Organism : Bacillus subtilis | Module List :
BSU05130 ydeB

putative transcriptional regulator (RefSeq)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulators, similar to M. xanthus CarD cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU05130
(Mouseover regulator name to see its description)

BSU05130 is regulated by 23 influences and regulates 11 modules.
Regulators for BSU05130 ydeB (23)
Regulator Module Operator
BSU05130 91 tf
BSU08990 91 tf
BSU10560 91 tf
BSU13150 91 tf
BSU29700 91 tf
BSU30150 91 tf
BSU33230 91 tf
BSU35050 91 tf
BSU35110 91 tf
BSU35490 91 tf
BSU38070 91 tf
BSU05130 404 tf
BSU05850 404 tf
BSU09270 404 tf
BSU09650 404 tf
BSU10560 404 tf
BSU10860 404 tf
BSU24220 404 tf
BSU24610 404 tf
BSU29270 404 tf
BSU35050 404 tf
BSU35110 404 tf
BSU35490 404 tf

Warning: BSU05130 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
5136 2.00e+00 TGGAGG
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5137 4.70e+03 Tcc.accctTT.cCTATTtttTA
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5716 9.60e-02 tAtaaTtAaaa.AtAgGgagatgg
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5717 2.70e+03 CCGGaCtGgCT
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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 BSU05130

BSU05130 is enriched for 3 functions in 3 categories.
Module neighborhood information for BSU05130

BSU05130 has total of 60 gene neighbors in modules 91, 404
Gene neighbors (60)
Gene Common Name Description Module membership
BSU02650 pcp pyrrolidone-carboxylate peptidase (RefSeq) 208, 404
BSU03470 hxlR positive regulator of hxlAB expression (RefSeq) 91, 296
BSU03660 yclE putative hydrolase (RefSeq) 208, 404
BSU04480 ydbI putative integral inner membrane protein (RefSeq) 208, 404
BSU05130 ydeB putative transcriptional regulator (RefSeq) 91, 404
BSU08720 ygaF putative bacterioferritin comigratory protein; putative peroxiredoxin (RefSeq) 222, 404
BSU08740 ygzB hypothetical protein (RefSeq) 22, 404
BSU09260 yhxA aminotransferase (RefSeq) 330, 404
BSU09270 glpP glycerol-3-phosphate responding transcription antiterminator (RefSeq) 208, 404
BSU09540 plsC 1-acylglycerol-phosphate (1-acyl-G3P) acyltransferase (RefSeq) 64, 404
BSU09650 yhdZ NAD-dependent deacetylase (RefSeq) 208, 404
BSU10440 yhjA hypothetical protein (RefSeq) 208, 404
BSU10560 yhjM transcriptional regulator of the ntd operon; (LacI family) (RefSeq) 49, 91
BSU11990 yjdB hypothetical protein (RefSeq) 25, 91
BSU12450 yjpA putative enzyme (RefSeq) 25, 404
BSU13640 spo0E negative regulatory phosphatase acting on Spo0A-P (sporulation) (RefSeq) 70, 91
BSU14220 ykuU putative 2-cys peroxiredoxin (RefSeq) 91, 359
BSU14230 ykuV thiol-disulfide isomerase (RefSeq) 91, 359
BSU14510 ktrC potassium uptake protein (RefSeq) 310, 404
BSU14560 def peptide deformylase (RefSeq) 91, 373
BSU14940 ylbA hypothetical protein (RefSeq) 25, 404
BSU15090 ylbO putative spore coat protein regulator protein YlbO (RefSeq) 91, 126
BSU17020 ymcA master regulator for biofilm formation (RefSeq) 208, 404
BSU17100 pksC malonyl-CoA-acyltransferase involved in polyketide synthesis (RefSeq) 25, 91
BSU17500 ynaB hypothetical protein (RefSeq) 70, 91
BSU17690 yncM hypothetical protein (RefSeq) 39, 91
BSU18530 yoaA putative N-acetyltransferase (RefSeq) 91, 323
BSU21830 ypjQ putative phosphatidylglycerophosphatase (RefSeq) 64, 404
BSU23300 ypuD hypothetical protein (RefSeq) 59, 91
BSU24110 yqzF hypothetical protein (RefSeq) 208, 404
BSU24220 spo0A response regulator (RefSeq) 208, 404
BSU24490 yqhQ hypothetical protein (RefSeq) 208, 404
BSU24500 yqhP hypothetical protein (RefSeq) 208, 404
BSU24610 sinR transcriptional regulator for post-exponential-phase response (RefSeq) 219, 404
BSU24800 yqgW hypothetical protein (RefSeq) 25, 404
BSU25860 yqcG putative phage DNA manipulating enzyme; skin element (RefSeq) 31, 91
BSU25870 yqcF hypothetical protein; skin element (RefSeq) 31, 91
BSU26780 yrdA hypothetical protein (RefSeq) 304, 404
BSU26790 aadK aminoglycoside 6-adenylyltransferase (RefSeq) 94, 404
BSU26900 yraL hypothetical protein (RefSeq) 208, 404
BSU26910 yraK putative hydrolase (RefSeq) 91, 379
BSU26920 yraJ hypothetical protein (RefSeq) 208, 404
BSU26930 yraI hypothetical protein (RefSeq) 208, 404
BSU29260 ytpI hypothetical protein (RefSeq) 91, 304
BSU29270 ytoI hypothetical protein (RefSeq) 206, 404
BSU30000 ythQ putative ABC transporter (permease) (RefSeq) 91, 166
BSU30010 ythP putative ABC transporter (ATP-binding protein) (RefSeq) 91, 166
BSU30020 ytzE putative transcriptional regulator (DeoR family) (RefSeq) 91, 249
BSU32760 yusD hypothetical protein (RefSeq) 49, 404
BSU33140 yvqJ putative efflux protein (RefSeq) 91, 141
BSU33960 araE arabinose-related compounds permease (RefSeq) 91, 329
BSU34430 racX amino acid racemase (RefSeq) 91, 329
BSU34440 pbpE penicillin-binding protein 4* (RefSeq) 91, 329
BSU34660 yvdB putative anion transporter (RefSeq) 208, 404
BSU35050 yvnA putative transcriptional regulator (RefSeq) 25, 91
BSU35490 degU two-component response regulator (RefSeq) 208, 404
BSU36380 rapD response regulator aspartate phosphatase (RefSeq) 91, 237
BSU37800 yweA member of the processed secretome (RefSeq) 25, 91
BSU39080 licT transcriptional antiterminator (BglG family) (RefSeq) 68, 91
BSU39090 yxiP putative lipoprotein (RefSeq) 90, 91
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 BSU05130
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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