Organism : Bacillus subtilis | Module List :
BSU05460 ydfL

putative transcriptional regulator of efflux transporter (RefSeq)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator, effector-binding domain/component cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU05460
(Mouseover regulator name to see its description)

BSU05460 is regulated by 19 influences and regulates 9 modules.
Regulators for BSU05460 ydfL (19)
Regulator Module Operator
BSU00560 115 tf
BSU03880 115 tf
BSU05060 115 tf
BSU05150 115 tf
BSU05180 115 tf
BSU05240 115 tf
BSU05460 115 tf
BSU05850 115 tf
BSU09430 115 tf
BSU11930 115 tf
BSU01810 157 tf
BSU03880 157 tf
BSU05060 157 tf
BSU05180 157 tf
BSU05460 157 tf
BSU05850 157 tf
BSU19200 157 tf
BSU25100 157 tf
BSU29030 157 tf
Regulated by BSU05460 (9)
Module Residual Genes
106 0.34 19
115 0.50 34
157 0.49 30
263 0.48 13
289 0.36 21
292 0.47 22
310 0.45 29
316 0.52 8
343 0.44 22
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
5184 1.50e+00 TtATGaaCAGCa.GcTTcaaTAAA
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5185 5.90e-02 ctaTttaa.AtaAaGtgAatg
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5262 1.60e-03 CTCCTTtctcA
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5263 6.40e-02 ctTtcCaTT.attA.TcgCcGg.C
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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 BSU05460

BSU05460 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Transcriptional regulator, effector-binding domain/component cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BSU05460

BSU05460 has total of 58 gene neighbors in modules 115, 157
Gene neighbors (58)
Gene Common Name Description Module membership
BSU00440 veg hypothetical protein (RefSeq) 94, 115
BSU01800 alkA DNA-3-methyladenine glycosylase (RefSeq) 115, 157
BSU01810 adaA methylphosphotriester-DNA alkyltransferase and transcriptional regulator (AraC/XylS family) (RefSeq) 157, 406
BSU03020 ycgA putative integral inner membrane protein (RefSeq) 157, 161
BSU03140 tmrB ATP-binding tunicamycin resistance protein (RefSeq) 94, 115
BSU03150 aroK shikimate kinase (RefSeq) 94, 115
BSU03540 ycxB hypothetical protein (RefSeq) 49, 115
BSU03880 yczG putative transcriptional regulator (ArsR family) (RefSeq) 94, 115
BSU04610 ydcA hypothetical protein (RefSeq) 115, 123
BSU05060 lrpB transcriptional regulator (Lrp/AsnC family) (RefSeq) 115, 157
BSU05090 yddS putative permease (RefSeq) 38, 115
BSU05110 ydeA putative enzyme (RefSeq) 49, 115
BSU05150 ydeC putative transcriptional regulator (AraC/XylS family) (RefSeq) 157, 216
BSU05170 ydeE putative transcriptional regulator (AraC/XylS family) (RefSeq) 115, 157
BSU05180 ydeF putative PLP-dependent transcriptional regulator (RefSeq) 115, 216
BSU05200 ydeH putative integral inner membrane protein (RefSeq) 115, 159
BSU05210 ydeI hypothetical protein (RefSeq) 115, 157
BSU05240 ydeL putative PLP-dependent transcriptional regulator (RefSeq) 115, 291
BSU05460 ydfL putative transcriptional regulator of efflux transporter (RefSeq) 115, 157
BSU07970 yfjT hypothetical protein (RefSeq) 94, 157
BSU08360 yfiQ putative membrane component involved in biofilm formation (RefSeq) 115, 285
BSU09600 crcBA camphor resistance protein CrcB (RefSeq) 64, 115
BSU09760 yheE hypothetical protein (RefSeq) 115, 171
BSU11110 yitS hypothetical protein (RefSeq) 157, 215
BSU11270 yjzD hypothetical protein (RefSeq) 64, 157
BSU11280 yjaU hypothetical protein (RefSeq) 64, 157
BSU11510 yjbE putative transporter component (RefSeq) 64, 115
BSU11890 yjcK putative ribosomal-protein-alanine N-acetyltransferase (RefSeq) 157, 216
BSU12200 yjiA hypothetical protein (RefSeq) 115, 157
BSU13370 ykoQ putative metallophosphoesterase (RefSeq) 115, 226
BSU14080 ykuH hypothetical protein (RefSeq) 151, 157
BSU17060 ymzD putative integral inner membrane protein (RefSeq) 115, 159
BSU18390 yoeC putative bacteriophage integrase (RefSeq) 94, 157
BSU18790 yoaZ putative factor of the oxidative stress response (RefSeq) 115, 226
BSU19020 yobN putative amine oxidase (RefSeq) 114, 157
BSU19190 desK two-component sensor histidine kinase [DesR] (RefSeq) 157, 406
BSU19200 desR two-component response regulator [DesK] (RefSeq) 157, 378
BSU19350 yocS putative sodium-dependent transporter (RefSeq) 157, 365
BSU21750 scuA assembly factor BSco of the Cu(A) site of cytochrome c oxidase (RefSeq) 157, 219
BSU21970 ypeP hypothetical protein (RefSeq) 157, 311
BSU21980 ypdP putative integral inner membrane protein (RefSeq) 157, 311
BSU23320 ypzC hypothetical protein (RefSeq) 121, 157
BSU26580 bltR transcriptional regulator (RefSeq) 115, 409
BSU26590 blt efflux transporter (RefSeq) 115, 409
BSU26600 bltD spermine/spermidine acetyltransferase (RefSeq) 115, 129
BSU26620 yrdR putative efflux transporter (RefSeq) 157, 226
BSU27190 yrzI hypothetical protein (RefSeq) 49, 157
BSU29030 ytcD putative transcriptional regulator (MarD family) (RefSeq) 157, 161
BSU30680 ytjA hypothetical protein (RefSeq) 64, 115
BSU32190 yuzB hypothetical protein (RefSeq) 96, 115
BSU33130 liaI permease (RefSeq) 19, 115
BSU36540 ywnJ putative integral inner membrane protein (RefSeq) 157, 311
BSU37540 ywhB 4-oxalocrotonate tautomerase (RefSeq) 111, 115
BSU37740 bacA bacilysin biosynthesis protein, dehydratase (RefSeq) 157, 217
BSU38360 ywbD putative AdoMet-dependent methyltransferase (RefSeq) 116, 157
BSU40140 yydJ putative permease for export of a regulatory peptide (RefSeq) 36, 115
BSU40150 yydI ABC transporter (ATP-binding protein) (RefSeq) 32, 115
BSU40980 yyaB putative integral inner membrane protein (RefSeq) 115, 291
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 BSU05460
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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