beta subunit/140 kD 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
rpoB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0122
(Mouseover regulator name to see its description)

BC0122 is regulated by 16 influences and regulates 55 modules.
Regulators for BC0122 (16)
Regulator Module Operator
BC0059 366 tf
BC0116 366 tf
BC0123 366 tf
BC1004 366 tf
BC3814 366 tf
BC3826 366 tf
BC4277 366 tf
BC0051 357 tf
BC0122 357 tf
BC0123 357 tf
BC0518 357 tf
BC1059 357 tf
BC1710 357 tf
BC2340 357 tf
BC4072 357 tf
BC4703 357 tf

Warning: BC0122 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
4624 2.20e-01 AGatgctaggG
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4625 5.40e+02 AaGgGgtGcttgTTT
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4642 2.30e+01 AGCAcgtA
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4643 6.10e+02 gcggagcCTtc
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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 BC0122

BC0122 is enriched for 12 functions in 3 categories.
Enrichment Table (12)
Function System
DNA-directed RNA polymerase, beta subunit/140 kD 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
rpoB tigr/ tigrfam
Module neighborhood information for BC0122

BC0122 has total of 36 gene neighbors in modules 357, 366
Gene neighbors (36)
Gene Common Name Description Module membership
BC0006 BC0006 DNA gyrase subunit A (NCBI ptt file) 75, 357
BC0109 BC0109 Serine acetyltransferase (NCBI ptt file) 240, 357
BC0110 BC0110 Cysteinyl-tRNA synthetase (NCBI ptt file) 240, 357
BC0111 BC0111 hypothetical protein (NCBI ptt file) 240, 357
BC0112 BC0112 23S rRNA methyltransferase (NCBI ptt file) 240, 357
BC0113 BC0113 hypothetical Cytosolic Protein (NCBI ptt file) 357, 484
BC0121 BC0121 16S rRNA m(2)G 1207 methyltransferase (NCBI ptt file) 92, 366
BC0122 BC0122 DNA-directed RNA polymerase beta chain (NCBI ptt file) 357, 366
BC0123 BC0123 DNA-directed RNA polymerase beta' chain (NCBI ptt file) 357, 366
BC0160 BC0160 Cobalt transport ATP-binding protein cbiO (NCBI ptt file) 157, 366
BC0161 BC0161 Cobalt transport ATP-binding protein cbiO (NCBI ptt file) 157, 366
BC0162 BC0162 Cobalt transport protein cbiQ (NCBI ptt file) 157, 366
BC1474 BC1474 ResB protein (NCBI ptt file) 150, 357
BC1475 BC1475 ResB protein (NCBI ptt file) 150, 357
BC1476 BC1476 Protein resC (NCBI ptt file) 150, 357
BC2984 BC2984 Immune inhibitor A precursor (NCBI ptt file) 357, 509
BC3809 BC3809 Ribosome-binding factor A (NCBI ptt file) 71, 366
BC3814 BC3814 N utilization substance protein A (NCBI ptt file) 366, 476
BC3815 BC3815 hypothetical Cytosolic Protein (NCBI ptt file) 71, 366
BC3819 BC3819 1-deoxy-D-xylulose 5-phosphate reductoisomerase (NCBI ptt file) 182, 366
BC3821 BC3821 Undecaprenyl pyrophosphate synthetase (NCBI ptt file) 366, 471
BC3835 BC3835 Ribonuclease HII (NCBI ptt file) 366, 476
BC3836 BC3836 GTP-binding protein (NCBI ptt file) 269, 366
BC3837 BC3837 Signal peptidase I (NCBI ptt file) 312, 366
BC3941 BC3941 Cytochrome c oxidase polypeptide IVB (NCBI ptt file) 357, 405
BC3942 BC3942 Cytochrome c oxidase polypeptide III (NCBI ptt file) 357, 405
BC3943 BC3943 Cytochrome c oxidase polypeptide I (NCBI ptt file) 161, 357
BC3944 BC3944 Cytochrome c oxidase polypeptide II (NCBI ptt file) 161, 357
BC4434 BC4434 GTP-binding protein (NCBI ptt file) 14, 366
BC4435 BC4435 Sporulation initiation phosphotransferase B (NCBI ptt file) 14, 366
BC4492 BC4492 putative phosphoesterase (NCBI ptt file) 182, 357
BC4494 BC4494 Ribonuclease PH (NCBI ptt file) 313, 357
BC5305 BC5305 ATP synthase epsilon chain (NCBI ptt file) 182, 357
BC5306 BC5306 ATP synthase beta chain (NCBI ptt file) 182, 357
BC5307 BC5307 ATP synthase gamma chain (NCBI ptt file) 182, 357
BC5308 BC5308 F0F1 ATP synthase subunit alpha (RefSeq) 182, 357
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 BC0122
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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