Organism : Bacillus subtilis | Module List :
BSU32040 yuiF

amino acid transporter (RefSeq)

CircVis
Functional Annotations (5)
Function System
Predicted permease cog/ cog
sodium ion transport go/ biological_process
regulation of pH go/ biological_process
sodium:hydrogen antiporter activity go/ molecular_function
integral to membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU32040
(Mouseover regulator name to see its description)

BSU32040 is regulated by 24 influences and regulates 0 modules.
Regulators for BSU32040 yuiF (24)
Regulator Module Operator
BSU01080 72 tf
BSU01690 72 tf
BSU04100 72 tf
BSU05670 72 tf
BSU15330 72 tf
BSU35050 72 tf
BSU37550 72 tf
BSU37620 72 tf
BSU01010 319 tf
BSU01810 319 tf
BSU02680 319 tf
BSU03080 319 tf
BSU03850 319 tf
BSU04650 319 tf
BSU05330 319 tf
BSU08300 319 tf
BSU13210 319 tf
BSU15470 319 tf
BSU15970 319 tf
BSU19070 319 tf
BSU33080 319 tf
BSU34170 319 tf
BSU36300 319 tf
BSU38600 319 tf

Warning: BSU32040 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
5100 1.50e+02 AacTAAAGGAT
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5101 1.10e+03 cggatTTTTC
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5576 1.70e+00 ctTTttTaTcg
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5577 7.10e+01 GCCgctTC
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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 BSU32040

BSU32040 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Predicted permease cog/ cog
sodium ion transport go/ biological_process
regulation of pH go/ biological_process
sodium:hydrogen antiporter activity go/ molecular_function
integral to membrane go/ cellular_component
Module neighborhood information for BSU32040

BSU32040 has total of 48 gene neighbors in modules 72, 319
Gene neighbors (48)
Gene Common Name Description Module membership
BSU03580 yczE integral inner membrane protein regulating antibiotic production (RefSeq) 132, 319
BSU03590 tcyC cystine ABC transporter (ATP-binding protein) (RefSeq) 13, 72
BSU03600 tcyB cystine ABC transporter (permease) (RefSeq) 13, 72
BSU03610 tcyA cystine ABC transporter (substrate-binding lipoprotein) (RefSeq) 13, 72
BSU07340 yfnA metabolite permease (RefSeq) 190, 319
BSU08030 dusC tRNA-dihydrouridine synthase 2 (RefSeq) 319, 397
BSU08930 cspR putative rRNA methylase (RefSeq) 197, 319
BSU13730 queD 6-pyruvoyl tetrahydrobiopterin synthase-like; queuosine biosynthesis (RefSeq) 319, 409
BSU13740 queE queuosine biosynthesis enzyme (RefSeq) 319, 409
BSU19440 yojI multidrug efflux protein (RefSeq) 319, 397
BSU19650 yodM putative phospholipid phosphatase (RefSeq) 48, 319
BSU22150 ypvA putative ATP-dependent helicase (RefSeq) 271, 319
BSU23950 yqjA hypothetical protein (RefSeq) 67, 319
BSU24830 yqgT putative gamma-D-glutamyl-L-diamino acid endopeptidase (RefSeq) 37, 319
BSU28840 ysdA putative membrane component (RefSeq) 72, 202
BSU29600 braB branched-chain amino acid-Na+ symporter (RefSeq) 13, 319
BSU30490 ytqB putative RNA methylase (RefSeq) 271, 319
BSU30820 menD 2-succinyl-5-enolpyruvyl-6-hydroxy-3- cyclohexene-1-carboxylate synthase (RefSeq) 132, 319
BSU30990 thiT thiamin permease (RefSeq) 13, 319
BSU31600 mrpA monovalent cation/H+ antiporter subunit A (RefSeq) 72, 193
BSU31610 mrpB putative monovalent cation/H+ antiporter subunit B (RefSeq) 72, 193
BSU31620 mrpC putative monovalent cation/H+ antiporter subunit C (RefSeq) 72, 193
BSU31630 mrpD putative monovalent cation/H+ antiporter subunit D (RefSeq) 72, 193
BSU31640 mrpE putative monovalent cation/H+ antiporter subunit E (RefSeq) 72, 193
BSU31650 mrpF putative monovalent cation/H+ antiporter subunit F (RefSeq) 72, 193
BSU31660 mrpG putative monovalent cation/H+ antiporter subunit G (RefSeq) 72, 193
BSU32040 yuiF amino acid transporter (RefSeq) 72, 319
BSU33080 liaR two-component response regulator [YvqE] responding to cell wall stress (RefSeq) 48, 319
BSU33090 liaS two-component sensor histidine kinase [YvqC] sensing cell wall stress (RefSeq) 48, 319
BSU33100 liaF integral inner membrane protein (RefSeq) 66, 319
BSU33330 lysP lysine permease (RefSeq) 319, 339
BSU33350 yvsG putative membrane hydrolase (RefSeq) 11, 319
BSU34100 rsbQ regulator of RsbP phosphatase (RefSeq) 132, 319
BSU34860 hisI bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein (RefSeq) 6, 72
BSU34870 hisF imidazole glycerol phosphate synthase subunit HisF (RefSeq) 6, 72
BSU34880 hisA 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase (RefSeq) 6, 72
BSU34890 hisH imidazole glycerol phosphate synthase subunit HisH (RefSeq) 6, 72
BSU34900 hisB imidazoleglycerol-phosphate dehydratase (RefSeq) 6, 72
BSU34910 hisD histidinol dehydrogenase (RefSeq) 6, 72
BSU34920 hisG ATP phosphoribosyltransferase catalytic subunit (RefSeq) 6, 72
BSU34930 hisZ ATP phosphoribosyltransferase regulatory subunit (RefSeq) 6, 72
BSU36290 ywpJ putative phosphatase (RefSeq) 319, 327
BSU36300 glcR transcriptional regulator (DeoR family) (RefSeq) 319, 327
BSU36610 ywnC putative integral inner membrane protein (RefSeq) 132, 319
BSU37150 pyrG CTP synthetase (RefSeq) 190, 319
VIMSS37141 VIMSS37141 None 45, 72
VIMSS38543 VIMSS38543 None 72, 120
VIMSS39723 VIMSS39723 None 72, 271
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 BSU32040
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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