Organism : Bacillus subtilis | Module List :
BSU26340 yqaF

putative transcriptional regulator; skin element (RefSeq)

CircVis
Functional Annotations (1)
Function System
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU26340
(Mouseover regulator name to see its description)

BSU26340 is regulated by 23 influences and regulates 18 modules.
Regulators for BSU26340 yqaF (23)
Regulator Module Operator
BSU02000 206 tf
BSU02070 206 tf
BSU06140 206 tf
BSU09500 206 tf
BSU26220 206 tf
BSU26320 206 tf
BSU26340 206 tf
BSU26840 206 tf
BSU30150 206 tf
BSU36600 206 tf
BSU02320 205 tf
BSU03890 205 tf
BSU04820 205 tf
BSU05170 205 tf
BSU05970 205 tf
BSU06140 205 tf
BSU06700 205 tf
BSU22120 205 tf
BSU25760 205 tf
BSU26220 205 tf
BSU26340 205 tf
BSU35030 205 tf
BSU36600 205 tf

Warning: BSU26340 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
5354 5.70e+00 aaaataAaaaAgGGc
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5355 6.30e+03 GAAcATTTTCGGT
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5356 1.20e+00 CCtcTCCTTtAtCtTTAT
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5357 1.90e+02 TgCcTccT.TTTTTaATCaTt
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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 BSU26340

BSU26340 is enriched for 1 functions in 2 categories.
Enrichment Table (1)
Function System
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for BSU26340

BSU26340 has total of 40 gene neighbors in modules 205, 206
Gene neighbors (40)
Gene Common Name Description Module membership
BSU02250 ybfJ putative lipoprotein (RefSeq) 8, 205
BSU02380 ybgB hypothetical protein (RefSeq) 206, 285
BSU04360 mntH manganese transport protein MntH (RefSeq) 95, 205
BSU04540 ydbO putative cation efflux system (RefSeq) 74, 205
BSU05780 ydhJ putative metal-dependent phosphohydrolase (RefSeq) 142, 205
BSU06130 ydjC hypothetical protein (RefSeq) 205, 364
BSU07410 yfmN hypothetical protein (RefSeq) 83, 205
BSU07560 pel pectate lyase (RefSeq) 8, 205
BSU08760 spo0M sporulation-control gene (RefSeq) 183, 205
BSU10870 yisU putative aminoacid related metabolite efflux transporter (RefSeq) 52, 206
BSU11100 nprB extracellular neutral protease B (RefSeq) 10, 205
BSU13330 ykoL hypothetical protein (RefSeq) 74, 205
BSU13990 kinA sporulation-specific ATP-dependent protein histidine kinase (RefSeq) 205, 359
BSU14330 yknV putative ABC transporter (ATP-binding protein) (RefSeq) 88, 205
BSU17560 ynaI hypothetical protein (RefSeq) 205, 222
BSU17740 ynzB hypothetical protein (RefSeq) 39, 206
BSU17760 yndE putative spore germination integral inner membrane protein (RefSeq) 205, 278
BSU18680 yoaO hypothetical protein (RefSeq) 39, 205
BSU21950 ypzA hypothetical protein (RefSeq) 8, 205
BSU23530 spoIIM autolysin component for dissolution of the septal cell wall (stage II sporulation) (RefSeq) 206, 286
BSU25220 antE hypothetical protein (RefSeq) 205, 233
BSU25900 cwlA N-acetylmuramoyl-L-alanine amidase; skin element (RefSeq) 44, 206
BSU25910 yqxH putative holin; skin element (RefSeq) 44, 206
BSU25920 yqxG putative phage-related lytic exoenzyme; skin element (RefSeq) 206, 371
BSU25930 yqcE conserved hypothetical protein; skin element (RefSeq) 205, 206
BSU26140 yqbE putative phage capsid protein; skin element (RefSeq) 206, 371
BSU26150 yqbD putative DNA wielding protein; skin element (RefSeq) 129, 206
BSU26220 yqaQ conserved hypothetical protein; skin element (RefSeq) 205, 305
BSU26250 yqaN putative Holliday junction resolvase; skin element (RefSeq) 52, 206
BSU26300 yqaI hypothetical protein; skin element (RefSeq) 205, 371
BSU26330 yqdA hypothetical protein; skin element (RefSeq) 205, 206
BSU26340 yqaF putative transcriptional regulator; skin element (RefSeq) 205, 206
BSU26840 sigZ RNA polymerase sigma factor SigZ (RefSeq) 44, 206
BSU26850 yrpG putative oxidoreductase (RefSeq) 206, 301
BSU29270 ytoI hypothetical protein (RefSeq) 206, 404
BSU29320 ytnI putative redoxin (RefSeq) 206, 333
BSU31590 yufS putative bacteriocin (RefSeq) 39, 206
BSU37450 ywhK factor interacting with DNA helicase PcrA (RefSeq) 108, 206
BSU38060 ywcJ formate/nitrite transporter (RefSeq) 74, 206
BSU39040 yxiS hypothetical protein (RefSeq) 47, 206
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 BSU26340
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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