Organism : Bacillus subtilis | Module List :
BSU09480 yhdI

putative PLP-dependent transcriptional regulator (RefSeq)

CircVis
Functional Annotations (7)
Function System
Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
biosynthetic process go/ biological_process
transferase activity, transferring nitrogenous groups go/ molecular_function
pyridoxal phosphate binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU09480
(Mouseover regulator name to see its description)

BSU09480 is regulated by 21 influences and regulates 25 modules.
Regulators for BSU09480 yhdI (21)
Regulator Module Operator
BSU02000 294 tf
BSU02160 294 tf
BSU05970 294 tf
BSU06700 294 tf
BSU07820 294 tf
BSU09480 294 tf
BSU13870 294 tf
BSU17850 294 tf
BSU35030 294 tf
BSU36600 294 tf
BSU03890 95 tf
BSU04730 95 tf
BSU05970 95 tf
BSU09480 95 tf
BSU13870 95 tf
BSU17850 95 tf
BSU26220 95 tf
BSU26840 95 tf
BSU35030 95 tf
BSU36600 95 tf
BSU37080 95 tf

Warning: BSU09480 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
5144 2.80e+02 aTgcct.tttcaTtTgcAg.gAAa
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5145 8.20e+03 tgAaGagCTTG
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5526 2.50e-03 AaaAAAGGgGagt
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5527 5.10e+00 gtTCgcTctgcaggc
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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 BSU09480

BSU09480 is enriched for 7 functions in 3 categories.
Module neighborhood information for BSU09480

BSU09480 has total of 37 gene neighbors in modules 95, 294
Gene neighbors (37)
Gene Common Name Description Module membership
BSU02060 ybxG putative amino acid permease (RefSeq) 95, 199
BSU02300 ybfN hypothetical protein (RefSeq) 75, 294
BSU02850 adcA Zn(II)-binding lipoprotein (RefSeq) 294, 395
BSU04360 mntH manganese transport protein MntH (RefSeq) 95, 205
BSU05040 yddN putative alkanal monooxygenase (RefSeq) 44, 95
BSU05510 ydfQ putative thioredoxin or thiol-disulfide isomerase (RefSeq) 95, 294
BSU05690 ydhB putative integral inner membrane protein (RefSeq) 270, 294
BSU05960 moaC molybdenum cofactor biosynthesis protein MoaC (RefSeq) 95, 201
BSU06370 pbuG hypoxanthine/guanine permease (RefSeq) 190, 294
BSU06660 opuE proline transporter (RefSeq) 142, 294
BSU07180 yetI hypothetical protein (RefSeq) 154, 294
BSU07190 yezD hypothetical protein (RefSeq) 95, 199
BSU07210 yetK putative efflux transporter (RefSeq) 95, 199
BSU07720 yflD hypothetical protein (RefSeq) 95, 294
BSU09250 yhcX putative amidohydrolase (RefSeq) 39, 95
BSU09480 yhdI putative PLP-dependent transcriptional regulator (RefSeq) 95, 294
BSU13440 ykoY putative transporter (RefSeq) 178, 294
BSU13720 queC pre-queuosine 0 synthase (RefSeq) 75, 95
BSU13870 ykvZ putative transcriptional regulator (LacI family) (RefSeq) 95, 389
BSU17290 ebrB small multidrug efflux transporter (RefSeq) 38, 294
BSU17310 ymaG putative cell wall associated protein (RefSeq) 294, 358
BSU17340 hfq RNA-binding protein Hfq (RefSeq) 95, 359
BSU17360 ymzA hypothetical protein (RefSeq) 95, 200
BSU17450 glnR transcriptional regulator (nitrogen metabolism) (RefSeq) 30, 294
BSU17880 ynzC hypothetical protein (RefSeq) 244, 294
BSU18060 yneR hypothetical protein (RefSeq) 20, 294
BSU19420 yojK putative glycosyltransferase (RefSeq) 95, 244
BSU25010 yqgE putative efflux transporter (RefSeq) 174, 294
BSU26110 yqbH conserved hypothetical protein; skin element (RefSeq) 175, 294
BSU27240 yrhC hypothetical protein (RefSeq) 95, 201
BSU28320 ysnD hypothetical protein (RefSeq) 108, 294
BSU29280 ytnM putative transporter (RefSeq) 95, 333
BSU34400 padC phenolic acid decarboxylase (RefSeq) 95, 294
BSU36740 ywmC hypothetical protein (RefSeq) 95, 364
BSU37200 uvsE putative UV damage endonuclease (RefSeq) 26, 294
BSU38780 yxkI putative membrane protease (RefSeq) 10, 95
BSU39530 yxeJ hypothetical protein (RefSeq) 95, 389
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 BSU09480
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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