Organism : Bacillus subtilis | Module List :
BSU01430 rpoA

DNA-directed RNA polymerase subunit alpha (RefSeq)

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 BSU01430
(Mouseover regulator name to see its description)

BSU01430 is regulated by 14 influences and regulates 29 modules.
Regulators for BSU01430 rpoA (14)
Regulator Module Operator
BSU01080 355 tf
BSU01430 355 tf
BSU01810 355 tf
BSU04680 355 tf
BSU16470 355 tf
BSU23210 355 tf
BSU25250 355 tf
BSU28820 355 tf
BSU33950 355 tf
BSU00470 139 tf
BSU01010 139 tf
BSU01080 139 tf
BSU01430 139 tf
BSU33950 139 tf

Warning: BSU01430 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
5230 1.80e+02 atAcggaTgT.AacaagGG
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5231 7.10e+02 AtAA.gGgTT
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5634 5.70e+02 aAAAGGaAtG
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5635 1.10e+03 cGcTTtaAcgGaa.gtTTTatG
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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 BSU01430

BSU01430 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 BSU01430

BSU01430 has total of 27 gene neighbors in modules 139, 355
Gene neighbors (27)
Gene Common Name Description Module membership
BSU00460 ipk 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (RefSeq) 139, 221
BSU00470 purR pur operon repressor (RefSeq) 139, 221
BSU01070 rpoB DNA-directed RNA polymerase subunit beta (RefSeq) 15, 139
BSU01080 rpoC DNA-directed RNA polymerase subunit beta' (RefSeq) 15, 139
BSU01120 fusA elongation factor G (RefSeq) 112, 139
BSU01390 infA translation initiation factor IF-1 (RefSeq) 139, 140
BSU01400 rpmJ 50S ribosomal protein L36 (RefSeq) 139, 140
BSU01410 rpsM 30S ribosomal protein S13 (RefSeq) 139, 140
BSU01420 rpsK 30S ribosomal protein S11 (RefSeq) 139, 140
BSU01430 rpoA DNA-directed RNA polymerase subunit alpha (RefSeq) 139, 355
BSU01440 rplQ 50S ribosomal protein L17 (RefSeq) 139, 355
BSU01870 ybcH hypothetical protein (RefSeq) 139, 377
BSU01880 ybcI hypothetical protein (RefSeq) 139, 377
BSU06690 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B (RefSeq) 15, 355
BSU13900 ptsH phosphocarrier protein HPr (RefSeq) 119, 355
BSU13910 ptsI phosphotransferase system (PTS) enzyme I (RefSeq) 119, 355
BSU14580 pdhA pyruvate dehydrogenase (E1 alpha subunit) (RefSeq) 247, 355
BSU14590 pdhB pyruvate dehydrogenase (E1 beta subunit) (RefSeq) 247, 355
BSU14600 pdhC branched-chain alpha-keto acid dehydrogenase subunit E2 (RefSeq) 194, 355
BSU14610 pdhD dihydrolipoamide dehydrogenase (RefSeq) 128, 355
BSU32740 metP methionine ABC transporter, permease component (RefSeq) 139, 191
BSU32750 metQ methionine ABC transporter (ATP-binding protein) (RefSeq) 139, 191
BSU33900 eno phosphopyruvate hydratase (RefSeq) 194, 355
BSU33910 pgm phosphoglyceromutase (RefSeq) 194, 355
BSU33920 tpiA triosephosphate isomerase (RefSeq) 194, 355
BSU33930 pgk phosphoglycerate kinase (RefSeq) 194, 355
BSU33940 gapA glyceraldehyde-3-phosphate dehydrogenase (RefSeq) 237, 355
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 BSU01430
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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