Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1949 nifA-1

nif-specific regulatory protein

CircVis
Functional Annotations (8)
Function System
Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
Two-component system kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1949
(Mouseover regulator name to see its description)

DVU1949 is regulated by 17 influences and regulates 40 modules.
Regulators for DVU1949 nifA-1 (17)
Regulator Module Operator
DVU0277
DVU2394
28 combiner
DVU0629 28 tf
DVU1788
DVU0436
28 combiner
DVU2547
DVU2251
28 combiner
DVU2557 28 tf
DVU2567 28 tf
DVU2567
DVU1788
28 combiner
DVU2909 28 tf
DVU3066 28 tf
DVU1063 270 tf
DVU1754
DVU1561
270 combiner
DVU1788
DVU0804
270 combiner
DVU1949 270 tf
DVU2788
DVU0916
270 combiner
DVU2799 270 tf
DVU2832
DVU1745
270 combiner
DVU2909
DVU1517
270 combiner

Warning: DVU1949 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.
Click on the RegPredict links to explore the motif in RegPredict.

Motif Table (4)
Motif Id e-value Consensus Motif Logo RegPredict
55 8.90e+02 GAaaaaAA
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RegPredict
56 4.70e+03 ACAGTtTt
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RegPredict
515 4.00e+03 gCAAcGcaACC
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RegPredict
516 2.10e+01 AttCgtTgaC.aaaTtCTG.AAG
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RegPredict
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 DVU1949

DVU1949 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
Two-component system kegg/ kegg pathway
Module neighborhood information for DVU1949

DVU1949 has total of 51 gene neighbors in modules 28, 270
Gene neighbors (51)
Gene Common Name Description Module membership
DVU0422 sensory box protein 208, 270
DVU0527 maF Maf-like protein 13, 270
DVU0668 methyl-accepting chemotaxis protein 193, 270
DVU0703 lepA GTP-binding protein LepA 28, 65
DVU0757 hypothetical protein DVU0757 28, 211
DVU0786 penicillin-binding protein 28, 270
DVU0807 trmU tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase 15, 28
DVU0808 gatA aspartyl/glutamyl-tRNA amidotransferase subunit A 28, 278
DVU0840 ffh signal recognition particle protein 28, 188
DVU0867 aromatic amino acid decarboxylase 28, 306
DVU0868 cdsA phosphatidate cytidylyltransferase 28, 65
DVU0869 uppS undecaprenyl diphosphate synthase 28, 278
DVU0871 pyrH uridylate kinase 28, 65
DVU0906 lipB lipoate-protein ligase B 28, 32
DVU1044 guaB inosine-5`-monophosphate dehydrogenase 28, 270
DVU1208 plsX glycerol-3-phosphate acyltransferase PlsX 28, 124
DVU1210 hypothetical protein DVU1210 28, 169
DVU1240 hypothetical protein DVU1240 28, 270
DVU1247 hypothetical protein DVU1247 28, 235
DVU1251 hypothetical protein DVU1251 65, 270
DVU1258 glnN glutamine synthetase, type III 254, 270
DVU1273 type II/III secretion system protein 65, 270
DVU1429 ychF GTP-dependent nucleic acid-binding protein EngD 254, 270
DVU1538 hypothetical protein DVU1538 28, 278
DVU1621 hypothetical protein DVU1621 28, 65
DVU1694 C4-type zinc finger DksA/TraR family protein 84, 270
DVU1703 type I restriction-modification enzyme, R subunit 118, 270
DVU1788 rpoD RNA polymerase sigma-70 factor 28, 227
DVU1789 dnaG DNA primase 28, 227
DVU1790 MutS2 family protein 1, 28
DVU1791 GatB/Yqey family protein 28, 94
DVU1878 ltaE threonine aldolase 65, 270
DVU1879 glycosyl transferase group 1 family protein 65, 270
DVU1890 hemC porphobilinogen deaminase 28, 270
DVU1897 glyS glycyl-tRNA synthetase subunit beta 28, 270
DVU1898 glyQ glycyl-tRNA synthetase subunit alpha 28, 270
DVU1949 nifA-1 nif-specific regulatory protein 28, 270
DVU1951 indolepyruvate ferredoxin oxidoreductase subunit alpha 28, 270
DVU1952 hypothetical protein DVU1952 28, 113
DVU2043 hypothetical protein DVU2043 270, 273
DVU2317 methyl-accepting chemotaxis protein 270, 311
DVU2343 amino acid ABC transporter ATP-binding protein 3, 28
DVU2567 hypothetical protein DVU2567 3, 270
DVU2579 hypothetical protein 208, 270
DVU2678 RNA pseudouridine synthase family protein 84, 270
DVU3052 ABC transporter ATP-binding protein 221, 270
DVU3066 DNA-binding protein 65, 270
DVU3243 dnaJ chaperone protein DnaJ 28, 227
DVU3258 murA UDP-N-acetylglucosamine 1-carboxyvinyltransferase 82, 270
DVU3279 cobT nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase 254, 270
DVU3365 fmt methionyl-tRNA formyltransferase 28, 227
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 DVU1949
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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