Organism : Bacillus subtilis | Module List :
BSU41010 gidA

tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA (RefSeq)

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

Cytoscape Web
Regulation information for BSU41010
(Mouseover regulator name to see its description)

BSU41010 is regulated by 23 influences and regulates 0 modules.
Regulators for BSU41010 gidA (23)
Regulator Module Operator
BSU00700 211 tf
BSU00800 211 tf
BSU01080 211 tf
BSU01640 211 tf
BSU01690 211 tf
BSU05670 211 tf
BSU16170 211 tf
BSU16600 211 tf
BSU24250 211 tf
BSU27520 211 tf
BSU35050 211 tf
BSU40990 211 tf
BSU00700 314 tf
BSU00800 314 tf
BSU05670 314 tf
BSU10860 314 tf
BSU16170 314 tf
BSU16600 314 tf
BSU24250 314 tf
BSU27520 314 tf
BSU35050 314 tf
BSU40410 314 tf
BSU40990 314 tf

Warning: BSU41010 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
5366 5.10e+02 GaAaGGggccT
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5367 5.50e+03 GCGGCtGG
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5566 3.20e+02 CCaCacCTgtTgtaaAagCCc
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5567 1.70e+04 GtTtcTCacCttTc
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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 BSU41010

BSU41010 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
NAD/FAD-utilizing enzyme apparently involved in cell division cog/ cog
electron transport go/ biological_process
tRNA processing go/ biological_process
flavin adenine dinucleotide binding go/ molecular_function
gidA tigr/ tigrfam
Module neighborhood information for BSU41010

BSU41010 has total of 30 gene neighbors in modules 211, 314
Gene neighbors (30)
Gene Common Name Description Module membership
BSU00700 coaX pantothenate kinase (RefSeq) 13, 314
BSU00710 hslO Hsp33-like chaperonin (RefSeq) 166, 314
BSU04640 alrA D-alanine racemase (RefSeq) 1, 314
BSU06600 pcrB geranylgeranylglyceryl phosphate synthase-like protein (RefSeq) 293, 314
BSU06610 pcrA ATP-dependent DNA helicase (RefSeq) 211, 314
BSU06620 ligA NAD-dependent DNA ligase LigA (RefSeq) 204, 211
BSU07955 BSU07955 None 211, 289
BSU08630 yfhQ A/G-specific adenine glycosylase or DNA-(apurinic or apyrimidinic site) lyase (RefSeq) 37, 314
BSU13300 mgtE magnesium transporter (RefSeq) 265, 314
BSU22830 gpsA NAD(P)H-dependent glycerol-3-phosphate dehydrogenase (RefSeq) 37, 314
BSU22840 engA GTP-binding protein EngA (RefSeq) 204, 211
BSU24260 yqxC putative methyltransferase with RNA binding domain (RefSeq) 211, 288
BSU24270 dxs 1-deoxy-D-xylulose-5-phosphate synthase (RefSeq) 211, 288
BSU25670 yqeH GTP-binding protein YqeH (RefSeq) 48, 314
BSU25680 yqeG putative hydrolase (RefSeq) 48, 314
BSU27490 yrrB putative tetratricopeptide repeat family protein (RefSeq) 211, 314
BSU27500 mnmA tRNA-specific 2-thiouridylase MnmA (RefSeq) 211, 314
BSU27510 iscS cysteine desulfurase involved in tRNA thiolation (RefSeq) 228, 314
BSU28570 yshE putative integral inner membrane protein (RefSeq) 211, 314
BSU28580 mutSB recombination and DNA strand exchange inhibitor protein (RefSeq) 211, 314
BSU28590 yshC hypothetical protein (RefSeq) 211, 314
BSU40360 htrC putative membrane serine protease Do (RefSeq) 228, 314
BSU40370 yycJ putative hydrolase (RefSeq) 211, 314
BSU40380 yycI regulator of YycFG (RefSeq) 228, 314
BSU40390 walH regulator of YycFG (RefSeq) 228, 314
BSU41000 gidB 16S rRNA methyltransferase GidB (RefSeq) 211, 314
BSU41010 gidA tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA (RefSeq) 211, 314
BSU41020 trmE tRNA modification GTPase TrmE (RefSeq) 211, 314
VIMSS37328 VIMSS37328 None 69, 211
VIMSS37621 VIMSS37621 None 69, 211
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 BSU41010
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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