Organism : Geobacter sulfurreducens | Module List :
GSU3445 nuoA-2

NADH dehydrogenase I, A subunit (NCBI)

CircVis
Functional Annotations (5)
Function System
NADH:ubiquinone oxidoreductase subunit 3 (chain A) cog/ cog
mitochondrial electron transport, NADH to ubiquinone go/ biological_process
NADH dehydrogenase (ubiquinone) activity go/ molecular_function
Oxidative phosphorylation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU3445
(Mouseover regulator name to see its description)

GSU3445 is regulated by 14 influences and regulates 0 modules.
Regulators for GSU3445 nuoA-2 (14)
Regulator Module Operator
GSU0682 299 tf
GSU1410 299 tf
GSU1626 299 tf
GSU2362 299 tf
GSU2753 299 tf
GSU3387 299 tf
GSU0187 119 tf
GSU0625 119 tf
GSU0776 119 tf
GSU1495 119 tf
GSU1569 119 tf
GSU2185 119 tf
GSU2753 119 tf
GSU3109 119 tf

Warning: GSU3445 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
2398 7.50e-03 atcAgCTtTcacgaA.cat.tTa
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2399 1.10e-02 Aagaaaag.GaaAgtATAgcA
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2756 2.90e+03 AaTCaAtGtAtTA
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2757 8.50e+03 AAAATgGtaTG
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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 GSU3445

GSU3445 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
NADH:ubiquinone oxidoreductase subunit 3 (chain A) cog/ cog
mitochondrial electron transport, NADH to ubiquinone go/ biological_process
NADH dehydrogenase (ubiquinone) activity go/ molecular_function
Oxidative phosphorylation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Module neighborhood information for GSU3445

GSU3445 has total of 35 gene neighbors in modules 119, 299
Gene neighbors (35)
Gene Common Name Description Module membership
GSU0080 degQ protease degQ (NCBI) 3, 119
GSU0100 GSU0100 hypothetical protein (VIMSS) 88, 299
GSU0152 argF ornithine carbamoyltransferase (NCBI) 119, 256
GSU0238 GSU0238 radical SAM domain protein (NCBI) 119, 283
GSU0239 GSU0239 conserved hypothetical protein (NCBI) 3, 119
GSU0240 GSU0240 malonyl Coa-acyl carrier protein transacylase, putative (VIMSS) 3, 119
GSU0241 GSU0241 BchE/P-methylase family protein (VIMSS) 119, 311
GSU0242 acpP-1 acyl carrier protein (NCBI) 3, 119
GSU0243 GSU0243 conserved hypothetical protein (VIMSS) 119, 128
GSU0244 GSU0244 radical SAM domain protein (NCBI) 119, 311
GSU0245 GSU0245 glycosyl transferase, group 2 family protein (VIMSS) 119, 294
GSU0246 GSU0246 polysaccharide deacetylase domain protein (VIMSS) 100, 119
GSU0247 GSU0247 radical SAM domain protein (NCBI) 3, 119
GSU0248 GSU0248 BchE/P-methylase family protein (VIMSS) 3, 119
GSU0641 GSU0641 hypothetical protein (VIMSS) 13, 299
GSU0682 GSU0682 DNA-binding response regulator, LuxR family (VIMSS) 275, 299
GSU0789 GSU0789 response regulator (VIMSS) 187, 299
GSU0984 GSU0984 hypothetical protein (VIMSS) 13, 299
GSU1153 GSU1153 outer membrane protein, OMP85 family (NCBI) 275, 299
GSU1301 cheW-5 purine-binding chemotaxis protein CheW (NCBI) 212, 299
GSU1338 GSU1338 heavy-metal-associated domain protein (VIMSS) 13, 299
GSU1361 GSU1361 Piwi domain protein (NCBI) 212, 299
GSU1508 GSU1508 conserved hypothetical protein (VIMSS) 124, 299
GSU1776 GSU1776 pilin domain protein (VIMSS) 245, 299
GSU2457 GSU2457 conserved hypothetical protein (NCBI) 13, 299
GSU2507 GSU2507 sensor histidine kinase (NCBI) 299, 341
GSU2810 GSU2810 hypothetical protein (VIMSS) 13, 299
GSU3204 GSU3204 conserved hypothetical protein (VIMSS) 212, 299
GSU3213 obg GTP-binding protein, GTP1/OBG family (NCBI) 119, 256
GSU3330 GSU3330 NADH-dependent flavin oxidoreductase, Oye family (VIMSS) 119, 256
GSU3333 GSU3333 3-deoxy-7-phosphoheptulonate synthase (RefSeq) 3, 119
GSU3438 GSU3438 conserved hypothetical protein (VIMSS) 187, 299
GSU3439 GSU3439 NADH dehydrogenase I, G subunit (VIMSS) 167, 299
GSU3445 nuoA-2 NADH dehydrogenase I, A subunit (NCBI) 119, 299
GSU3447 bcp AhpC/TSA family protein (NCBI) 119, 256
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 GSU3445
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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