Organism : Bacillus subtilis | Module List :
BSU26220 yqaQ

conserved hypothetical protein; skin element (RefSeq)

CircVis
Functional Annotations (6)
Function System
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU26220
(Mouseover regulator name to see its description)

BSU26220 is regulated by 22 influences and regulates 25 modules.
Regulators for BSU26220 yqaQ (22)
Regulator Module Operator
BSU02000 305 tf
BSU02160 305 tf
BSU03890 305 tf
BSU26220 305 tf
BSU26320 305 tf
BSU30150 305 tf
BSU35030 305 tf
BSU36600 305 tf
BSU37290 305 tf
BSU02320 205 tf
BSU03890 205 tf
BSU04820 205 tf
BSU05170 205 tf
BSU05970 205 tf
BSU06140 205 tf
BSU06700 205 tf
BSU22120 205 tf
BSU25760 205 tf
BSU26220 205 tf
BSU26340 205 tf
BSU35030 205 tf
BSU36600 205 tf

Warning: BSU26220 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
5354 5.70e+00 aaaataAaaaAgGGc
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5355 6.30e+03 GAAcATTTTCGGT
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5548 3.00e+04 AAaGGAGattAc
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5549 1.80e+02 atTCgTTtTgaaACg.tTc
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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 BSU26220

BSU26220 is enriched for 6 functions in 2 categories.
Enrichment Table (6)
Function System
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for BSU26220

BSU26220 has total of 44 gene neighbors in modules 205, 305
Gene neighbors (44)
Gene Common Name Description Module membership
BSU02250 ybfJ putative lipoprotein (RefSeq) 8, 205
BSU02420 glnT glutamine transporter (RefSeq) 295, 305
BSU02430 ybgJ glutaminase (RefSeq) 10, 305
BSU02610 ycbR hypothetical protein (RefSeq) 222, 305
BSU02620 phoD phosphodiesterase/alkaline phosphatase D (RefSeq) 305, 372
BSU02630 tatAD component of the twin-arginine pre-protein translocation pathway (RefSeq) 305, 372
BSU02640 tatCD component of the twin-arginine pre-protein translocation pathway (RefSeq) 84, 305
BSU03320 nasB assimilatory nitrate reductase (electron transfer subunit) (RefSeq) 305, 405
BSU04360 mntH manganese transport protein MntH (RefSeq) 95, 205
BSU04540 ydbO putative cation efflux system (RefSeq) 74, 205
BSU05310 ydeR putative efflux transporter (RefSeq) 175, 305
BSU05430 ydfJ putative proton metabolite efflux transporter (RefSeq) 175, 305
BSU05780 ydhJ putative metal-dependent phosphohydrolase (RefSeq) 142, 205
BSU06130 ydjC hypothetical protein (RefSeq) 205, 364
BSU07230 yetM hypothetical protein (RefSeq) 285, 305
BSU07410 yfmN hypothetical protein (RefSeq) 83, 205
BSU07560 pel pectate lyase (RefSeq) 8, 205
BSU08760 spo0M sporulation-control gene (RefSeq) 183, 205
BSU09190 yhcR non specific extracellular endonuclease cleaving RNA and DNA (RefSeq) 10, 305
BSU11070 yitP hypothetical protein (RefSeq) 282, 305
BSU11100 nprB extracellular neutral protease B (RefSeq) 10, 205
BSU13330 ykoL hypothetical protein (RefSeq) 74, 205
BSU13990 kinA sporulation-specific ATP-dependent protein histidine kinase (RefSeq) 205, 359
BSU14330 yknV putative ABC transporter (ATP-binding protein) (RefSeq) 88, 205
BSU17560 ynaI hypothetical protein (RefSeq) 205, 222
BSU17760 yndE putative spore germination integral inner membrane protein (RefSeq) 205, 278
BSU18680 yoaO hypothetical protein (RefSeq) 39, 205
BSU21950 ypzA hypothetical protein (RefSeq) 8, 205
BSU25220 antE hypothetical protein (RefSeq) 205, 233
BSU25930 yqcE conserved hypothetical protein; skin element (RefSeq) 205, 206
BSU25950 yqcC hypothetical protein (RefSeq) 130, 305
BSU25960 yqcB hypothetical protein; skin element (RefSeq) 305, 372
BSU25970 yqcA hypothetical protein (RefSeq) 130, 305
BSU25980 yqbT putative phage capsid assembly protein; skin element (RefSeq) 130, 305
BSU26000 yqbR conserved hypothetical protein; skin element (RefSeq) 130, 305
BSU26010 yqbQ conserved hypothetical protein; skin element (RefSeq) 130, 305
BSU26020 yqbP conserved hypothetical protein; skin element (RefSeq) 130, 305
BSU26030 yqbO putative lytic transglycosylase (RefSeq) 130, 305
BSU26220 yqaQ conserved hypothetical protein; skin element (RefSeq) 205, 305
BSU26300 yqaI hypothetical protein; skin element (RefSeq) 205, 371
BSU26330 yqdA hypothetical protein; skin element (RefSeq) 205, 206
BSU26340 yqaF putative transcriptional regulator; skin element (RefSeq) 205, 206
BSU30090 yteU putative membrane enzyme for rhamnogalaturonan degradation (RefSeq) 305, 371
BSU32430 pucJ uric acid permease (RefSeq) 84, 305
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 BSU26220
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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