Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVUA0143 nifA-2

Nif-specific regulatory protein

CircVis
Functional Annotations (12)
Function System
Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains cog/ cog
two-component signal transduction system (phosphorelay) go/ biological_process
nucleotide binding go/ molecular_function
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
nitrogen fixation go/ biological_process
transcription activator activity go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
Two-component system kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVUA0143
(Mouseover regulator name to see its description)

DVUA0143 is regulated by 16 influences and regulates 28 modules.
Regulators for DVUA0143 nifA-2 (16)
Regulator Module Operator
DVU0230 43 tf
DVU1517 43 tf
DVU1754 43 tf
DVU2588
DVU1967
43 combiner
DVU2690 43 tf
DVU2832 43 tf
DVU2836
DVU0653
43 combiner
DVU3334
DVU0230
43 combiner
DVUA0057 43 tf
DVUA0057
DVU0529
43 combiner
DVU1517 293 tf
DVU1754 293 tf
DVU2114 293 tf
DVU2690 293 tf
DVU2832 293 tf
DVUA0057 293 tf

Warning: DVUA0143 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
85 4.00e+00 ACgGaCGcGAGtCgcAtccCgcCa
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RegPredict
86 2.40e+01 AaggCCcgGCAtgCG
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RegPredict
561 3.60e+02 agcGGgCg.GGCag
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RegPredict
562 2.40e+03 CCgTg.CgCGca
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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 DVUA0143

DVUA0143 is enriched for 12 functions in 3 categories.
Enrichment Table (12)
Function System
Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains cog/ cog
two-component signal transduction system (phosphorelay) go/ biological_process
nucleotide binding go/ molecular_function
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
nitrogen fixation go/ biological_process
transcription activator activity go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
Two-component system kegg/ kegg pathway
Module neighborhood information for DVUA0143

DVUA0143 has total of 23 gene neighbors in modules 43, 293
Gene neighbors (23)
Gene Common Name Description Module membership
DVU1525 hypothetical protein DVU1525 43, 129
DVU1714 hypothetical protein DVU1714 43, 329
DVU1715 hypothetical protein DVU1715 73, 293
DVU1717 hypothetical protein DVU1717 73, 293
DVU1718 hypothetical protein DVU1718 42, 293
DVU1719 hypothetical protein DVU1719 73, 293
DVU1720 hypothetical protein DVU1720 73, 293
DVU1721 hypothetical protein DVU1721 293, 299
DVU1723 hypothetical protein DVU1723 73, 293
DVU1725 hypothetical protein DVU1725 73, 293
DVU1752 hypothetical protein DVU1752 43, 165
DVU2125 hypothetical protein 43, 59
DVU2163 hypothetical protein DVU2163 42, 43
DVU2164 lipoprotein 42, 43
DVU2166 holin 43, 73
DVU2541 CoA-substrate-specific enzyme activase 43, 329
DVU2542 hypothetical protein DVU2542 42, 43
DVU2597 hypothetical protein DVU2597 73, 293
DVU2789 Gpr1/Fun34/YaaH family protein 73, 293
DVU2820 amidohydrolase family protein 43, 149
DVUA0007 nifB nitrogenase cofactor biosynthesis protein NifB 276, 293
DVUA0008 nitrogenase molybdenum-iron cofactor biosynthesis protein NifN 257, 293
DVUA0143 nifA-2 Nif-specific regulatory protein 43, 293
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 DVUA0143
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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