Organism : Bacillus subtilis | Module List :
BSU20190 yosA

hypothetical protein from phage SPbeta (RefSeq)

CircVis
Functional Annotations (1)
Function System
tiny_TM_bacill tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU20190
(Mouseover regulator name to see its description)

BSU20190 is regulated by 24 influences and regulates 0 modules.
Regulators for BSU20190 yosA (24)
Regulator Module Operator
BSU00370 326 tf
BSU02000 326 tf
BSU05370 326 tf
BSU06960 326 tf
BSU07010 326 tf
BSU07590 326 tf
BSU08100 326 tf
BSU09480 326 tf
BSU17590 326 tf
BSU23090 326 tf
BSU23100 326 tf
BSU26320 326 tf
BSU28410 326 tf
BSU39850 326 tf
BSU01430 180 tf
BSU05370 180 tf
BSU06960 180 tf
BSU16600 180 tf
BSU23090 180 tf
BSU25250 180 tf
BSU26320 180 tf
BSU27320 180 tf
BSU29740 180 tf
BSU33650 180 tf

Warning: BSU20190 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
5308 4.80e-03 CTATaTTTtGaGGAGAActTacAC
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5309 5.20e-04 a.AagGaaAGG
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5590 3.80e-05 A.aAaaggGAGtTgaag
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5591 9.90e+01 AaGGAg
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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 BSU20190

BSU20190 is enriched for 1 functions in 4 categories.
Enrichment Table (1)
Function System
tiny_TM_bacill tigr/ tigrfam
Module neighborhood information for BSU20190

BSU20190 has total of 48 gene neighbors in modules 180, 326
Gene neighbors (48)
Gene Common Name Description Module membership
BSU02460 ycbC 5-dehydro-4-deoxyglucarate dehydratase (RefSeq) 168, 326
BSU02470 ycbD 2,5-dioxovalerate dehydrogenase (alpha-ketoglutaric semialdehyde dehydrogenase) (RefSeq) 168, 326
BSU02510 garD D-galactarate dehydratase (RefSeq) 180, 326
BSU03120 ycgI putative methyltransferase (RefSeq) 156, 180
BSU03690 yczF hypothetical protein (RefSeq) 180, 231
BSU03700 gerKA spore germination receptor subunit (RefSeq) 180, 290
BSU03710 gerKC spore germination receptor subunit (RefSeq) 180, 290
BSU03720 gerKB spore germination receptor subunit (RefSeq) 180, 290
BSU03730 yclH putative ABC transporter (ATPase component) (RefSeq) 180, 405
BSU03740 yclI putative transporter (RefSeq) 71, 180
BSU05230 ydeK putative permease (RefSeq) 84, 326
BSU05450 ydfK putative integral inner membrane protein (RefSeq) 180, 290
BSU05710 ydhD spore cortex lytic enzyme (RefSeq) 180, 304
BSU06150 gutB glucitol (sorbitol) dehydrogenase (RefSeq) 180, 326
BSU06160 gutP H+-glucitol symporter (RefSeq) 61, 326
BSU06300 cotA spore copper-dependent laccase (RefSeq) 84, 326
BSU08310 yfiL putative ABC transporter (ATP-binding protein) (RefSeq) 180, 406
BSU08320 yfiM putative ABC transporter (permease) (RefSeq) 180, 406
BSU10970 yitF putative enolase superfamily enzyme (RefSeq) 175, 326
BSU10980 yitG putative efflux transporter (RefSeq) 152, 326
BSU11130 ipi intracellular proteinase inhibitor BsuPI (RefSeq) 149, 180
BSU12190 yjhB putative ADP-ribose pyrophosphatase (RefSeq) 180, 257
BSU12300 uxaC glucuronate isomerase (RefSeq) 152, 180
BSU12310 exuM putative Na+:altronate/mannonate symporter (RefSeq) 152, 180
BSU12390 uxaA altronate hydrolase (RefSeq) 180, 318
BSU13350 ykoN putative glycosyltransferase (RefSeq) 43, 180
BSU13360 ykoP hypothetical protein (RefSeq) 43, 180
BSU13380 ykoS putative integral inner membrane protein (RefSeq) 180, 282
BSU18770 cyeA cysteine and O-acetyl serine efflux permease (RefSeq) 96, 180
BSU19510 yojB hypothetical protein (RefSeq) 21, 326
BSU19810 ypqP hypothetical protein (RefSeq) 86, 326
BSU20190 yosA hypothetical protein from phage SPbeta (RefSeq) 180, 326
BSU32470 pucE xanthine dehydrogenase, iron-sulfur subunit (RefSeq) 52, 326
BSU32480 pucD xanthine dehydrogenase, substrate and molybdenum cofactor subunit (RefSeq) 52, 326
BSU32490 pucC xanthine dehydrogenase, FAD-binding subunit (RefSeq) 52, 326
BSU34080 yvfS putative ABC transporter (permease) (RefSeq) 318, 326
BSU34090 yvfR putative ABC efflux transporter (ATP-binding protein) (RefSeq) 318, 326
BSU34530 cotR spore coat protein assembly factor CotR (RefSeq) 281, 326
BSU35190 yvkC putative phosphotransferase (RefSeq) 180, 248
BSU36030 ywrK putative Na+/H+ antiporter (RefSeq) 281, 326
BSU38440 ywaF putative integral inner membrane protein (RefSeq) 180, 278
BSU38640 yxlH putative efflux transporter (RefSeq) 180, 318
BSU38990 scoA succinyl CoA:3-oxoacid CoA-transferase (subunit A) (RefSeq) 156, 180
BSU39350 hutH histidine ammonia-lyase (RefSeq) 85, 326
BSU39360 hutU urocanate hydratase (RefSeq) 85, 326
BSU39370 hutI imidazolonepropionase (RefSeq) 85, 326
BSU39380 hutG formimidoylglutamase (RefSeq) 85, 326
BSU39390 hutM histidine permease (RefSeq) 84, 326
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 BSU20190
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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