Organism : Bacillus subtilis | Module List :
BSU38420 sacY

transcriptional antiterminator (RefSeq)

CircVis
Functional Annotations (2)
Function System
RNA binding go/ molecular_function
positive regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU38420
(Mouseover regulator name to see its description)

BSU38420 is regulated by 17 influences and regulates 5 modules.
Regulators for BSU38420 sacY (17)
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
BSU04460 246 tf
BSU07820 246 tf
BSU09480 246 tf
BSU27120 246 tf
BSU33950 246 tf

Warning: BSU38420 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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5434 3.80e-05 TtaTacttaAaaagggGgAt
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5435 4.20e-03 Aa.gAC.ttAaagGAgAAGcT
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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 BSU38420

BSU38420 is enriched for 2 functions in 2 categories.
Enrichment Table (2)
Function System
RNA binding go/ molecular_function
positive regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BSU38420

BSU38420 has total of 47 gene neighbors in modules 241, 246
Gene neighbors (47)
Gene Common Name Description Module membership
BSU00400 yabE putative cell wall shaping enzyme (RefSeq) 53, 246
BSU02730 natK two-component sensor histidine kinase [NatR] (RefSeq) 130, 246
BSU02740 natR two-component response regulator [NatK] (RefSeq) 130, 246
BSU02750 natA Na+ ABC efflux transporter (ATP-binding protein) (RefSeq) 130, 246
BSU02760 natB Na+ ABC efflux transporter (permease) (RefSeq) 130, 246
BSU04440 dctB C4-dicarboxylate binding protein (RefSeq) 246, 361
BSU04450 dctS two-component sensor histidine kinase (RefSeq) 246, 361
BSU04460 dctR two-component response regulator (RefSeq) 246, 361
BSU08120 yfjF hypothetical protein (RefSeq) 55, 246
BSU09150 yhcN putative lipoprotein (RefSeq) 43, 246
BSU09680 nhaC Na+/H+ antiporter (RefSeq) 22, 241
BSU12490 yjqC putative PBSX phage manganese-containing catalase (RefSeq) 231, 246
BSU15520 carB carbamoyl phosphate synthase large subunit (RefSeq) 241, 267
BSU17070 ymcC putative integral inner membrane protein (RefSeq) 246, 285
BSU17600 xylA xylose isomerase (RefSeq) 19, 241
BSU17640 alrB alanine racemase (RefSeq) 246, 301
BSU17700 cotC spore coat protein (outer) (RefSeq) 241, 283
BSU18860 yozH hypothetical protein (RefSeq) 246, 411
BSU22920 ypeB spore membrane component (RefSeq) 246, 357
BSU22930 sleB spore cortex-lytic enzyme (RefSeq) 246, 357
BSU23390 spoVAF stage V sporulation protein AF (RefSeq) 246, 357
BSU24230 spoIVB regulatory membrane-associated serine protease (RefSeq) 246, 357
BSU25080 yqfX hypothetical protein (RefSeq) 43, 246
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
BSU32720 yurZ hypothetical protein (RefSeq) 246, 301
BSU34410 yveG hypothetical protein (RefSeq) 161, 241
BSU36100 ywrD putative gamma-glutamyltransferase (RefSeq) 241, 246
BSU37190 clsB cardiolipin synthetase (RefSeq) 22, 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
BSU39029 yxiT 150, 246
BSU40320 argI arginase (RefSeq) 229, 246
BSU40330 rocE arginine/ornithine/gamma-aminobutyrate permease (RefSeq) 229, 246
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 BSU38420
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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