Organism : Bacillus subtilis | Module List :
BSU03250 ycgR

putative permease (RefSeq)

CircVis
Functional Annotations (1)
Function System
Predicted permeases cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU03250
(Mouseover regulator name to see its description)

BSU03250 is regulated by 16 influences and regulates 0 modules.
Regulators for BSU03250 ycgR (16)
Regulator Module Operator
BSU02500 233 tf
BSU04770 233 tf
BSU05320 233 tf
BSU06860 233 tf
BSU08340 233 tf
BSU09510 233 tf
BSU29740 233 tf
BSU31070 233 tf
BSU37580 233 tf
BSU38310 233 tf
BSU38910 233 tf
BSU40670 233 tf
BSU05420 89 tf
BSU26730 89 tf
BSU37080 89 tf
BSU39990 89 tf

Warning: BSU03250 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
5132 3.40e-03 CaGt.AaaCaGcaG
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5133 1.90e-01 ccTCCtcc
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5410 7.60e+00 cGgAGGaGGggAA
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5411 2.20e+04 GCCAGCGGTC
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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 BSU03250

BSU03250 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted permeases cog/ cog
Module neighborhood information for BSU03250

BSU03250 has total of 59 gene neighbors in modules 89, 233
Gene neighbors (59)
Gene Common Name Description Module membership
BSU00200 yaaK hypothetical protein (RefSeq) 188, 233
BSU01990 ybdG putative hydrolase/transferase (RefSeq) 89, 360
BSU02500 ycbG transcriptional regulator (GntR family) (RefSeq) 233, 293
BSU02950 yceI putative transporter (RefSeq) 89, 365
BSU03240 ycgQ hypothetical protein (RefSeq) 150, 233
BSU03250 ycgR putative permease (RefSeq) 89, 233
BSU04500 ydbK putative efflux ABC-transporter (permease component) (RefSeq) 89, 240
BSU04510 ydbL hypothetical protein (RefSeq) 189, 233
BSU05320 ydeS putative transcriptional regulator (TetR/AcrR family) (RefSeq) 233, 255
BSU06860 yezE putative transcriptional regulator (TetR family) (RefSeq) 233, 361
BSU09080 yhcH putative ABC transporter (ATP-binding protein) (RefSeq) 150, 233
BSU09890 natA Na+-efflux ABC transporter (ATP-binding protein) (RefSeq) 89, 313
BSU09900 natB Na+ exporter (ABC permease) (RefSeq) 89, 313
BSU11180 yitZ putative transport protein (RefSeq) 89, 313
BSU12480 yjqB putative PBSX phage-related replication protein (RefSeq) 89, 202
BSU12910 proG pyrroline-5-carboxylate reductase (RefSeq) 233, 323
BSU13430 ykoX putative integral inner membrane protein (RefSeq) 38, 89
BSU13890 ptsG phosphotransferase system (PTS) glucose-specific enzyme IICBA component (RefSeq) 89, 138
BSU14710 ylaA hypothetical protein (RefSeq) 89, 361
BSU14720 ylaB hypothetical protein (RefSeq) 89, 231
BSU15460 rluD pseudouridylate synthase (RefSeq) 62, 89
BSU23760 coaA pantothenate kinase (RefSeq) 116, 233
BSU23840 yqjK ribonuclease Z (RefSeq) 102, 233
BSU24520 mntR manganese transport transcriptional regulator (RefSeq) 233, 292
BSU24880 yqgO hypothetical protein (RefSeq) 89, 202
BSU24890 yqgN 5-formyltetrahydrofolate cyclo-ligase (RefSeq) 89, 385
BSU25220 antE hypothetical protein (RefSeq) 205, 233
BSU26680 yrdK hypothetical protein (RefSeq) 89, 270
BSU26748 yrdD 89, 199
BSU27830 coxA spore cortex protein (RefSeq) 233, 322
BSU31500 yuxK hypothetical protein (RefSeq) 233, 402
BSU31790 yueG putative spore germination protein (RefSeq) 233, 365
BSU32110 yumC ferredoxin-NADP+ reductase (RefSeq) 177, 233
BSU32530 yurH allantoate amidohydrolase (RefSeq) 89, 318
BSU32660 yurT putative methylglyoxalase (RefSeq) 50, 233
BSU33630 secG preprotein translocase subunit SecG (RefSeq) 233, 393
BSU34450 sacB levansucrase (RefSeq) 40, 89
BSU36110 ywrC putative transcriptional regulator (Lrp/AsnC family) (RefSeq) 233, 327
BSU36120 ywrB putative anion transporter (RefSeq) 233, 409
BSU36470 pucI allantoin permease (RefSeq) 84, 89
BSU36950 ywlC putative ribosome maturation factor; RNA binding protein (RefSeq) 37, 233
BSU37060 tdk thymidine kinase (RefSeq) 89, 142
BSU37930 ywdK hypothetical protein (RefSeq) 233, 241
BSU38710 yxlA putative purine-cytosine permease (RefSeq) 89, 177
BSU38880 yxjO putative transcriptional regulator (LysR family) (RefSeq) 167, 233
BSU38890 yxjN putative integral inner membrane protein (RefSeq) 38, 233
BSU38900 yxjM two-component sensor histidine kinase [YxjL] (RefSeq) 89, 233
BSU38910 yxjL two-component response regulator [YxjM] (RefSeq) 11, 233
BSU39280 yxxE hypothetical protein (RefSeq) 124, 233
BSU39290 yxxD hypothetical protein (RefSeq) 124, 233
BSU39550 yxeH putative hydrolase (RefSeq) 116, 233
BSU39560 yxeG putative integral inner membrane protein (RefSeq) 29, 233
BSU39570 yxeF hypothetical protein (RefSeq) 142, 233
BSU39620 yxeA hypothetical protein (RefSeq) 89, 208
BSU39630 yxdM ABC transporter (permease); efflux of cationic peptides (RefSeq) 84, 89
BSU39640 yxdL ABC transporter (ATP-binding protein); efflux of cationic peptides (RefSeq) 84, 89
BSU39650 yxdK two-component sensor histidine kinase [YxdJ] (RefSeq) 89, 361
BSU39660 yxdJ two-component response regulator [YxdK] (RefSeq) 89, 361
BSU40880 exoAA apurinic/apyrimidinic endonuclease (RefSeq) 89, 301
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 BSU03250
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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