Organism : Bacillus subtilis | Module List :
BSU19090 yobU

putative effector of transcriptional regulator (RefSeq)

CircVis
Functional Annotations (1)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU19090
(Mouseover regulator name to see its description)

BSU19090 is regulated by 21 influences and regulates 18 modules.
Regulators for BSU19090 yobU (21)
Regulator Module Operator
BSU05850 64 tf
BSU09650 64 tf
BSU00800 239 tf
BSU01740 239 tf
BSU04680 239 tf
BSU04730 239 tf
BSU10420 239 tf
BSU11500 239 tf
BSU12560 239 tf
BSU14240 239 tf
BSU14380 239 tf
BSU18760 239 tf
BSU19090 239 tf
BSU19100 239 tf
BSU19120 239 tf
BSU26580 239 tf
BSU29700 239 tf
BSU33970 239 tf
BSU34220 239 tf
BSU35650 239 tf
BSU37620 239 tf

Warning: BSU19090 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
5084 4.70e-02 aaaaAggggaG
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5085 1.20e+02 TaTATTTTaccATtAaActGTgAC
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5420 6.50e-02 aataaGgaGGAagaAa
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5421 2.70e-01 aCAGccg.taTTaTGaat.cA
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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 BSU19090

BSU19090 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
Module neighborhood information for BSU19090

BSU19090 has total of 60 gene neighbors in modules 64, 239
Gene neighbors (60)
Gene Common Name Description Module membership
BSU00990 rpmG 50S ribosomal protein L33 (RefSeq) 64, 200
BSU03450 hxlB 6-phospho-3-hexuloisomerase (PHI) (RefSeq) 64, 296
BSU03460 hxlA 3-hexulose-6-phosphate synthase (HPS) (RefSeq) 64, 296
BSU04020 yczH putative hydrolase (RefSeq) 64, 145
BSU05380 ydfE putative flavoprotein (RefSeq) 174, 239
BSU09540 plsC 1-acylglycerol-phosphate (1-acyl-G3P) acyltransferase (RefSeq) 64, 404
BSU09600 crcBA camphor resistance protein CrcB (RefSeq) 64, 115
BSU10010 trpP tryptophan transporter (RefSeq) 64, 94
BSU10880 yisV putative PLP-dependent transcriptional regulator (RefSeq) 64, 318
BSU10990 yitH putative N-acetyltransferase (RefSeq) 64, 171
BSU11000 yitI putative N-acetyltransferase (RefSeq) 64, 219
BSU11270 yjzD hypothetical protein (RefSeq) 64, 157
BSU11280 yjaU hypothetical protein (RefSeq) 64, 157
BSU11480 yjbB putative exporter (RefSeq) 64, 350
BSU11510 yjbE putative transporter component (RefSeq) 64, 115
BSU12460 xlyB N-acetylmuramoyl-L-alanine amidase; bacteriophage PBSX protein (RefSeq) 239, 306
BSU12500 xkdA PBSX phage protein, putative peptidase (RefSeq) 64, 96
BSU12680 xkdO conserved hypothetical protein; PBSX phage protein (RefSeq) 239, 269
BSU12710 xkdR conserved hypothetical protein; putative PBSX prophage protein (RefSeq) 239, 269
BSU12790 xhlA defective prophage PBSX putative enzyme (RefSeq) 7, 239
BSU13070 ykkA hypothetical protein (RefSeq) 64, 171
BSU13080 ykkB putative N-acetyltransferase (RefSeq) 64, 171
BSU13480 ykrK hypothetical protein (RefSeq) 150, 239
BSU14750 ylaE hypothetical protein (RefSeq) 239, 353
BSU14800 ylaJ putative lipoprotein (RefSeq) 239, 263
BSU15420 divIVA cell-division initiation protein (RefSeq) 64, 402
BSU18600 yozQ hypothetical protein (RefSeq) 55, 239
BSU18620 yoaI putative 4-hydroxyphenylacetate-3-hydroxylase (RefSeq) 64, 379
BSU18690 yoaP hypothetical protein (RefSeq) 64, 129
BSU18760 yoaU putative transcriptional regulator (LysR family) (RefSeq) 200, 239
BSU18920 phrK secreted regulator of the activity of phosphatase RapK (RefSeq) 239, 291
BSU19090 yobU putative effector of transcriptional regulator (RefSeq) 64, 239
BSU19100 yobV putative transcriptional regulator (RefSeq) 64, 170
BSU19400 sodC superoxide dismutase (exported lipoprotein) (RefSeq) 239, 359
BSU19410 cwlS peptidoglycan hydrolase (cell wall-binding d,l-endopeptidase) (RefSeq) 239, 353
BSU21830 ypjQ putative phosphatidylglycerophosphatase (RefSeq) 64, 404
BSU22000 sspL small acid-soluble spore protein (RefSeq) 200, 239
BSU24590 yqhG hypothetical protein (RefSeq) 239, 411
BSU25060 yqfZ factor involved in motility (RefSeq) 123, 239
BSU25120 yqfT hypothetical protein (RefSeq) 239, 280
BSU26120 yqbG conserved hypothetical protein; skin element (RefSeq) 96, 239
BSU26230 yqaP conserved hypothetical protein; skin element (RefSeq) 25, 64
BSU26240 yqaO conserved hypothetical protein; skin element (RefSeq) 64, 216
BSU26940 yraH putative lyase (RefSeq) 86, 239
BSU27570 yrzK hypothetical protein (RefSeq) 150, 239
BSU27670 spoVB putative putative translocase with flippase function for teichoic acid synthesis; involved in spore cortex synthesis (stage V sporulation) (RefSeq) 127, 239
BSU27800 yrzH hypothetical protein (RefSeq) 64, 258
BSU27810 yrbD sodium/proton-dependent alanine transporter (RefSeq) 64, 304
BSU29910 ytzH hypothetical protein (RefSeq) 127, 239
BSU30670 luxS S-ribosylhomocysteinase (RefSeq) 49, 64
BSU30680 ytjA hypothetical protein (RefSeq) 64, 115
BSU31580 maeN Na+/malate symporter (RefSeq) 64, 238
BSU32270 yutH spore coat-associated protein (RefSeq) 127, 239
BSU32280 yutG putative phosphatidylglycerophosphatase A (RefSeq) 27, 239
BSU32320 yutC putative lipoprotein (RefSeq) 239, 255
BSU35770 tagC putative polyglycerol phosphate assembly and export protein (teichoic acid biosynthesis) (RefSeq) 239, 307
BSU35880 pgsA capsular polyglutamate synthetase (RefSeq) 64, 318
BSU36090 ywrE hypothetical protein (RefSeq) 166, 239
BSU36320 ywpG hypothetical protein (RefSeq) 64, 318
BSU38800 yxkH putative exported polysaccharide deacetylase, lipoprotein (RefSeq) 96, 239
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 BSU19090
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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