Organism : Bacillus subtilis | Module List :
BSU27330 udk

uridine kinase (RefSeq)

CircVis
Functional Annotations (8)
Function System
Uridine kinase cog/ cog
cell killing go/ biological_process
uridine kinase activity go/ molecular_function
ATP binding go/ molecular_function
biosynthetic process go/ biological_process
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
udk tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU27330
(Mouseover regulator name to see its description)

BSU27330 is regulated by 19 influences and regulates 0 modules.
Regulators for BSU27330 udk (19)
Regulator Module Operator
BSU02370 176 tf
BSU04060 176 tf
BSU04100 176 tf
BSU10860 176 tf
BSU16600 176 tf
BSU24320 176 tf
BSU30020 176 tf
BSU35050 176 tf
BSU01070 227 tf
BSU01080 227 tf
BSU02370 227 tf
BSU02680 227 tf
BSU06700 227 tf
BSU13880 227 tf
BSU16170 227 tf
BSU17850 227 tf
BSU20820 227 tf
BSU21020 227 tf
BSU37080 227 tf

Warning: BSU27330 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
5300 1.80e+02 caGGAGgc
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5301 2.20e+03 GACTGGGG
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5398 1.40e+03 gGgGCTTT
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5399 2.90e+03 gAAAgcaAgaAAAaggGaAg
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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 BSU27330

BSU27330 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Uridine kinase cog/ cog
cell killing go/ biological_process
uridine kinase activity go/ molecular_function
ATP binding go/ molecular_function
biosynthetic process go/ biological_process
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
udk tigr/ tigrfam
Module neighborhood information for BSU27330

BSU27330 has total of 36 gene neighbors in modules 176, 227
Gene neighbors (36)
Gene Common Name Description Module membership
BSU01450 cbiO cobalt transporter ATP-binding subunit (RefSeq) 122, 176
BSU01460 cbiO cobalt transporter ATP-binding subunit (RefSeq) 176, 374
BSU01470 ybaF putative permease (RefSeq) 30, 176
BSU01480 truA tRNA pseudouridine synthase A (RefSeq) 176, 374
BSU02290 psd phosphatidylserine decarboxylase (RefSeq) 75, 227
BSU04050 ycsF LamB/YcsF family protein (RefSeq) 176, 240
BSU04060 ycsG putative branched chain amino acids transporter (RefSeq) 176, 240
BSU04070 ycsI hypothetical protein (RefSeq) 176, 240
BSU04080 kipI putative inhibitor of the autophosphorylation reaction of KinA (RefSeq) 176, 240
BSU04090 kipA putative hydrolase subunit antagonist of KipI (RefSeq) 176, 240
BSU04100 kipR transcriptional regulator (IclR family) (RefSeq) 176, 240
BSU06630 yerH putative lipoprotein (RefSeq) 75, 227
BSU06710 swrC transporter involved in surfactin self-resistance (RefSeq) 154, 227
BSU09165 BSU09165 None 67, 176
BSU12671 BSU12671 None 51, 176
BSU15220 murG undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase (RefSeq) 176, 193
BSU16140 xerC site-specific tyrosine recombinase XerC (RefSeq) 30, 227
BSU17370 nrdI ribonucleotide reductase stimulatory protein (RefSeq) 30, 227
BSU17380 nrdE ribonucleotide-diphosphate reductase subunit alpha (RefSeq) 30, 227
BSU17390 nrdF ribonucleotide-diphosphate reductase subunit beta (RefSeq) 30, 227
BSU17400 ymaB putative enzyme involved in deoxyribonucleotide synthesis (RefSeq) 30, 227
BSU18440 gltD glutamate synthase subunit beta (RefSeq) 1, 176
BSU18450 gltA glutamate synthase (large subunit) (RefSeq) 1, 176
BSU19390 yojN putative nitric-oxide reductase (RefSeq) 30, 227
BSU19450 rsbRC Component of the piezosome (stressosome) (RefSeq) 227, 271
BSU22400 dinG bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon (RefSeq) 227, 385
BSU22410 panD aspartate alpha-decarboxylase (RefSeq) 227, 382
BSU22420 panC pantoate--beta-alanine ligase (RefSeq) 227, 382
BSU22430 panB 3-methyl-2-oxobutanoate hydroxymethyltransferase (RefSeq) 227, 382
BSU25610 yqeM hypothetical protein (RefSeq) 75, 227
BSU26075 BSU26075 None 24, 176
BSU27330 udk uridine kinase (RefSeq) 176, 227
BSU27920 obgE GTPase ObgE (RefSeq) 30, 227
BSU35700 tagH ATP-binding teichoic acid precursor transporter component (RefSeq) 227, 265
VIMSS36726 VIMSS36726 None 176, 235
VIMSS39187 VIMSS39187 None 176, 235
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 BSU27330
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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