Organism : Bacillus subtilis | Module List :
BSU00230 bofA

inhibitor of the pro-sigma(K) processing machinery (RefSeq)

CircVis
Functional Annotations (1)
Function System
spore_BofA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU00230
(Mouseover regulator name to see its description)

BSU00230 is regulated by 21 influences and regulates 7 modules.
Regulators for BSU00230 bofA (21)
Regulator Module Operator
BSU00230 179 tf
BSU03560 179 tf
BSU04460 179 tf
BSU16470 179 tf
BSU21780 179 tf
BSU23590 179 tf
BSU37580 179 tf
BSU00230 377 tf
BSU00700 377 tf
BSU01730 377 tf
BSU07590 377 tf
BSU09480 377 tf
BSU09510 377 tf
BSU15970 377 tf
BSU29630 377 tf
BSU33680 377 tf
BSU34380 377 tf
BSU34630 377 tf
BSU35110 377 tf
BSU36420 377 tf
BSU37160 377 tf

Warning: BSU00230 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
5306 2.40e+01 TCttCTC.TTgCct
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5307 2.30e+03 AGGGaaGC
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5668 7.20e+03 gAcAgtt.AaAATggg.gggTgga
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5669 1.30e+04 CtGaCtaGTtctG
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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 BSU00230

BSU00230 is enriched for 1 functions in 4 categories.
Enrichment Table (1)
Function System
spore_BofA tigr/ tigrfam
Module neighborhood information for BSU00230

BSU00230 has total of 29 gene neighbors in modules 179, 377
Gene neighbors (29)
Gene Common Name Description Module membership
BSU00230 bofA inhibitor of the pro-sigma(K) processing machinery (RefSeq) 179, 377
BSU00600 yabP spore protein involved in the shaping of the spore coat (RefSeq) 324, 377
BSU00610 yabQ membrane protein of the forespore (RefSeq) 324, 377
BSU00630 yabR hypothetical protein (RefSeq) 7, 377
BSU01860 ybcF putative carbonic anhydrase (RefSeq) 220, 377
BSU01870 ybcH hypothetical protein (RefSeq) 139, 377
BSU01880 ybcI hypothetical protein (RefSeq) 139, 377
BSU04630 ydcC putative lipoprotein (RefSeq) 124, 377
BSU08610 yfhO hypothetical protein (RefSeq) 40, 377
BSU08690 ygaD putative ABC transporter (ATP-binding protein) (RefSeq) 54, 377
BSU12420 yjoB ATPase possibly involved in protein degradation (RefSeq) 166, 377
BSU15130 yllB cell division protein MraZ (RefSeq) 166, 377
BSU15150 ftsL cell-division protein (RefSeq) 170, 377
BSU15160 pbpB penicillin-binding protein 2B (RefSeq) 170, 377
BSU18650 pelB pectin lyase (RefSeq) 159, 179
BSU21850 ypiP putative methyltransferase (RefSeq) 164, 179
BSU22030 ypbR putative GTP-binding protein (RefSeq) 102, 179
BSU22040 ypbQ putative integral inner membrane enzyme (RefSeq) 179, 276
BSU22050 bcsA terpene family molecule synthase (RefSeq) 179, 276
BSU22990 ypbF hypothetical protein (RefSeq) 377, 402
BSU25030 yqgC putative integral inner membrane protein (RefSeq) 187, 377
BSU30700 rpmE2 50S ribosomal protein L31 type B (RefSeq) 377, 402
BSU32130 guaC guanosine 5'-monophosphate oxidoreductase (RefSeq) 14, 377
BSU35100 yvlD putative integral inner membrane protein (RefSeq) 166, 377
BSU35110 yvlC putative regulator (stress mediated) (RefSeq) 166, 377
BSU35120 yvlB hypothetical protein (RefSeq) 166, 377
BSU35130 yvlA hypothetical protein (RefSeq) 166, 377
BSU39980 qodI quercetin dioxygenase (RefSeq) 179, 406
BSU40930 yyaE putative oxidoreductase (RefSeq) 179, 370
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 BSU00230
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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