Organism : Bacillus subtilis | Module List :
BSU07520 yfmC

iron-dicitrate ABC transporter (binding lipoprotein) (RefSeq)

CircVis
Functional Annotations (4)
Function System
ABC-type Fe3+-citrate transport system, periplasmic component cog/ cog
iron ion transmembrane transporter activity go/ molecular_function
high-affinity iron ion transport go/ biological_process
ABC transporters kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU07520
(Mouseover regulator name to see its description)

BSU07520 is regulated by 19 influences and regulates 0 modules.
Regulators for BSU07520 yfmC (19)
Regulator Module Operator
BSU01640 93 tf
BSU03960 93 tf
BSU12560 93 tf
BSU13210 93 tf
BSU15470 93 tf
BSU19100 93 tf
BSU20820 93 tf
BSU29700 93 tf
BSU40350 93 tf
BSU02070 395 tf
BSU03890 395 tf
BSU05970 395 tf
BSU06540 395 tf
BSU06700 395 tf
BSU07820 395 tf
BSU13670 395 tf
BSU17850 395 tf
BSU26220 395 tf
BSU35030 395 tf

Warning: BSU07520 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
5140 7.80e-20 T.tAaaTGAtAATGAtTaTCAaT
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5141 2.80e-01 ccTTTTTGcag
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5700 2.00e-02 aatgAGaaGgaggat
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5701 1.00e+04 gaAaAaAgtaagca
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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 BSU07520

BSU07520 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
ABC-type Fe3+-citrate transport system, periplasmic component cog/ cog
iron ion transmembrane transporter activity go/ molecular_function
high-affinity iron ion transport go/ biological_process
ABC transporters kegg/ kegg pathway
Module neighborhood information for BSU07520

BSU07520 has total of 41 gene neighbors in modules 93, 395
Gene neighbors (41)
Gene Common Name Description Module membership
BSU01620 feuB iron-uptake protein (RefSeq) 65, 93
BSU01630 feuA iron hydroxamate-binding lipoprotein (RefSeq) 65, 93
BSU02450 glnL two-component response regulator [GlnJ] for glutamine utilisation (RefSeq) 244, 395
BSU02810 cwlK murein L,D:-endopeptidase (RefSeq) 83, 395
BSU02850 adcA Zn(II)-binding lipoprotein (RefSeq) 294, 395
BSU03270 ycgT putative thioredoxin reductase (RefSeq) 65, 93
BSU03800 yclN putative iron-siderophore ABC transporter (permease) (RefSeq) 93, 266
BSU03810 yclO putative iron-siderophore ABC transporter (permease) (RefSeq) 93, 266
BSU03820 yclP putative iron-siderophore ABC transporter (ATP-binding protein) (RefSeq) 93, 266
BSU03830 yclQ putative iron-siderophore ABC transporter (binding lipoprotein) (RefSeq) 93, 266
BSU06070 ydiP DNA-methyltransferase (cytosine-specific) (RefSeq) 83, 395
BSU06320 yeaB putative cation efflux transporter (RefSeq) 201, 395
BSU06410 yebG hypothetical protein (RefSeq) 83, 395
BSU06650 sapB membrane component (RefSeq) 83, 395
BSU07510 yfmD iron-dicitrate ABC transporter (permease) (RefSeq) 244, 395
BSU07520 yfmC iron-dicitrate ABC transporter (binding lipoprotein) (RefSeq) 93, 395
BSU08440 yfiY putative iron(III) dicitrate transporter binding lipoprotein (RefSeq) 65, 93
BSU08450 yfiZ iron(III) siderophore transport permease (RefSeq) 93, 325
BSU08460 yfhA iron(III) siderophore transport permease (RefSeq) 93, 325
BSU08480 yfhC putative oxidoreductase (nitroreductase family) (RefSeq) 65, 93
BSU08770 ygzA hypothetical protein (RefSeq) 295, 395
BSU09850 yhaU transporter involved in K+ efflux (RefSeq) 295, 395
BSU10330 yhfQ putative iron(III) dicitrate-binding lipoprotein (RefSeq) 93, 295
BSU17920 ynzD Spo0A-P phosphatase (RefSeq) 83, 395
BSU17940 yneI putative response regulator (CheY homolog) (RefSeq) 83, 395
BSU21880 ypgR putative lyase (RefSeq) 244, 395
BSU22360 asnC asparaginyl-tRNA synthetase (RefSeq) 244, 395
BSU22520 ypjB spore formation membrane associated protein (RefSeq) 244, 395
BSU24900 rpmG 50S ribosomal protein L33 (RefSeq) 154, 395
BSU27680 yrbG hypothetical protein (RefSeq) 295, 395
BSU30520 ytoA hypothetical protein (RefSeq) 244, 395
BSU32930 yusU hypothetical protein (RefSeq) 65, 93
BSU32940 yusV iron(III)-siderophore transporter (ATP binding component) (RefSeq) 65, 93
BSU33290 fhuC ferrichrome ABC transporter (ATP-binding protein) (RefSeq) 93, 218
BSU33300 fhuG ferrichrome ABC transporter (permease) (RefSeq) 93, 218
BSU33310 fhuB ferrichrome ABC transporter (permease) (RefSeq) 93, 218
BSU34940 yvpB putative hydrolase (RefSeq) 83, 395
BSU36250 ptkA protein tyrosine kinase (RefSeq) 75, 395
BSU38260 efeN iron-dependent peroxidase convert ferric iron into ferrous iron (RefSeq) 65, 93
BSU38270 efeM lipoprotein binding ferrous or ferric iron for transport (RefSeq) 65, 93
BSU38280 efeU ferrous ion permease (RefSeq) 65, 93
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 BSU07520
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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