Organism : Bacillus subtilis | Module List :
BSU11650 tenA

thiaminase II (RefSeq)

CircVis
Functional Annotations (3)
Function System
Putative transcription activator cog/ cog
thiaminase activity go/ molecular_function
Thiamine metabolism kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU11650
(Mouseover regulator name to see its description)

BSU11650 is regulated by 20 influences and regulates 6 modules.
Regulators for BSU11650 tenA (20)
Regulator Module Operator
BSU03890 6 tf
BSU04100 6 tf
BSU08250 6 tf
BSU11650 6 tf
BSU11660 6 tf
BSU13150 6 tf
BSU13210 6 tf
BSU16900 6 tf
BSU19070 6 tf
BSU23100 6 tf
BSU24020 6 tf
BSU35050 6 tf
BSU37550 6 tf
BSU09270 146 tf
BSU11650 146 tf
BSU11660 146 tf
BSU13210 146 tf
BSU19050 146 tf
BSU26720 146 tf
BSU33840 146 tf

Warning: BSU11650 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
4974 1.50e+02 CgTagggAaGtgaAGc
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4975 3.80e+03 GGaGcTCGG
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5242 1.60e-03 GgtTcA.acc.gcgtaGgGaAGcG
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5243 5.10e+02 CGgaaTccgtTTtTTTttatag
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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 BSU11650

BSU11650 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Putative transcription activator cog/ cog
thiaminase activity go/ molecular_function
Thiamine metabolism kegg/ kegg pathway
Module neighborhood information for BSU11650

BSU11650 has total of 33 gene neighbors in modules 6, 146
Gene neighbors (33)
Gene Common Name Description Module membership
BSU08790 thiC thiamine biosynthesis protein ThiC (RefSeq) 6, 146
BSU11055 BSU11055 None 6, 235
BSU11650 tenA thiaminase II (RefSeq) 6, 146
BSU11660 tenI transcriptional regulator TenI (RefSeq) 6, 146
BSU11670 thiO FAD-dependent glycine oxidase (RefSeq) 6, 146
BSU11680 thiS Sulfur carrier for synthesis of hydroxyethylthiazole phosphate (RefSeq) 6, 146
BSU11690 thiG thiazole synthase (RefSeq) 6, 146
BSU11700 thiF thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein (RefSeq) 6, 146
BSU11710 yjbV phosphomethylpyrimidine kinase (RefSeq) 6, 146
BSU13210 thiX thiamine transporter, permease component (RefSeq) 6, 146
BSU13220 thiW thiamine ABC transporter (ATP-binding protein) (RefSeq) 6, 146
BSU13230 thiV thiamine transporter, permease component (RefSeq) 6, 146
BSU13240 thiU thiamine binding protein (RefSeq) 6, 146
BSU13250 ykoG two-component response regulator [YkoH] (RefSeq) 146, 150
BSU13260 ykoH two-component sensor histidine kinase [YkoG] (RefSeq) 146, 150
BSU13270 ykoI hypothetical protein (RefSeq) 146, 150
BSU13280 ykoJ hypothetical protein (RefSeq) 116, 146
BSU15350 ylmB acetylornithine deacetylase (RefSeq) 146, 370
BSU22530 ypjA putative integral inner membrane protein (RefSeq) 146, 370
BSU30200 bioB biotin synthase (RefSeq) 146, 192
BSU30210 bioD dithiobiotin synthetase (RefSeq) 146, 192
BSU30220 bioF 8-amino-7-oxononanoate synthase (RefSeq) 146, 192
BSU30230 bioA adenosylmethionine--8-amino-7-oxononanoate transaminase (RefSeq) 146, 192
BSU30240 bioW 6-carboxyhexanoate--CoA ligase (RefSeq) 146, 192
BSU34860 hisI bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein (RefSeq) 6, 72
BSU34870 hisF imidazole glycerol phosphate synthase subunit HisF (RefSeq) 6, 72
BSU34880 hisA 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase (RefSeq) 6, 72
BSU34890 hisH imidazole glycerol phosphate synthase subunit HisH (RefSeq) 6, 72
BSU34900 hisB imidazoleglycerol-phosphate dehydratase (RefSeq) 6, 72
BSU34910 hisD histidinol dehydrogenase (RefSeq) 6, 72
BSU34920 hisG ATP phosphoribosyltransferase catalytic subunit (RefSeq) 6, 72
BSU34930 hisZ ATP phosphoribosyltransferase regulatory subunit (RefSeq) 6, 72
VIMSS37714 VIMSS37714 None 6, 120
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 BSU11650
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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