Organism : Bacillus subtilis | Module List :
BSU32140 paiB

putative enzyme (RefSeq)

CircVis
Functional Annotations (2)
Function System
Transcriptional regulator cog/ cog
FMN binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU32140
(Mouseover regulator name to see its description)

BSU32140 is regulated by 24 influences and regulates 5 modules.
Regulators for BSU32140 paiB (24)
Regulator Module Operator
BSU11930 241 tf
BSU13880 241 tf
BSU14240 241 tf
BSU14380 241 tf
BSU17080 241 tf
BSU17450 241 tf
BSU27320 241 tf
BSU29700 241 tf
BSU32140 241 tf
BSU32420 241 tf
BSU37580 241 tf
BSU38420 241 tf
BSU04770 270 tf
BSU05370 270 tf
BSU05850 270 tf
BSU08410 270 tf
BSU09480 270 tf
BSU10510 270 tf
BSU25100 270 tf
BSU26430 270 tf
BSU29000 270 tf
BSU33670 270 tf
BSU39990 270 tf
BSU40010 270 tf

Warning: BSU32140 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
5424 5.20e-01 aaaTtctTaatAAaGGGGa
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5425 4.00e+03 TGttccgGaA.acAt
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5478 8.40e-01 cTgTgcaGaAcGcaggTcgtc
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5479 8.10e-01 AAAcCCcTggctcATtTTTttTGc
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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 BSU32140

BSU32140 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Transcriptional regulator cog/ cog
FMN binding go/ molecular_function
Module neighborhood information for BSU32140

BSU32140 has total of 50 gene neighbors in modules 241, 270
Gene neighbors (50)
Gene Common Name Description Module membership
BSU04320 ydaO putative metabolite transporter (RefSeq) 38, 270
BSU05690 ydhB putative integral inner membrane protein (RefSeq) 270, 294
BSU05700 ydhC putative transcriptional regulator (GntR family) (RefSeq) 270, 323
BSU07400 yfmO metal efflux transporter (RefSeq) 161, 270
BSU08400 yfiU putative efflux transporter (RefSeq) 270, 327
BSU08530 yfhH hypothetical protein (RefSeq) 94, 270
BSU09680 nhaC Na+/H+ antiporter (RefSeq) 22, 241
BSU15520 carB carbamoyl phosphate synthase large subunit (RefSeq) 241, 267
BSU17600 xylA xylose isomerase (RefSeq) 19, 241
BSU17700 cotC spore coat protein (outer) (RefSeq) 241, 283
BSU21810 dfrA dihydrofolate reductase (RefSeq) 228, 270
BSU21820 thyA thymidylate synthase (RefSeq) 270, 301
BSU23540 yqkK hypothetical protein (RefSeq) 129, 270
BSU23700 yqjX hypothetical protein (RefSeq) 161, 270
BSU23710 yqjW DNA polymerase IV (RefSeq) 161, 270
BSU23720 yqzH hypothetical protein (RefSeq) 159, 270
BSU26190 yqaT putative phage-related terminase large subunit; skin element (RefSeq) 238, 270
BSU26420 yrkQ two-component sensor histidine kinase [YrkP] (RefSeq) 129, 270
BSU26540 yrkE hypothetical protein (RefSeq) 71, 270
BSU26660 yrdN putative tautomerase (RefSeq) 129, 270
BSU26670 gltR transcriptional regulator (LysR family) (RefSeq) 38, 270
BSU26680 yrdK hypothetical protein (RefSeq) 89, 270
BSU26810 yrpC glutamate racemase (RefSeq) 270, 310
BSU27140 oatA peptidoglycan O-acetyltransferase (RefSeq) 38, 270
BSU28180 ysxD putative integral inner membrane protein (RefSeq) 151, 270
BSU29000 nrdR transcriptional regulator NrdR (RefSeq) 94, 270
BSU29010 speD S-adenosylmethionine decarboxylase proenzyme (RefSeq) 22, 241
BSU29020 gapB glyceraldehyde-3-phosphate dehydrogenase (RefSeq) 55, 241
BSU29200 accA acetyl-CoA carboxylase carboxyltransferase subunit alpha (RefSeq) 241, 293
BSU29210 accD acetyl-CoA carboxylase subunit beta (RefSeq) 241, 293
BSU30560 pckA phosphoenolpyruvate carboxykinase (RefSeq) 55, 241
BSU32140 paiB putative enzyme (RefSeq) 241, 270
BSU32150 paiA polyamine N-acetyltransferase (RefSeq) 241, 317
BSU34410 yveG hypothetical protein (RefSeq) 161, 241
BSU36100 ywrD putative gamma-glutamyltransferase (RefSeq) 241, 246
BSU37370 albA putative antilisterial bacteriocin (subtilosin) production enzyme (RefSeq) 189, 241
BSU37380 albB putative membrane component involved in subtilosin production (RefSeq) 189, 241
BSU37390 albC putative transporter involved in subtilosin production (RefSeq) 241, 335
BSU37400 albD putative integral inner membrane protein involved in subtilosin production and immunity (RefSeq) 241, 335
BSU37410 albE putative hydrolase involved in subtilosin production (RefSeq) 241, 335
BSU37420 albF putative peptidase involved in subtilosin production (RefSeq) 241, 335
BSU37430 albG putative integral inner membrane protein involved in subtilosin production and immunity (RefSeq) 241, 405
BSU37630 ywfM putative transporter (RefSeq) 98, 241
BSU37930 ywdK hypothetical protein (RefSeq) 233, 241
BSU38420 sacY transcriptional antiterminator (RefSeq) 241, 246
BSU39990 yxaF transcriptional regulator (RefSeq) 38, 270
BSU40010 yxaD putative transcriptional regulator (MarR family) (RefSeq) 161, 270
BSU40710 yybA putative transcriptional regulator (MarR family) (RefSeq) 270, 310
BSU40720 yyaT putative acetyltransferase (RefSeq) 151, 270
BSU40730 yyaS putative integral inner membrane protein (RefSeq) 151, 270
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 BSU32140
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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