Organism : Bacillus subtilis | Module List :
BSU29400 ytlI

transcriptional regulator (LysR family) (RefSeq)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU29400
(Mouseover regulator name to see its description)

BSU29400 is regulated by 19 influences and regulates 7 modules.
Regulators for BSU29400 ytlI (19)
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
BSU02220 333 tf
BSU05170 333 tf
BSU15320 333 tf
BSU18420 333 tf
BSU20820 333 tf
BSU24250 333 tf
BSU29270 333 tf
BSU29400 333 tf
BSU29690 333 tf
BSU34380 333 tf
BSU38070 333 tf

Warning: BSU29400 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
5250 8.20e-01 AggaAGgGGaaAagA
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5251 3.60e+02 TaTtTTaccgAaAAgacGagG
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5602 5.00e+00 TTgtcAcTCctCatCAcaA
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5603 7.00e+00 ATgatGaaaaacaGaaaGGAGc
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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 BSU29400

BSU29400 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BSU29400

BSU29400 has total of 39 gene neighbors in modules 150, 333
Gene neighbors (39)
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
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
BSU09080 yhcH putative ABC transporter (ATP-binding protein) (RefSeq) 150, 233
BSU11030 yitL putative RNA-binding protein (RefSeq) 150, 247
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
BSU18300 ppsE plipastatin synthetase (RefSeq) 98, 150
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
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
BSU29280 ytnM putative transporter (RefSeq) 95, 333
BSU29290 ytnL putative aminohydrolase (RefSeq) 333, 336
BSU29300 rbfK RNA-binding riboflavin kinase (RefSeq) 333, 336
BSU29310 ytnJ putative monooxygenase (RefSeq) 333, 336
BSU29320 ytnI putative redoxin (RefSeq) 206, 333
BSU29330 ytmO putative monooxygenase (RefSeq) 333, 336
BSU29340 tcyN sulfur-containing amino-acid ABC transporter (ATP-binding protein) (RefSeq) 333, 336
BSU29350 tcyM sulfur-containing amino acid ABC transporter (permease) (RefSeq) 333, 336
BSU29360 tcyL sulfur-containing amino acid ABC transporter (permease) (RefSeq) 333, 336
BSU29370 tcyK sulfur-containing amino acid ABC transporter binding lipoprotein (RefSeq) 333, 336
BSU29380 tcyJ sulfur containing amino acid ABC transporter binding lipoprotein (RefSeq) 333, 336
BSU29390 ytmI putative N-acetyltransferase (RefSeq) 333, 336
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
BSU38340 ywbF putative sugar permease (RefSeq) 19, 150
BSU39029 yxiT 150, 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 BSU29400
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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