Organism : Halobacterium salinarum NRC-1 | Module List :
VNG0536G sirR

transcription repressor

CircVis
Functional Annotations (4)
Function System
Mn-dependent transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
iron ion binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VNG0536G
(Mouseover regulator name to see its description)

VNG0536G is regulated by 13 influences and regulates 12 modules.
Regulators for VNG0536G sirR (13)
Regulator Module Operator
VNG1405C 174 tf
VNG1899G 174 tf
VNG2441G 174 tf
VNG2441G
VNG2094G
174 combiner
VNG0530G
VNG0654C
163 combiner
VNG1377G
VNG1816G
163 combiner
VNG1405C 163 tf
VNG1899G
VNG2094G
163 combiner
VNG1899G
VNG2476C
163 combiner
VNG2441G
VNG2094G
163 combiner
VNG2476C 163 tf
VNG5028G
VNG1899G
163 combiner
VNG5182G
VNG2094G
163 combiner

Warning: VNG0536G 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
1287 9.20e-04 AtataaatTtcgac
Loader icon
1288 5.60e-01 tAtTAtAAa
Loader icon
1307 7.10e-04 attagata.a.cTaAattTctaTt
Loader icon
1308 7.90e+01 GGgT.GAAttAtacA
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 VNG0536G

VNG0536G is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Mn-dependent transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
iron ion binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for VNG0536G

VNG0536G has total of 45 gene neighbors in modules 163, 174
Gene neighbors (45)
Gene Common Name Description Module membership
VNG0451G phoU hypothetical protein VNG0451G 6, 76, 124, 163, 174, 205, 226
VNG0452G pstB2 phosphate ABC transporter ATP-binding protein 6, 76, 124, 163, 174, 205, 226
VNG0453G pstA2 phosphate ABC transporter permease 6, 76, 124, 163, 174, 205, 226
VNG0455G pstC2 phosphate ABC transporter permease 6, 76, 124, 163, 174, 205, 226
VNG0457G phoX phosphate ABC transporter periplasmic phosphate-binding protein 6, 76, 124, 163, 174, 205, 226
VNG0458G prp1 phosphate regulatory protein-like protein 6, 76, 124, 163, 174, 205, 226
VNG0535C hypothetical protein VNG0535C 76, 163, 174, 226
VNG0536G sirR transcription repressor 163, 174
VNG1295H hypothetical protein VNG1295H 6, 77, 163, 205, 226
VNG1543G zim CTAG modification methylase 114, 124, 174, 184
VNG1557G cbiH cobalamin biosynthesis protein 45, 61, 67, 114, 124, 174, 227
VNG1558H hypothetical protein VNG1558H 45, 61, 67, 114, 124, 174, 227
VNG1559H hypothetical protein VNG1559H 45, 114, 124, 174, 227
VNG1562H hypothetical protein VNG1562H 45, 114, 124, 174, 205, 227
VNG1564H hypothetical protein VNG1564H 114, 124, 174, 205, 226, 227
VNG1632G cbiQ hypothetical protein VNG1632G 76, 114, 163, 174, 205, 226, 227
VNG1635G cbiM cobalt transport protein CbiM 76, 163, 205, 226, 227
VNG1644G nrdB2 ribonucleoside reductase large chain 174
VNG2093G glnA hypothetical protein VNG2093G 75, 76, 163, 174
VNG2218G pdhB hypothetical protein VNG2218G 45, 61, 124, 174
VNG2219G dsa branched-chain alpha-keto acid dehydrogenase subunit E2 45, 61, 124, 174
VNG2220G lpdA LpdA 45, 61, 124, 174, 184
VNG2302G yuxL acylaminoacyl-peptidase 76, 174, 184
VNG2343G ykfD oligopeptide ABC transporter ATP-binding protein 174
VNG2344G oppD2 oligopeptide ABC transporter 163
VNG2477H hypothetical protein VNG2477H 6, 77, 163, 205, 226
VNG2480Hm hypothetical protein VNG2480Hm 6, 163, 205
VNG2482G pstB1 phosphate ABC transporter ATP-binding protein 6, 76, 77, 163, 174, 205, 226
VNG2483G pstA1 phosphate ABC transporter permease 6, 76, 77, 163, 174, 205
VNG2484G pstC1 phosphate transporter permease 6, 76, 77, 163, 205
VNG2486G yqgG phosphate ABC transporter binding protein 6, 76, 77, 163
VNG2529G dppB2 hypothetical protein VNG2529G 6, 76, 77, 163, 205, 226
VNG2531G dppC1 dipeptide ABC transporter permease 6, 76, 77, 163, 174, 205, 226
VNG2546G pepB3 aminopeptidase-like protein 174
VNG2615C ATPase 174
VNG2616G cxp putative carboxypeptidase 77, 163, 174
VNG6262G zurM ABC transporter permease 6, 76, 163, 174, 205, 226, 249
VNG6264G zurA ABC transporter ATP-binding protein 6, 76, 163, 205, 226, 249
VNG6265G ycdH adhesion protein 6, 76, 163, 174, 205, 226, 249
VNG6277G ugpB glycerol-3-phosphate-binding protein 6, 76, 163, 205
VNG6279G ugpA sn-glycerol-3-phosphate transport system permease 6, 76, 163, 205, 226
VNG6280G ugpE sn-glycerol-3-phosphate transport system permease 6, 76, 163, 205, 226
VNG6281G ugpC sn-glycerol-3-phosphate transport system ATP-binding protein 6, 76, 163, 205
VNG6301G aph alkaline phosphatase 6, 77, 163, 205, 226
VNG6311G pyrI aspartate carbamoyltransferase regulatory subunit 174
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 VNG0536G
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