Organism : Bacillus subtilis | Module List :
BSU29230 dnaE

DNA polymerase III DnaE (RefSeq)

CircVis
Functional Annotations (13)
Function System
DNA polymerase III, alpha subunit cog/ cog
DNA binding go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
cytoplasm go/ cellular_component
DNA replication go/ biological_process
3'-5' exonuclease activity go/ molecular_function
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
DNA replication kegg/ kegg pathway
Mismatch repair kegg/ kegg pathway
Homologous recombination kegg/ kegg pathway
polc tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU29230
(Mouseover regulator name to see its description)

BSU29230 is regulated by 22 influences and regulates 0 modules.
Regulators for BSU29230 dnaE (22)
Regulator Module Operator
BSU00560 160 tf
BSU00830 160 tf
BSU02220 160 tf
BSU02500 160 tf
BSU04680 160 tf
BSU06960 160 tf
BSU15690 160 tf
BSU27080 160 tf
BSU27320 160 tf
BSU29110 160 tf
BSU31210 160 tf
BSU31530 160 tf
BSU37550 160 tf
BSU38700 160 tf
BSU40050 160 tf
BSU40410 160 tf
BSU40710 160 tf
BSU00330 54 tf
BSU09560 54 tf
BSU10840 54 tf
BSU38700 54 tf
BSU40410 54 tf

Warning: BSU29230 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
5066 1.30e-08 a.aaaaAaagaGggG
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5067 3.00e+03 AaAaGaAtATt
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5268 5.70e-02 GgaGGt.agca
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5269 4.60e+02 gAgaCAaAaaA
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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 BSU29230

BSU29230 is enriched for 13 functions in 3 categories.
Enrichment Table (13)
Function System
DNA polymerase III, alpha subunit cog/ cog
DNA binding go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
cytoplasm go/ cellular_component
DNA replication go/ biological_process
3'-5' exonuclease activity go/ molecular_function
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
DNA replication kegg/ kegg pathway
Mismatch repair kegg/ kegg pathway
Homologous recombination kegg/ kegg pathway
polc tigr/ tigrfam
Module neighborhood information for BSU29230

BSU29230 has total of 52 gene neighbors in modules 54, 160
Gene neighbors (52)
Gene Common Name Description Module membership
BSU00210 recR recombination protein RecR (RefSeq) 160, 188
BSU00250 xpaC putative phosphatase (RefSeq) 54, 68
BSU00260 yaaN hypothetical protein (RefSeq) 54, 166
BSU00270 yaaO putative lysine decarboxylase (RefSeq) 54, 225
BSU00280 tmk thymidylate kinase (RefSeq) 54, 225
BSU00290 yaaQ hypothetical protein (RefSeq) 54, 317
BSU00300 yaaR hypothetical protein (RefSeq) 54, 173
BSU00310 holB DNA polymerase III subunit delta' (RefSeq) 54, 173
BSU00320 yaaT hypothetical protein (RefSeq) 54, 225
BSU00330 yabA DNA replication intiation control protein YabA (RefSeq) 54, 173
BSU00690 ftsH cell-division protein and general stress protein (class III heat-shock) (RefSeq) 160, 243
BSU00890 yacL hypothetical protein (RefSeq) 54, 388
BSU00920 gltX glutamyl-tRNA synthetase (RefSeq) 160, 243
BSU04670 rsbRA component of the piezosome (stressosome); positive regulation of sigma(B) activity in response to salt and heat stress (RefSeq) 160, 243
BSU04680 rsbS antagonist of RsbT (RefSeq) 160, 243
BSU04690 rsbT switch protein/serine-threonine kinase; controls the activity of the piezosome (stressosome) (RefSeq) 160, 243
BSU04700 rsbU serine phosphatase; controls the activity of the piezosome (stressosome) (RefSeq) 160, 243
BSU04760 ydcG hypothetical protein (RefSeq) 54, 323
BSU08690 ygaD putative ABC transporter (ATP-binding protein) (RefSeq) 54, 377
BSU08960 yhbF hypothetical protein (RefSeq) 54, 317
BSU09640 yhdY putative integral membrane protein; putative small conductance mechano-sensitive channel (RefSeq) 54, 379
BSU10620 addB ATP-dependent deoxyribonuclease (subunit B) (RefSeq) 54, 370
BSU23050 fmnP FMN permease (RefSeq) 51, 54
BSU24850 glcK glucose kinase (RefSeq) 54, 323
BSU24860 yqgQ hypothetical protein (RefSeq) 54, 323
BSU29080 mutM formamidopyrimidine-DNA glycosylase (RefSeq) 160, 188
BSU29090 polA DNA polymerase I (RefSeq) 160, 188
BSU29230 dnaE DNA polymerase III DnaE (RefSeq) 54, 160
BSU31770 yueI hypothetical protein (RefSeq) 160, 252
BSU31780 yueH hypothetical protein (RefSeq) 31, 160
BSU33000 htrB HtrA-like serine protease (RefSeq) 54, 323
BSU33010 cssR two-component response regulator (RefSeq) 54, 310
BSU34730 yvcN putative acetyltransferase (RefSeq) 160, 188
BSU34740 crh phosphocarrier protein Chr (RefSeq) 160, 188
BSU34750 whiA putative morphogen (RefSeq) 160, 188
BSU34760 yvcK gluconeogenesis factor (RefSeq) 160, 188
BSU34770 yvcJ hypothetical protein (RefSeq) 160, 188
BSU34780 yvcI putative triphosphate pyrophosphate hydrolase (RefSeq) 160, 188
BSU35160 uvrA excinuclease ABC subunit A (RefSeq) 54, 68
BSU35170 uvrB excinuclease ABC subunit B (RefSeq) 54, 68
BSU36700 moaA molybdenum cofactor biosynthesis protein A (RefSeq) 160, 237
BSU36710 fdhD formate dehydrogenase accessory protein (RefSeq) 160, 237
BSU36910 ywlG hypothetical protein (RefSeq) 77, 160
BSU36920 ywlF ribose-5-phosphate isomerase B (RefSeq) 77, 160
BSU38020 thiD pyridoxal kinase (RefSeq) 82, 160
BSU38650 yxlG putative ABC-transporter (permease) (RefSeq) 54, 164
BSU38670 yxlE negative regulator of sigma-Y activity (RefSeq) 54, 164
BSU38680 yxlD putative sigma-Y antisigma factor component (RefSeq) 54, 164
BSU38690 yxlC sigma-Y antisigma factor (RefSeq) 54, 164
BSU38700 sigY RNA polymerase sigma factor SigY (RefSeq) 54, 164
BSU40060 gntK gluconate kinase (RefSeq) 54, 323
BSU40190 fbp fructose-1,6-bisphosphatase (RefSeq) 160, 252
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 BSU29230
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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