Organism : Bacillus subtilis | Module List :
BSU15880 ylpC

fatty acid biosynthesis transcriptional regulator (RefSeq)

CircVis
Functional Annotations (1)
Function System
Uncharacterized protein, possibly involved in aromatic compounds catabolism cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU15880
(Mouseover regulator name to see its description)

BSU15880 is regulated by 20 influences and regulates 13 modules.
Regulators for BSU15880 ylpC (20)
Regulator Module Operator
BSU01010 309 tf
BSU02500 309 tf
BSU04650 309 tf
BSU15880 309 tf
BSU25200 309 tf
BSU29740 309 tf
BSU31680 309 tf
BSU35520 309 tf
BSU01070 343 tf
BSU01810 343 tf
BSU04650 343 tf
BSU05460 343 tf
BSU10560 343 tf
BSU15880 343 tf
BSU16600 343 tf
BSU24100 343 tf
BSU26390 343 tf
BSU28400 343 tf
BSU28820 343 tf
BSU33030 343 tf

Warning: BSU15880 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
5556 5.10e+01 AgaATTaGtaCcTgaTc.TaA
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5557 3.50e+02 gtTTTtcaT.T
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5620 7.50e+02 GGTGGTACCGCG
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5621 1.60e+04 AAGCGaaAATGcGATGAAG
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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 BSU15880

BSU15880 is enriched for 1 functions in 3 categories.
Module neighborhood information for BSU15880

BSU15880 has total of 37 gene neighbors in modules 309, 343
Gene neighbors (37)
Gene Common Name Description Module membership
BSU02720 yccF hypothetical protein (RefSeq) 309, 322
BSU04260 topB DNA topoisomerase III (RefSeq) 97, 309
BSU09660 yheN putative polysaccharide deacetylase (RefSeq) 309, 322
BSU11330 fabHA 3-oxoacyl-(acyl carrier protein) synthase III (RefSeq) 309, 343
BSU11340 fabF 3-oxoacyl-(acyl carrier protein) synthase II (RefSeq) 309, 343
BSU11720 fabI enoyl-(acyl carrier protein) reductase (RefSeq) 255, 309
BSU15880 ylpC fatty acid biosynthesis transcriptional regulator (RefSeq) 309, 343
BSU15890 plsX putative glycerol-3-phosphate acyltransferase PlsX (RefSeq) 309, 343
BSU15900 fabD malonyl CoA:acyl carrier protein transacylase (RefSeq) 273, 343
BSU15910 fabG beta-ketoacyl-acyl carrier protein reductase (RefSeq) 273, 309
BSU15920 acpP acyl carrier protein (RefSeq) 273, 343
BSU15930 rnc ribonuclease III (RefSeq) 245, 343
BSU16530 uppS undecaprenyl pyrophosphate synthase (RefSeq) 325, 343
BSU16540 cdsA phosphatidate cytidylyltransferase (CDP-diglyceride synthase) (RefSeq) 253, 343
BSU19590 ctpA carboxy-terminal processing protease (RefSeq) 102, 309
BSU21860 yphP hypothetical protein (RefSeq) 197, 309
BSU21930 cspD cold-shock protein, molecular chaperone, RNA-helicase co-factor (RefSeq) 7, 309
BSU22690 aroH chorismate mutase (RefSeq) 107, 343
BSU22700 aroB 3-dehydroquinate synthase (RefSeq) 107, 343
BSU22710 aroF chorismate synthase (RefSeq) 107, 343
BSU25200 sigA RNA polymerase sigma factor RpoD (RefSeq) 220, 309
BSU25210 dnaG DNA primase (RefSeq) 191, 309
BSU25230 yqxD hypothetical protein (RefSeq) 292, 309
BSU28080 folC folyl-polyglutamate synthase (RefSeq) 245, 343
BSU28090 valS valyl-tRNA synthetase (RefSeq) 245, 343
BSU28630 pheT phenylalanyl-tRNA synthetase subunit beta (RefSeq) 158, 343
BSU28640 pheS phenylalanyl-tRNA synthetase subunit alpha (RefSeq) 158, 343
BSU28960 ytxC hypothetical protein (RefSeq) 309, 322
BSU31680 comA two-component response regulator (RefSeq) 309, 322
BSU32620 yurQ putative excinuclease (RefSeq) 116, 309
BSU37090 glpX fructose 1,6-bisphosphatase II (RefSeq) 273, 343
BSU37100 murAB UDP-N-acetylglucosamine 1-carboxyvinyltransferase (RefSeq) 63, 343
BSU38140 qoxD cytochrome aa3-600 quinol oxidase (subunit IV) (RefSeq) 107, 343
BSU38150 qoxC cytochrome aa3-600 quinol oxidase (subunit III) (RefSeq) 107, 343
BSU38160 qoxB cytochrome aa3-600 quinol oxidase (subunit I) (RefSeq) 107, 343
BSU38170 qoxA cytochrome aa3-600 quinol oxidase (subunit II) (RefSeq) 107, 343
BSU39020 yxjA purine nucleoside transporter (RefSeq) 309, 334
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 BSU15880
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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