Organism : Bacillus subtilis | Module List :
BSU03340 yciA

putative GTP cyclohydrolase (RefSeq)

CircVis
Functional Annotations (4)
Function System
Uncharacterized conserved protein cog/ cog
urate oxidase activity go/ molecular_function
purine base metabolic process go/ biological_process
TIGR00294 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU03340
(Mouseover regulator name to see its description)

BSU03340 is regulated by 21 influences and regulates 0 modules.
Regulators for BSU03340 yciA (21)
Regulator Module Operator
BSU00980 406 tf
BSU01810 406 tf
BSU03560 406 tf
BSU03620 406 tf
BSU05850 406 tf
BSU08300 406 tf
BSU19200 406 tf
BSU25760 406 tf
BSU26220 406 tf
BSU26320 406 tf
BSU26430 406 tf
BSU27320 406 tf
BSU04730 307 tf
BSU08300 307 tf
BSU12560 307 tf
BSU18760 307 tf
BSU26320 307 tf
BSU26340 307 tf
BSU34220 307 tf
BSU38070 307 tf
BSU40990 307 tf

Warning: BSU03340 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
5552 1.70e+01 aAGGaG
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5553 1.10e+05 GCGcGG
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5720 2.00e+02 AtAaaAAagaa
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5721 7.20e+03 CCGCtC
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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 BSU03340

BSU03340 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Uncharacterized conserved protein cog/ cog
urate oxidase activity go/ molecular_function
purine base metabolic process go/ biological_process
TIGR00294 tigr/ tigrfam
Module neighborhood information for BSU03340

BSU03340 has total of 44 gene neighbors in modules 307, 406
Gene neighbors (44)
Gene Common Name Description Module membership
BSU01810 adaA methylphosphotriester-DNA alkyltransferase and transcriptional regulator (AraC/XylS family) (RefSeq) 157, 406
BSU01900 ybcM putative enzyme (RefSeq) 393, 406
BSU02710 yczC putative integral inner membrane protein (RefSeq) 96, 307
BSU03050 ldh L-lactate dehydrogenase (RefSeq) 238, 406
BSU03340 yciA putative GTP cyclohydrolase (RefSeq) 307, 406
BSU03350 yciB putative metal uptake system lipoprotein (RefSeq) 178, 406
BSU04110 lipC lysophopholipase (RefSeq) 11, 307
BSU06870 yesE hypothetical protein (RefSeq) 307, 361
BSU08230 catD catechol-2,3-dioxygenase membrane subunit (RefSeq) 178, 307
BSU08240 catE catechol-2,3-dioxygenase subunit (RefSeq) 238, 307
BSU08290 yfiJ two-component sensor histidine kinase [YfiK] (RefSeq) 132, 307
BSU08300 yfiK two-component response regulator [YfiJ] (RefSeq) 48, 307
BSU08310 yfiL putative ABC transporter (ATP-binding protein) (RefSeq) 180, 406
BSU08320 yfiM putative ABC transporter (permease) (RefSeq) 180, 406
BSU10170 fabHB 3-oxoacyl-(acyl carrier protein) synthase III (RefSeq) 307, 411
BSU11040 yitM hypothetical protein (RefSeq) 217, 307
BSU11320 yjzB hypothetical protein (RefSeq) 307, 411
BSU17270 ymaC putative phage-related replication protein (RefSeq) 200, 406
BSU19180 des fatty acid desaturase (RefSeq) 393, 406
BSU19190 desK two-component sensor histidine kinase [DesR] (RefSeq) 157, 406
BSU20210 yorY hypothetical protein; phage SPbeta (RefSeq) 405, 406
BSU21310 yozP hypothetical protein; phage SPbeta (RefSeq) 174, 307
BSU21530 yolB conserved hypothetical protein; phage SPbeta (RefSeq) 298, 307
BSU21540 yolA exported protein of unknown function; phage SPbeta (RefSeq) 298, 307
BSU23940 yqjB hypothetical protein (RefSeq) 291, 406
BSU25710 cwlH N-acetylmuramoyl-L-alanine amidase (RefSeq) 291, 406
BSU26740 cypA cytochrome P450 (RefSeq) 280, 307
BSU30380 bceA bacitracin ABC efflux transporter (ATP-binding protein) (RefSeq) 71, 406
BSU31560 yufP putative permease of ABC transporter (RefSeq) 344, 406
BSU32070 yuiC hypothetical protein (RefSeq) 291, 307
BSU32650 yurS hypothetical protein (RefSeq) 280, 307
BSU34000 cyeB cysteine and O-acetylserine efflux permease (RefSeq) 96, 307
BSU35060 cypX putative monooxygenase (cytochrome P450) (RefSeq) 257, 406
BSU35070 yvmC hypothetical protein (RefSeq) 257, 406
BSU35280 yvjA putative integral inner membrane protein (RefSeq) 307, 411
BSU35770 tagC putative polyglycerol phosphate assembly and export protein (teichoic acid biosynthesis) (RefSeq) 239, 307
BSU36480 ywoD putative efflux transporter (RefSeq) 50, 307
BSU36490 ywoC putative hydrolase (RefSeq) 50, 307
BSU36500 ywoB putative integral inner membrane protein (RefSeq) 130, 307
BSU37050 ywkA malate dehydrogenase (RefSeq) 238, 406
BSU38250 ywbO putative sulfur oxido-reductase (RefSeq) 96, 307
BSU38790 yxzE putative bacteriocin (RefSeq) 231, 406
BSU39980 qodI quercetin dioxygenase (RefSeq) 179, 406
BSU40940 yyaD putative integral membrane protein; putative transporter (RefSeq) 156, 406
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 BSU03340
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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