Organism : Bacillus subtilis | Module List :
BSU30000 ythQ

putative ABC transporter (permease) (RefSeq)

CircVis
Functional Annotations (1)
Function System
Predicted ABC-type exoprotein transport system, permease component cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU30000
(Mouseover regulator name to see its description)

BSU30000 is regulated by 15 influences and regulates 0 modules.
Regulators for BSU30000 ythQ (15)
Regulator Module Operator
BSU01730 166 tf
BSU01740 166 tf
BSU35110 166 tf
BSU35650 166 tf
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

Warning: BSU30000 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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5280 3.70e-05 TGAAAccTtTT
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5281 9.10e+02 CTcCGAtTTacGGAAAttGG
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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 BSU30000

BSU30000 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted ABC-type exoprotein transport system, permease component cog/ cog
Module neighborhood information for BSU30000

BSU30000 has total of 60 gene neighbors in modules 91, 166
Gene neighbors (60)
Gene Common Name Description Module membership
BSU00260 yaaN hypothetical protein (RefSeq) 54, 166
BSU00710 hslO Hsp33-like chaperonin (RefSeq) 166, 314
BSU00720 yacD putative protein secretion PrsA homolog (RefSeq) 13, 166
BSU01130 tufA elongation factor Tu (RefSeq) 7, 166
BSU01730 sigW RNA polymerase sigma factor SigW (RefSeq) 159, 166
BSU01740 rsiW anti-sigma(W) factor (RefSeq) 159, 166
BSU03470 hxlR positive regulator of hxlAB expression (RefSeq) 91, 296
BSU05130 ydeB putative transcriptional regulator (RefSeq) 91, 404
BSU05750 ydhG hypothetical protein (RefSeq) 166, 167
BSU10560 yhjM transcriptional regulator of the ntd operon; (LacI family) (RefSeq) 49, 91
BSU11990 yjdB hypothetical protein (RefSeq) 25, 91
BSU12070 yjdJ hypothetical protein (RefSeq) 166, 291
BSU12420 yjoB ATPase possibly involved in protein degradation (RefSeq) 166, 377
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
BSU14560 def peptide deformylase (RefSeq) 91, 373
BSU15090 ylbO putative spore coat protein regulator protein YlbO (RefSeq) 91, 126
BSU15130 yllB cell division protein MraZ (RefSeq) 166, 377
BSU15140 mraW S-adenosyl-methyltransferase MraW (RefSeq) 79, 166
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
BSU18590 yoaG putative permease (RefSeq) 162, 166
BSU18980 yobJ hypothetical protein (RefSeq) 159, 166
BSU19290 yozO hypothetical protein (RefSeq) 36, 166
BSU23220 scpA segregation and condensation protein A (RefSeq) 145, 166
BSU23300 ypuD hypothetical protein (RefSeq) 59, 91
BSU24810 yqgV hypothetical protein (RefSeq) 70, 166
BSU25370 yqfB hypothetical protein (RefSeq) 162, 166
BSU25380 yqfA hypothetical protein (RefSeq) 162, 166
BSU25390 yqeZ putative membrane bound hydrolase (RefSeq) 162, 166
BSU25640 nadD nicotinic acid mononucleotide adenylyltransferase (RefSeq) 166, 170
BSU25660 aroE shikimate 5-dehydrogenase (RefSeq) 166, 170
BSU25860 yqcG putative phage DNA manipulating enzyme; skin element (RefSeq) 31, 91
BSU25870 yqcF hypothetical protein; skin element (RefSeq) 31, 91
BSU26910 yraK putative hydrolase (RefSeq) 91, 379
BSU27380 yrzB hypothetical protein (RefSeq) 70, 166
BSU29260 ytpI hypothetical protein (RefSeq) 91, 304
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
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
BSU35050 yvnA putative transcriptional regulator (RefSeq) 25, 91
BSU35100 yvlD putative integral inner membrane protein (RefSeq) 166, 377
BSU35110 yvlC putative regulator (stress mediated) (RefSeq) 166, 377
BSU35120 yvlB hypothetical protein (RefSeq) 166, 377
BSU35130 yvlA hypothetical protein (RefSeq) 166, 377
BSU35140 yvkN hypothetical protein (RefSeq) 31, 166
BSU35650 lytR membrane-bound transcriptional regulator LytR (RefSeq) 145, 166
BSU36090 ywrE hypothetical protein (RefSeq) 166, 239
BSU36380 rapD response regulator aspartate phosphatase (RefSeq) 91, 237
BSU37800 yweA member of the processed secretome (RefSeq) 25, 91
BSU38940 yxjI hypothetical protein (RefSeq) 166, 263
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 BSU30000
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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