Organism : Bacillus subtilis | Module List :
BSU38700 sigY

RNA polymerase sigma factor SigY (RefSeq)

CircVis
Functional Annotations (7)
Function System
DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
RNA polymerase kegg/ kegg pathway
sigma70-ECF tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU38700
(Mouseover regulator name to see its description)

BSU38700 is regulated by 15 influences and regulates 12 modules.
Regulators for BSU38700 sigY (15)
Regulator Module Operator
BSU00330 54 tf
BSU09560 54 tf
BSU10840 54 tf
BSU38700 54 tf
BSU40410 54 tf
BSU00330 164 tf
BSU03750 164 tf
BSU04460 164 tf
BSU10830 164 tf
BSU10840 164 tf
BSU14380 164 tf
BSU28550 164 tf
BSU31210 164 tf
BSU34180 164 tf
BSU38700 164 tf

Warning: BSU38700 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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5276 8.60e-02 AaaaGGaGaaA
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5277 3.30e+02 AAACgcTtctt
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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 BSU38700

BSU38700 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
RNA polymerase kegg/ kegg pathway
sigma70-ECF tigr/ tigrfam
Module neighborhood information for BSU38700

BSU38700 has total of 53 gene neighbors in modules 54, 164
Gene neighbors (53)
Gene Common Name Description Module membership
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
BSU00890 yacL hypothetical protein (RefSeq) 54, 388
BSU01845 BSU01845 None 24, 164
BSU04330 mutT putative NTP pyrophosphohydrolase (RefSeq) 164, 341
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
BSU10820 yisQ putative Na+driven efflux transporter (RefSeq) 50, 164
BSU10830 yisR putative transcriptional regulator (AraC/XylS family) (RefSeq) 50, 164
BSU10840 degA transcriptional regulator (LacI family) (RefSeq) 50, 164
BSU14380 fruR transcriptional regulator (DeoR family) (RefSeq) 22, 164
BSU14390 fruK fructose-1-phosphate kinase (RefSeq) 22, 164
BSU14400 fruA phosphotransferase system (PTS) fructose-specific enzyme IIABC component (RefSeq) 50, 164
BSU15850 sdaAB L-serine dehydratase (beta chain) (RefSeq) 164, 228
BSU15860 sdaAA L-serine dehydratase (alpha chain) (RefSeq) 164, 228
BSU15870 recG ATP-dependent DNA helicase RecG (RefSeq) 164, 228
BSU17010 ymcB (dimethylallyl)adenosine tRNA methylthiotransferase (RefSeq) 22, 164
BSU19230 yocJ azoreductase (RefSeq) 66, 164
BSU21850 ypiP putative methyltransferase (RefSeq) 164, 179
BSU23050 fmnP FMN permease (RefSeq) 51, 54
BSU24850 glcK glucose kinase (RefSeq) 54, 323
BSU24860 yqgQ hypothetical protein (RefSeq) 54, 323
BSU29230 dnaE DNA polymerase III DnaE (RefSeq) 54, 160
BSU32170 dapF diaminopimelate epimerase (RefSeq) 164, 258
BSU33000 htrB HtrA-like serine protease (RefSeq) 54, 323
BSU33010 cssR two-component response regulator (RefSeq) 54, 310
BSU33370 yvgK putative molybdate binding regulator (RefSeq) 164, 258
BSU35160 uvrA excinuclease ABC subunit A (RefSeq) 54, 68
BSU35170 uvrB excinuclease ABC subunit B (RefSeq) 54, 68
BSU38650 yxlG putative ABC-transporter (permease) (RefSeq) 54, 164
BSU38660 yxlF putative ABC transporter component (ATP-binding protein) (RefSeq) 52, 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
BSU39400 pdp pyrimidine-nucleoside phosphorylase (RefSeq) 22, 164
BSU39410 nupC pyrimidine-nucleoside Na+(H+) cotransporter (RefSeq) 4, 164
BSU40060 gntK gluconate kinase (RefSeq) 54, 323
VIMSS37306 VIMSS37306 None 24, 164
VIMSS37406 VIMSS37406 None 164, 187
VIMSS37650 VIMSS37650 None 164, 189
VIMSS37717 VIMSS37717 None 34, 164
VIMSS38219 VIMSS38219 None 164, 235
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 BSU38700
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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