Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVUA0012 nifD

nitrogenase molybdenum-iron protein subunit alpha

CircVis
Functional Annotations (16)
Function System
Nitrogenase molybdenum-iron protein, alpha and beta chains cog/ cog
electron transport go/ biological_process
nitrogen fixation go/ biological_process
nitrogenase activity go/ molecular_function
iron-iron nitrogenase complex go/ cellular_component
molybdenum-iron nitrogenase complex go/ cellular_component
vanadium-iron nitrogenase complex go/ cellular_component
iron-iron nitrogenase activity go/ molecular_function
molybdenum-iron nitrogenase activity go/ molecular_function
vanadium-iron nitrogenase activity go/ molecular_function
iron-sulfur cluster binding go/ molecular_function
Chloroalkane and chloroalkene degradation kegg/ kegg pathway
Nitrogen metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
nifD tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVUA0012
(Mouseover regulator name to see its description)

DVUA0012 is regulated by 16 influences and regulates 0 modules.
Regulators for DVUA0012 nifD (16)
Regulator Module Operator
DVU0619
DVU2832
197 combiner
DVU0744
DVU0230
197 combiner
DVU1572 197 tf
DVU1572
DVU3255
197 combiner
DVU1754
DVU0619
197 combiner
DVU1754
DVU0804
197 combiner
DVU2690 197 tf
DVU2832 197 tf
DVU3305
DVU2832
197 combiner
DVU0269
DVU2251
335 combiner
DVU0525 335 tf
DVU0813
DVU0230
335 combiner
DVU0936
DVU0269
335 combiner
DVU0936
DVU2275
335 combiner
DVU3167 335 tf
DVUA0057 335 tf

Warning: DVUA0012 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
377 1.10e+04 ACTTGAaaaTaTATTA
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RegPredict
378 1.30e+04 tgaaAcgAgGAGAa
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RegPredict
635 4.80e+03 T.c.gCA.CttCGgC
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RegPredict
636 9.40e+03 CaACTACA
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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 DVUA0012

DVUA0012 is enriched for 16 functions in 3 categories.
Enrichment Table (16)
Function System
Nitrogenase molybdenum-iron protein, alpha and beta chains cog/ cog
electron transport go/ biological_process
nitrogen fixation go/ biological_process
nitrogenase activity go/ molecular_function
iron-iron nitrogenase complex go/ cellular_component
molybdenum-iron nitrogenase complex go/ cellular_component
vanadium-iron nitrogenase complex go/ cellular_component
iron-iron nitrogenase activity go/ molecular_function
molybdenum-iron nitrogenase activity go/ molecular_function
vanadium-iron nitrogenase activity go/ molecular_function
iron-sulfur cluster binding go/ molecular_function
Chloroalkane and chloroalkene degradation kegg/ kegg pathway
Nitrogen metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
nifD tigr/ tigrfam
Module neighborhood information for DVUA0012

DVUA0012 has total of 29 gene neighbors in modules 197, 335
Gene neighbors (29)
Gene Common Name Description Module membership
DVU0621 sigma-54 dependent DNA-binding response regulator 15, 197
DVU1724 phage protein 197, 340
DVU2692 hypothetical protein DVU2692 182, 197
DVU2706 hypothetical protein DVU2706 197, 253
DVU2846 hypothetical protein DVU2846 90, 335
DVU2881 P4 family phage/plasmid primase 2, 197
DVU3142 sigma-54 dependent transcriptional regulator 197, 203
DVUA0010 ferredoxin, 2fe-2s 276, 335
DVUA0012 nifD nitrogenase molybdenum-iron protein subunit alpha 197, 335
DVUA0015 nifH nitrogenase reductase 328, 335
DVUA0024 sigma-54 factor interaction domain-containing protein 61, 335
DVUA0031 hypothetical protein DVUA0031 115, 197
DVUA0032 hypothetical protein DVUA0032 136, 197
DVUA0034 hypothetical protein DVUA0034 197, 340
DVUA0035 hypothetical protein DVUA0035 61, 197
DVUA0037 sugar transferase domain-containing protein 257, 335
DVUA0038 capsular polysaccharide transport protein 197, 340
DVUA0041 hypothetical protein DVUA0041 257, 335
DVUA0042 putative lipoprotein 197, 328
DVUA0043 polysaccharide deacetylase family protein 234, 335
DVUA0051 glycosyl transferase, group 1 family protein 328, 335
DVUA0054 glycosyl transferase, group 1 family protein 197, 340
DVUA0064 hypothetical protein DVUA0064 61, 335
DVUA0090 hypothetical protein DVUA0090 257, 335
DVUA0093 chromate transport family protein 97, 197
DVUA0102 escT type III secretion inner membrane protein 131, 197
DVUA0128 hypothetical protein DVUA0128 131, 197
DVUA0136 zupT zinc transporter ZupT 138, 197
DVUA0152 hypothetical protein DVUA0152 335, 340
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 DVUA0012
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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