Organism : Bacillus subtilis | Module List :
BSU10150 yhgD

putative transcriptional regulator (RefSeq)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU10150
(Mouseover regulator name to see its description)

BSU10150 is regulated by 22 influences and regulates 8 modules.
Regulators for BSU10150 yhgD (22)
Regulator Module Operator
BSU00800 1 tf
BSU03470 1 tf
BSU04460 1 tf
BSU10560 1 tf
BSU10860 1 tf
BSU24250 1 tf
BSU27170 1 tf
BSU27520 1 tf
BSU29740 1 tf
BSU35050 1 tf
BSU37580 1 tf
BSU37620 1 tf
BSU39990 1 tf
BSU02680 132 tf
BSU03080 132 tf
BSU04060 132 tf
BSU10150 132 tf
BSU15970 132 tf
BSU28400 132 tf
BSU33740 132 tf
BSU35200 132 tf
BSU37160 132 tf

Warning: BSU10150 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
4966 1.10e+00 GAattggaAaaagC
Loader icon
4967 9.00e+03 CC.gcCtGcTTGA.gAGC
Loader icon
5216 2.70e-09 CTCCttTtTtT
Loader icon
5217 6.40e+01 aACAgCAttTT
Loader icon
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 BSU10150

BSU10150 is enriched for 5 functions in 3 categories.
Module neighborhood information for BSU10150

BSU10150 has total of 50 gene neighbors in modules 1, 132
Gene neighbors (50)
Gene Common Name Description Module membership
BSU00220 yaaL hypothetical protein (RefSeq) 1, 188
BSU00390 yabD metal-dependent DNase (RefSeq) 1, 243
BSU03080 ycgE putative transcriptional regulator (RefSeq) 132, 339
BSU03569 sfp 38, 132
BSU03580 yczE integral inner membrane protein regulating antibiotic production (RefSeq) 132, 319
BSU04640 alrA D-alanine racemase (RefSeq) 1, 314
BSU05470 ydfM putative divalent cation efflux transporter (RefSeq) 132, 197
BSU05900 thiL thiamine monophosphate kinase (RefSeq) 1, 245
BSU05930 rimI ribosomal protein S18 alanine N-acetyltransferase (RefSeq) 1, 48
BSU08290 yfiJ two-component sensor histidine kinase [YfiK] (RefSeq) 132, 307
BSU08700 ygaE hypothetical protein (RefSeq) 132, 397
BSU09965 BSU09965 None 132, 271
BSU10150 yhgD putative transcriptional regulator (RefSeq) 1, 132
BSU12240 yjkA putative ABC transporter (permease) (RefSeq) 132, 339
BSU12250 yjkB putative phosphate ABC transporter (ATP-binding protein) (RefSeq) 132, 339
BSU12260 yjlA putative permease (RefSeq) 107, 132
BSU15230 murB UDP-N-acetylenolpyruvoylglucosamine reductase (RefSeq) 1, 50
BSU16050 rbgA ribosomal biogenesis GTPase (RefSeq) 1, 292
BSU18440 gltD glutamate synthase subunit beta (RefSeq) 1, 176
BSU18450 gltA glutamate synthase (large subunit) (RefSeq) 1, 176
BSU23770 dsdA D-serine dehydratase (RefSeq) 1, 37
BSU23780 yqjQ putative metabolite dehydrogenase, NAD-binding (RefSeq) 1, 37
BSU25180 trmK tRNA: m1A22 methyltransferase (RefSeq) 1, 202
BSU27520 cymR transcriptional regulator of cysteine biosynthesis (RefSeq) 1, 228
BSU28650 ysgA putative RNA methylase (RefSeq) 132, 339
BSU29900 trmB tRNA (guanine-N(7)-)-methyltransferase (RefSeq) 132, 397
BSU29990 pbuO hypoxanthine/guanine permease (RefSeq) 1, 37
BSU30810 ytxM putative esterase (RefSeq) 132, 339
BSU30820 menD 2-succinyl-5-enolpyruvyl-6-hydroxy-3- cyclohexene-1-carboxylate synthase (RefSeq) 132, 319
BSU31400 alaT hypothetical protein (RefSeq) 67, 132
BSU31510 yufK putative integral inner membrane protein (RefSeq) 132, 240
BSU33150 yvqK ATP:cob(I)alamin adenosyltransferase (RefSeq) 1, 48
BSU33170 yvrB putative vitamin B12 permease (RefSeq) 1, 48
BSU33450 helD DNA 3'-5' helicase IV (RefSeq) 1, 37
BSU33460 yvgT putative integral inner membrane protein (RefSeq) 132, 339
BSU33470 bdbC thiol-disulfide oxidoreductase (RefSeq) 4, 132
BSU33740 yvaV putative transcriptional regulator (RefSeq) 132, 339
BSU34100 rsbQ regulator of RsbP phosphatase (RefSeq) 132, 319
BSU34110 rsbP serine phosphatase (RefSeq) 75, 132
BSU35200 yvkB putative transcriptional regulator (TetR/AcrR family) (RefSeq) 38, 132
BSU36240 ywqE protein tyrosine-phosphatase (RefSeq) 1, 339
BSU36360 mscL large-conductance mechanosensitive channel (RefSeq) 1, 240
BSU36610 ywnC putative integral inner membrane protein (RefSeq) 132, 319
BSU37970 ung uracil-DNA glycosylase (RefSeq) 1, 50
BSU37980 ywdF putative glycosyltransferase (RefSeq) 1, 243
BSU38320 ywbH holin-like protein (RefSeq) 132, 409
BSU40490 yycA putative integral inner membrane protein; putative glycosyl transferase (RefSeq) 132, 339
BSU40510 yybT putative phosphodiesterase (RefSeq) 1, 292
BSU40520 yybS putative integral inner membrane protein (RefSeq) 1, 243
VIMSS37450 VIMSS37450 None 132, 184
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 BSU10150
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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