Organism : Bacillus cereus ATCC14579 | Module List :
BC0158

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

CircVis
Functional Annotations (13)
Function System
DNA-directed RNA polymerase, alpha subunit/40 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
protein dimerization activity go/ molecular_function
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
rpoA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0158
(Mouseover regulator name to see its description)

BC0158 is regulated by 18 influences and regulates 15 modules.
Regulators for BC0158 (18)
Regulator Module Operator
BC0158 82 tf
BC0601 82 tf
BC1537 82 tf
BC2108 82 tf
BC3592 82 tf
BC3844 82 tf
BC3868 82 tf
BC5141 82 tf
BC0122 292 tf
BC0158 292 tf
BC1996 292 tf
BC2766 292 tf
BC3253 292 tf
BC3356 292 tf
BC3720 292 tf
BC3844 292 tf
BC4212 292 tf
BC5352 292 tf

Warning: BC0158 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 2 motifs predicted.

Motif Table (2)
Motif Id e-value Consensus Motif Logo
4500 5.60e+01 CGGcCGC
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4501 1.50e+02 cAgGgAGAA.G.CT
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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 BC0158

BC0158 is enriched for 13 functions in 3 categories.
Enrichment Table (13)
Function System
DNA-directed RNA polymerase, alpha subunit/40 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
protein dimerization activity go/ molecular_function
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
rpoA tigr/ tigrfam
Module neighborhood information for BC0158

BC0158 has total of 29 gene neighbors in modules 82, 292
Gene neighbors (29)
Gene Common Name Description Module membership
BC0124 BC0124 LSU ribosomal protein L7AE (NCBI ptt file) 39, 292
BC0128 BC0128 Protein Translation Elongation Factor G (EF-G) (NCBI ptt file) 188, 292
BC0130 BC0130 SSU ribosomal protein S10P (NCBI ptt file) 39, 292
BC0131 BC0131 LSU ribosomal protein L3P (NCBI ptt file) 39, 292
BC0132 BC0132 LSU ribosomal protein L1E/L4P (NCBI ptt file) 39, 292
BC0133 BC0133 LSU ribosomal protein L23P (NCBI ptt file) 39, 292
BC0134 BC0134 LSU ribosomal protein L2P (NCBI ptt file) 39, 292
BC0135 BC0135 SSU ribosomal protein S19P (NCBI ptt file) 39, 292
BC0138 BC0138 LSU ribosomal protein L16P (NCBI ptt file) 82, 348
BC0139 BC0139 LSU ribosomal protein L29P (NCBI ptt file) 82, 348
BC0140 BC0140 SSU ribosomal protein S17P (NCBI ptt file) 82, 348
BC0141 BC0141 LSU ribosomal protein L14P (NCBI ptt file) 82, 348
BC0142 BC0142 LSU ribosomal protein L24P (NCBI ptt file) 82, 348
BC0143 BC0143 LSU ribosomal protein L5P (NCBI ptt file) 82, 348
BC0144 BC0144 SSU ribosomal protein S14P (NCBI ptt file) 82, 348
BC0145 BC0145 SSU ribosomal protein S8P (NCBI ptt file) 82, 348
BC0146 BC0146 LSU ribosomal protein L6P (NCBI ptt file) 82, 348
BC0147 BC0147 LSU ribosomal protein L18P (NCBI ptt file) 82, 348
BC0148 BC0148 SSU ribosomal protein S5P (NCBI ptt file) 82, 348
BC0149 BC0149 LSU ribosomal protein L30P (NCBI ptt file) 82, 348
BC0150 BC0150 LSU ribosomal protein L15P (NCBI ptt file) 82, 348
BC0151 BC0151 None 82, 292
BC0152 BC0152 Adenylate kinase (NCBI ptt file) 82, 292
BC0153 BC0153 Methionine aminopeptidase (NCBI ptt file) 292, 430
BC0154 BC0154 Bacterial Protein Translation Initiation Factor 1 (IF-1) (NCBI ptt file) 82, 292
BC0155 BC0155 LSU ribosomal protein L36P (NCBI ptt file) 292, 430
BC0156 BC0156 SSU ribosomal protein S13P (NCBI ptt file) 82, 292
BC0157 BC0157 SSU ribosomal protein S11P (NCBI ptt file) 82, 292
BC0158 BC0158 DNA-directed RNA polymerase alpha chain (NCBI ptt file) 82, 292
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 BC0158
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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