Organism : Halobacterium salinarum NRC-1 | Module List :
VNG2527G dppD

hypothetical protein VNG2527G

CircVis
Functional Annotations (5)
Function System
ABC-type dipeptide transport system, periplasmic component cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
ABC transporters kegg/ kegg pathway
TAT_signal_seq tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VNG2527G
(Mouseover regulator name to see its description)

VNG2527G is regulated by 7 influences and regulates 0 modules.
Regulators for VNG2527G dppD (7)
Regulator Module Operator
VNG0458G
VNG1922G
77 combiner
VNG0458G
VNG2476C
77 combiner
VNG1483C 77 tf
VNG1899G
VNG0536G
77 combiner
VNG1899G
VNG2094G
77 combiner
VNG2441G
VNG0751C
77 combiner
VNG5028G
VNG1899G
77 combiner

Warning: VNG2527G Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 2 motifs predicted.

Motif Table (2)
Motif Id e-value Consensus Motif Logo
1129 3.60e-01 TG.gA.cAaacCCcaTaaTaaTaT
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1130 7.40e+02 AcAccccacAc
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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 VNG2527G

VNG2527G is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
ABC-type dipeptide transport system, periplasmic component cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
ABC transporters kegg/ kegg pathway
TAT_signal_seq tigr/ tigrfam
Module neighborhood information for VNG2527G

VNG2527G has total of 33 gene neighbors in modules 77
Gene neighbors (33)
Gene Common Name Description Module membership
VNG0745G spoVR hypothetical protein VNG0745G 77
VNG0746C hypothetical protein VNG0746C 77
VNG0748G prkA hypothetical protein VNG0748G 77
VNG0749G prk serine protein kinase 77
VNG0750C hypothetical protein VNG0750C 77, 284
VNG1018G adh3 alcohol dehydrogenase 77
VNG1021C GTP cyclohydrolase III 77
VNG1023C hypothetical protein VNG1023C 77
VNG1024C hypothetical protein VNG1024C 77
VNG1025H hypothetical protein VNG1025H 77
VNG1295H hypothetical protein VNG1295H 6, 77, 163, 205, 226
VNG1760G htr5 Htr5 77
VNG1821G adh4 alcohol dehydrogenase 77
VNG1925H hypothetical protein VNG1925H 77
VNG2358G appA oligopeptide binding protein 6, 76, 77
VNG2359G appB oligopeptide ABC permease 6, 76, 77
VNG2361G appC oligopeptide transport permease 6, 76, 77
VNG2363Gm oppD1 oligopeptide ABC transporter ATP-binding protein 6, 77, 226
VNG2365G appF oligopeptide ABC transporter ATP-binding protein 6, 76, 77
VNG2430G thrC1 threonine synthase 61, 77
VNG2436G argH argininosuccinate lyase 77
VNG2437G argG argininosuccinate synthase 77
VNG2477H hypothetical protein VNG2477H 6, 77, 163, 205, 226
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
VNG2527G dppD hypothetical protein VNG2527G 77
VNG2529G dppB2 hypothetical protein VNG2529G 6, 76, 77, 163, 205, 226
VNG2531G dppC1 dipeptide ABC transporter permease 6, 76, 77, 163, 174, 205, 226
VNG2532H hypothetical protein VNG2532H 6, 76, 77
VNG2616G cxp putative carboxypeptidase 77, 163, 174
VNG6301G aph alkaline phosphatase 6, 77, 163, 205, 226
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 VNG2527G
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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