Organism : Bacillus subtilis | Module List :
BSU38340 ywbF

putative sugar permease (RefSeq)

CircVis
Functional Annotations (4)
Function System
transporter activity go/ molecular_function
sugar:hydrogen symporter activity go/ molecular_function
transport go/ biological_process
integral to membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU38340
(Mouseover regulator name to see its description)

BSU38340 is regulated by 17 influences and regulates 0 modules.
Regulators for BSU38340 ywbF (17)
Regulator Module Operator
BSU02370 150 tf
BSU05050 150 tf
BSU05320 150 tf
BSU15640 150 tf
BSU18850 150 tf
BSU26580 150 tf
BSU28820 150 tf
BSU29400 150 tf
BSU01690 19 tf
BSU15320 19 tf
BSU15970 19 tf
BSU16600 19 tf
BSU19090 19 tf
BSU24320 19 tf
BSU29270 19 tf
BSU29630 19 tf
BSU30020 19 tf

Warning: BSU38340 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
5000 1.10e-02 AGGaGGgA
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5001 1.10e+02 GCc.GCTGCtacag.c.GgCGC
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5250 8.20e-01 AggaAGgGGaaAagA
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5251 3.60e+02 TaTtTTaccgAaAAgacGagG
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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 BSU38340

BSU38340 is enriched for 4 functions in 2 categories.
Enrichment Table (4)
Function System
transporter activity go/ molecular_function
sugar:hydrogen symporter activity go/ molecular_function
transport go/ biological_process
integral to membrane go/ cellular_component
Module neighborhood information for BSU38340

BSU38340 has total of 49 gene neighbors in modules 19, 150
Gene neighbors (49)
Gene Common Name Description Module membership
BSU00080 yaaC hypothetical protein (RefSeq) 105, 150
BSU00090 guaB inosine 5'-monophosphate dehydrogenase (RefSeq) 42, 150
BSU00730 cysK cysteine synthase (RefSeq) 80, 150
BSU01680 ybbF putative sugar phosphotransferase enzyme II (RefSeq) 19, 407
BSU03240 ycgQ hypothetical protein (RefSeq) 150, 233
BSU06020 groES co-chaperonin GroES (RefSeq) 39, 150
BSU06030 groEL chaperonin GroEL (RefSeq) 39, 150
BSU06120 ydjB hypothetical protein (RefSeq) 150, 409
BSU07830 yfkO NAD(P)H-flavin oxidoreductase (RefSeq) 19, 161
BSU09080 yhcH putative ABC transporter (ATP-binding protein) (RefSeq) 150, 233
BSU11030 yitL putative RNA-binding protein (RefSeq) 150, 247
BSU12430 rapA response regulator aspartate phosphatase (RefSeq) 12, 19
BSU12440 phrA secreted inhibitor of the activity of phosphatase RapA (RefSeq) 12, 19
BSU13250 ykoG two-component response regulator [YkoH] (RefSeq) 146, 150
BSU13260 ykoH two-component sensor histidine kinase [YkoG] (RefSeq) 146, 150
BSU13270 ykoI hypothetical protein (RefSeq) 146, 150
BSU13480 ykrK hypothetical protein (RefSeq) 150, 239
BSU14310 moaD molybdopterin synthase (small subunit) (RefSeq) 128, 150
BSU17600 xylA xylose isomerase (RefSeq) 19, 241
BSU17610 xylB xylulose kinase (RefSeq) 19, 405
BSU18300 ppsE plipastatin synthetase (RefSeq) 98, 150
BSU18410 ggt membrane bound gamma-glutamyltranspeptidase (RefSeq) 12, 19
BSU18660 yoaM hypothetical protein (RefSeq) 19, 150
BSU18800 penP beta-lactamase precursor (RefSeq) 150, 274
BSU22140 kduD 2-deoxy-D-gluconate 3-dehydrogenase (RefSeq) 150, 168
BSU25420 yqeW putative Na+/anion cotransporter (RefSeq) 86, 150
BSU26640 yrdP putative oxidoreductase (RefSeq) 19, 161
BSU26650 czcD potassium/proton-divalent cation antiporter (RefSeq) 19, 161
BSU27250 yrhB cystathionine beta-lyase (RefSeq) 80, 150
BSU27260 mccA cystathionine beta-synthase for the reverse transsulfuration pathway (RefSeq) 80, 150
BSU27280 yrrT putative AdoMet-dependent methyltransferase (RefSeq) 150, 195
BSU27570 yrzK hypothetical protein (RefSeq) 150, 239
BSU29400 ytlI transcriptional regulator (LysR family) (RefSeq) 150, 333
BSU31460 kapB factor required for KinB signal transduction and activation of the phosphorelay to sporulation (RefSeq) 145, 150
BSU33120 liaH modulator of liaIHGFSR (yvqIHGFEC) operon expression (RefSeq) 19, 49
BSU33130 liaI permease (RefSeq) 19, 115
BSU35540 tuaH putative glycosyltransferase (RefSeq) 19, 349
BSU35550 tuaG putative glycosyltransferase (RefSeq) 19, 349
BSU35560 tuaF putative hydrolase involved in teichuronic acid synthesis (RefSeq) 19, 349
BSU35570 tuaE putative polymerase of teichuronic acid repeating units (RefSeq) 19, 349
BSU35580 tuaD UDP-glucose 6-dehydrogenase (RefSeq) 19, 349
BSU35590 tuaC putative glycosyltransferase (RefSeq) 19, 349
BSU38090 vpr extracellular serine protease (RefSeq) 19, 101
BSU38340 ywbF putative sugar permease (RefSeq) 19, 150
BSU39029 yxiT 150, 246
BSU39880 yxbC hypothetical protein (RefSeq) 12, 19
BSU39890 yxbB putative S-adenosylmethionine-dependent methyltransferase (RefSeq) 19, 141
BSU39900 aslA D-Aspartate ligase (RefSeq) 12, 19
BSU39910 yxnB hypothetical protein (RefSeq) 19, 141
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 BSU38340
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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