Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1974

pyridine nucleotide-disulfide oxidoreductase

CircVis
Functional Annotations (4)
Function System
NADH dehydrogenase, FAD-containing subunit cog/ cog
NADH dehydrogenase activity go/ molecular_function
flavin adenine dinucleotide binding go/ molecular_function
Nterm_to_SelD tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1974
(Mouseover regulator name to see its description)

DVU1974 is regulated by 20 influences and regulates 0 modules.
Regulators for DVU1974 (20)
Regulator Module Operator
DVU0030
DVU3080
283 combiner
DVU0629 283 tf
DVU1561 283 tf
DVU1561
DVU1584
283 combiner
DVU1561
DVU1964
283 combiner
DVU1759 283 tf
DVU2106 283 tf
DVU2686 283 tf
DVU3167 283 tf
DVU3313
DVU2106
283 combiner
DVU0309
DVU1949
274 combiner
DVU0309
DVU2275
274 combiner
DVU1402 274 tf
DVU1572
DVU2547
274 combiner
DVU2547
DVU1340
274 combiner
DVU2547
DVU2394
274 combiner
DVU2557
DVU2547
274 combiner
DVU2557
DVU2675
274 combiner
DVU2675 274 tf
DVU3066 274 tf

Warning: DVU1974 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
523 1.70e+02 ATg.atcgaTgtaatGgatt
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RegPredict
524 8.90e+03 gTaCaTggcGcAaGcctcTGaacA
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RegPredict
541 0.00e+00 CAcgACCtCtTCcttTtGcAGaGa
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RegPredict
542 2.00e-06 CTtcAtcAgCCaCCAacaAGG
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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 DVU1974

DVU1974 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
NADH dehydrogenase, FAD-containing subunit cog/ cog
NADH dehydrogenase activity go/ molecular_function
flavin adenine dinucleotide binding go/ molecular_function
Nterm_to_SelD tigr/ tigrfam
Module neighborhood information for DVU1974

DVU1974 has total of 54 gene neighbors in modules 274, 283
Gene neighbors (54)
Gene Common Name Description Module membership
DVU0023 hypothetical protein DVU0023 215, 283
DVU0111 response regulator 143, 274
DVU0239 hypothetical protein DVU0239 153, 274
DVU0453 ATP-dependent DNA helicase UvrD 71, 274
DVU0564 ISDvu4, transposase, truncation 279, 283
DVU0577 formate dehydrogenase formation protein FdhE 274, 281
DVU0579 molybdopterin-guanine dinucleotide biosynthesis protein A 274, 281
DVU0587 fdnG-1 formate dehydrogenase subunit alpha, selenocysteine-containing 167, 274
DVU0604 hypothetical protein DVU0604 170, 283
DVU0717 GGDEF domain/EAL domain-containing protein 31, 283
DVU0819 FMN reductase, NADPH-dependent 153, 274
DVU0879 hypothetical protein DVU0879 56, 283
DVU0923 L-PSP family endoribonuclease 283, 339
DVU1111 hypothetical protein DVU1111 160, 283
DVU1144 Cro/CI family transcriptional regulator 143, 283
DVU1145 hypothetical protein DVU1145 279, 283
DVU1184 None 126, 283
DVU1396 hypothetical protein DVU1396 192, 274
DVU1397 bfr bacterioferritin 60, 274
DVU1400 methyl-accepting chemotaxis protein 283, 326
DVU1412 glycerate dehydrogenase 236, 274
DVU1511 hypothetical protein DVU1511 165, 283
DVU1512 hypothetical protein DVU1512 239, 283
DVU1564 hypothetical protein DVU1564 263, 274
DVU1592 arginine N-succinyltransferase subunit beta 192, 274
DVU1593 cheY-1 chemotaxis protein CheY 123, 274
DVU1594 cheA-1 chemotaxis protein CheA 192, 274
DVU1595 cheR-1 chemotaxis protein methyltransferase 274, 277
DVU1596 cheB-1 protein-glutamate methylesterase CheB 192, 274
DVU1597 sulfite reductase, assimilatory-type 123, 274
DVU1758 lipoprotein 143, 283
DVU1915 hypothetical protein DVU1915 245, 283
DVU1973 rhodanese-like domain-containing protein 269, 274
DVU1974 pyridine nucleotide-disulfide oxidoreductase 274, 283
DVU1992 antibiotic acetyltransferase 224, 283
DVU2004 ISDvu4, transposase 279, 283
DVU2107 hypothetical protein DVU2107 11, 283
DVU2128 hypothetical protein DVU2128 187, 283
DVU2176 hypothetical protein DVU2176 283, 313
DVU2184 DNA-binding protein 239, 283
DVU2221 hypothetical protein DVU2221 224, 283
DVU2246 S1 RNA-binding domain-containing protein 17, 283
DVU2354 glycosyl transferase group 2 family protein 283, 332
DVU2421 4-oxalocrotonate tautomerase family protein 192, 274
DVU2422 nitroreductase family protein 192, 274
DVU2972 chemotaxis protein CheD 37, 274
DVU3041 cytochrome c553 178, 274
DVU3042 lipoprotein 60, 274
DVU3076 hypothetical protein DVU3076 269, 274
DVU3079 glyoxalase family protein 110, 274
DVU3135 flavodoxin-like fold domain-containing protein 110, 274
DVU3136 nitroreductase family protein 110, 274
DVUA0023 ABC transporter permease 192, 274
DVUA0091 katA catalase 192, 274
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 DVU1974
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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