Organism : Bacillus subtilis | Module List :
BSU16130 gid

tRNA (uracil-5-)-methyltransferase Gid (RefSeq)

CircVis
Functional Annotations (5)
Function System
NAD(FAD)-utilizing enzyme possibly involved in translation cog/ cog
electron transport go/ biological_process
tRNA processing go/ biological_process
flavin adenine dinucleotide binding go/ molecular_function
gid_trmFO tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU16130
(Mouseover regulator name to see its description)

BSU16130 is regulated by 19 influences and regulates 0 modules.
Regulators for BSU16130 gid (19)
Regulator Module Operator
BSU01010 397 tf
BSU02680 397 tf
BSU05330 397 tf
BSU10150 397 tf
BSU15970 397 tf
BSU23120 397 tf
BSU24250 397 tf
BSU29000 397 tf
BSU33080 397 tf
BSU33740 397 tf
BSU37650 397 tf
BSU38600 397 tf
BSU04060 190 tf
BSU15970 190 tf
BSU30020 190 tf
BSU33080 190 tf
BSU33740 190 tf
BSU37620 190 tf
BSU38600 190 tf

Warning: BSU16130 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
5326 3.40e-02 aAGatagaAGggAAacAaa
Loader icon
5327 2.20e+00 AAgtCcgAtG.GT.gagtgcgaaT
Loader icon
5704 4.30e+02 aagaAAGcCGctCC
Loader icon
5705 4.50e+04 CaGGTGCctCGG
Loader icon
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 BSU16130

BSU16130 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
NAD(FAD)-utilizing enzyme possibly involved in translation cog/ cog
electron transport go/ biological_process
tRNA processing go/ biological_process
flavin adenine dinucleotide binding go/ molecular_function
gid_trmFO tigr/ tigrfam
Module neighborhood information for BSU16130

BSU16130 has total of 38 gene neighbors in modules 190, 397
Gene neighbors (38)
Gene Common Name Description Module membership
BSU00410 rnmV ribonuclease M5 (RefSeq) 48, 397
BSU00420 ksgA dimethyladenosine transferase (RefSeq) 48, 397
BSU01010 nusG transcription antitermination protein NusG (RefSeq) 212, 397
BSU01580 ybaR putative permease (RefSeq) 48, 397
BSU06370 pbuG hypoxanthine/guanine permease (RefSeq) 190, 294
BSU06720 yerQ putative lipid kinase (RefSeq) 271, 397
BSU06730 yefA putative RNA methyltransferase (RefSeq) 67, 190
BSU07340 yfnA metabolite permease (RefSeq) 190, 319
BSU07940 yfkC putative mechanosensitive ion channel (RefSeq) 69, 397
BSU08030 dusC tRNA-dihydrouridine synthase 2 (RefSeq) 319, 397
BSU08700 ygaE hypothetical protein (RefSeq) 132, 397
BSU09120 yhcK putative diguanylate cyclase or phosphodiesterase (RefSeq) 190, 325
BSU09130 tcyP sodium-cystine symporter (RefSeq) 80, 190
BSU09840 hemZ coproporphyrinogen III oxidase (RefSeq) 190, 397
BSU13500 ktrD K+-transporting ATPase (RefSeq) 271, 397
BSU14780 ylaH hypothetical protein (RefSeq) 212, 397
BSU16130 gid tRNA (uracil-5-)-methyltransferase Gid (RefSeq) 190, 397
BSU18120 alsT amino acid carrier protein (RefSeq) 75, 190
BSU19160 yocC hypothetical protein (RefSeq) 37, 397
BSU19440 yojI multidrug efflux protein (RefSeq) 319, 397
BSU29730 ytxD flagellar motor protein MotP (RefSeq) 48, 190
BSU29900 trmB tRNA (guanine-N(7)-)-methyltransferase (RefSeq) 132, 397
BSU30050 ytgP putative enzyme involved in polysaccharide biosynthesis (RefSeq) 271, 397
BSU30410 ytrF metabolite permease (RefSeq) 125, 190
BSU30420 ytrE ABC transporter (ATP-binding protein) (RefSeq) 125, 190
BSU30430 ytrD ABC transporter, permease component (RefSeq) 190, 339
BSU30440 ytrC ABC transporter, permease component (RefSeq) 190, 339
BSU30450 ytrB ABC transporter (ATP-binding protein) (RefSeq) 190, 339
BSU30460 ytrA transcriptional regulator (GntR family) (RefSeq) 190, 339
BSU31090 ktrA potassium uptake protein (RefSeq) 48, 397
BSU31100 ktrB potassium transporter ATPase (RefSeq) 37, 397
BSU33160 yvrA putative vitamin B12 transport system, ATPase component (RefSeq) 48, 190
BSU35710 tagG teichoic acid precursors permease (RefSeq) 204, 397
BSU36270 ywqB putative replication initiation protein (RefSeq) 190, 397
BSU36280 ywqA putative ATP-binding SNF2 helicase or protein kinase (RefSeq) 190, 271
BSU37150 pyrG CTP synthetase (RefSeq) 190, 319
BSU37490 speB agmatinase (RefSeq) 48, 190
BSU37610 ywzC hypothetical protein (RefSeq) 151, 397
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 BSU16130
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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