Organism : Geobacter sulfurreducens | Module List :
GSU3433 nuoJ

NADH dehydrogenase I, J subunit (NCBI)

CircVis
Functional Annotations (5)
Function System
NADH:ubiquinone oxidoreductase subunit 6 (chain J) 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 GSU3433
(Mouseover regulator name to see its description)

GSU3433 is regulated by 21 influences and regulates 0 modules.
Regulators for GSU3433 nuoJ (21)
Regulator Module Operator
GSU0280 256 tf
GSU0625 256 tf
GSU1013 256 tf
GSU1277 256 tf
GSU1293 256 tf
GSU1569 256 tf
GSU2506 256 tf
GSU2520 256 tf
GSU2523 256 tf
GSU2524 256 tf
GSU2753 256 tf
GSU2941 256 tf
GSU3109 256 tf
GSU3206 256 tf
GSU3457 256 tf
GSU0551 145 tf
GSU0735 145 tf
GSU0770 145 tf
GSU1495 145 tf
GSU2041 145 tf
GSU2185 145 tf

Warning: GSU3433 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
2450 5.00e+00 ttaCaccgt..taAccaagggga
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2451 4.70e+03 CctCcgctGt.cTcCCgcc.c.Tt
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2672 1.20e+01 TTcTGCtATagTT
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2673 1.30e+03 Gc.acctcCcGGgattG..T
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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 GSU3433

GSU3433 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
NADH:ubiquinone oxidoreductase subunit 6 (chain J) 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 GSU3433

GSU3433 has total of 41 gene neighbors in modules 145, 256
Gene neighbors (41)
Gene Common Name Description Module membership
GSU0152 argF ornithine carbamoyltransferase (NCBI) 119, 256
GSU0228 fkpB peptidyl-prolyl cis-trans isomerase, FKBP-type, putative (NCBI) 145, 324
GSU0255 GSU0255 sensory box histidine kinase (VIMSS) 87, 145
GSU0302 GSU0302 hypothetical protein (VIMSS) 145, 319
GSU0367 GSU0367 radical SAM protein, TIGR01212 family (NCBI) 145, 280
GSU0650 GSU0650 conserved hypothetical protein TIGR00252 (VIMSS) 87, 145
GSU0690 GSU0690 conserved hypothetical protein (VIMSS) 145, 245
GSU0933 upp uracil phosphoribosyltransferase (NCBI) 145, 260
GSU1043 GSU1043 sensory box histidine kinase (VIMSS) 98, 145
GSU1540 GSU1540 lipoprotein, putative (VIMSS) 33, 145
GSU2430 GSU2430 SPFH/Band 7 domain protein (VIMSS) 23, 256
GSU2443 GSU2443 dehydrogenase complex, E1 component, alpha subunit (VIMSS) 167, 256
GSU2445 GSU2445 aconitate hydratase, putative (VIMSS) 167, 256
GSU2469 GSU2469 hypothetical protein (VIMSS) 33, 145
GSU2550 drpA DNA processing protein DprA (NCBI) 87, 145
GSU2606 aroA 3-phosphoshikimate 1-carboxyvinyltransferase (NCBI) 13, 145
GSU2607 tyrA prephenate dehydrogenase (NCBI) 81, 145
GSU2667 GSU2667 sensory box histidine kinase (VIMSS) 145, 244
GSU2702 GSU2702 ABC transporter, ATP-binding protein (VIMSS) 23, 256
GSU2703 moeA molybdopterin biosynthesis protein MoeA (NCBI) 23, 256
GSU2704 moaC molybdenum cofactor biosynthesis protein MoaC (NCBI) 23, 256
GSU2723 GSU2723 molybdopterin binding domain protein (NCBI) 145, 244
GSU2882 GSU2882 cytochrome c family protein (VIMSS) 23, 256
GSU3057 gltA glutamate synthase (NADPH), homotetrameric (NCBI) 100, 145
GSU3058 GSU3058 dihydroorotate dehydrogenase, electron transfer subunit, putative (NCBI) 99, 145
GSU3105 GSU3105 conserved hypothetical protein (VIMSS) 194, 256
GSU3213 obg GTP-binding protein, GTP1/OBG family (NCBI) 119, 256
GSU3254 mpg phosphoglucomutase/phosphomannomutase family protein (NCBI) 100, 256
GSU3330 GSU3330 NADH-dependent flavin oxidoreductase, Oye family (VIMSS) 119, 256
GSU3331 pyk pyruvate kinase (NCBI) 237, 256
GSU3332 GSU3332 cytochrome c family protein, putative (NCBI) 133, 256
GSU3422 GSU3422 conserved hypothetical protein (VIMSS) 145, 333
GSU3430 nuoM-2 NADH dehydrogenase I, M subunit (NCBI) 23, 256
GSU3432 nuoI NADH dehydrogenase I, K subunit (NCBI) 23, 256
GSU3433 nuoJ NADH dehydrogenase I, J subunit (NCBI) 145, 256
GSU3436 nuoH-2 NADH dehydrogenase I, H subunit (NCBI) 23, 256
GSU3441 nuoF NADH dehydrogenase I, F subunit (NCBI) 167, 256
GSU3443 nuoE-2 NADH dehydrogenase I, E subunit (NCBI) 23, 256
GSU3447 bcp AhpC/TSA family protein (NCBI) 119, 256
GSU3449 GSU3449 ferredoxin family protein, putative (VIMSS) 145, 288
GSU3452 GSU3452 hypothetical protein (VIMSS) 145, 233
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 GSU3433
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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