Organism : Halobacterium salinarum NRC-1 | Module List :
VNG0641C
NADH dehydrogenase subunit J
Functional Annotations (4)
Function | System |
---|---|
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 |
Regulation information for VNG0641C
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
VNG2661G VNG0424C |
45 | combiner |
VNG2661G VNG1029C |
45 | combiner |
VNG6143H | 45 | tf |
VNG6389G | 45 | tf |
VNG0258H | 199 | tf |
VNG0258H | 19 | tf |
VNG0458G VNG0258H |
19 | combiner |
VNG0703H | 19 | tf |
VNG1029C | 19 | tf |
VNG1617H | 19 | tf |
VNG2661G VNG1029C |
19 | combiner |
VNG0101G VNG2163H |
24 | combiner |
VNG0194H | 24 | tf |
VNG2661G VNG1029C |
24 | combiner |
VNG0194H | 29 | tf |
VNG0258H | 29 | tf |
VNG2661G VNG1029C |
29 | combiner |
Motif information (de novo identified motifs for modules)
There are 10 motifs predicted.
Motif Id | e-value | Consensus | Motif Logo |
---|---|---|---|
1017 | 1.70e+01 | AATtaacct.TatcA | |
1018 | 1.60e+03 | acgtgGTTT.A | |
1025 | 3.90e-02 | tttaaaacgtTtgc | |
1026 | 8.10e+02 | cACgaAgA.cc | |
1035 | 1.80e+00 | Cag.AaTtaacgTttataa | |
1036 | 3.80e+02 | tTTAtaacCgt | |
1067 | 6.20e+01 | AcaACGT | |
1068 | 6.80e+03 | AATCAAaaTTGTtT | |
1351 | 1.20e+02 | aCgaataaaCa | |
1352 | 8.70e+02 | AACAaTTAA |
Functional Enrichment for VNG0641C
Function | System |
---|---|
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 VNG0641C
Gene | Common Name | Description | Module membership |
---|---|---|---|
VNG0043H | hypothetical protein VNG0043H | 45, 114 | |
VNG0208H | hypothetical protein VNG0208H | 2, 3, 7, 12, 16, 24, 29, 49, 67, 71, 78, 79, 113, 123 | |
VNG0209H | hypothetical protein VNG0209H | 2, 3, 7, 12, 16, 24, 29, 49, 67, 71, 78, 79, 113, 123 | |
VNG0584H | hypothetical protein VNG0584H | 2, 16, 24 | |
VNG0585H | hypothetical protein VNG0585H | 2, 16, 24 | |
VNG0635G | nolB | NADH dehydrogenase/oxidoreductase-like protein | 2, 16, 19, 24, 29, 199 |
VNG0636G | ndhG1 | NADH dehydrogenase/oxidoreductase | 19, 24, 29 |
VNG0637G | ndhG5 | NADH dehydrogenase/oxidoreductase | 2, 16, 19, 24, 29 |
VNG0639G | ndhG4 | NADH dehydrogenase/oxidoreductase | 19, 24, 29, 199 |
VNG0640G | nolD | NADH dehydrogenase/oxidoreductase-like protein | 2, 3, 16, 19, 24, 29, 45, 123 |
VNG0641C | NADH dehydrogenase subunit J | 19, 24, 29, 45, 199 | |
VNG0642C | hypothetical protein VNG0642C | 2, 24, 29, 45 | |
VNG0643G | nolC | NADH dehydrogenase/oxidoreductase-like protein | 19, 29, 199 |
VNG0646G | nuoL | F420H2:quinone oxidoreductase subunit L | 29, 45 |
VNG0715G | thiC | thiamine biosynthesis protein ThiC | 19 |
VNG0940Gm | ACS3 | Acetyl-CoA synthetase | 7, 19, 24, 25, 29, 49 |
VNG0964C | hypothetical protein VNG0964C | 12, 24, 49, 100, 109 | |
VNG1048G | udg1 | UDP-glucose dehydrogenase | 45 |
VNG1088C | hypothetical protein VNG1088C | 199, 283 | |
VNG1089G | purA | adenylosuccinate synthetase | 199 |
VNG1090H | hypothetical protein VNG1090H | 199 | |
VNG1125G | korB | KorB | 7, 12, 24, 29 |
VNG1128G | korA | KorA | 3, 7, 12, 24, 29, 49, 71, 78, 113 |
VNG1292H | hypothetical protein VNG1292H | 24, 33 | |
VNG1310G | sdhC | hypothetical protein VNG1310G | 2, 24, 236 |
VNG1542G | sucD | hypothetical protein VNG1542G | 33, 45, 67, 114, 124 |
VNG1550G | cbiT | cobalamin biosynthesis protein | 45, 67, 114, 227 |
VNG1551G | cbiL | cobalt-precorrin-2 C(20)-methyltransferase | 45, 67, 114, 124, 227 |
VNG1553G | cbiF | cobalamin biosynthesis protein | 45, 114, 227 |
VNG1554G | cbiG | cobalamin biosynthesis protein CbiG | 45, 61, 67, 114, 124, 227 |
VNG1557G | cbiH | cobalamin biosynthesis protein | 45, 61, 67, 114, 124, 174, 227 |
VNG1558H | hypothetical protein VNG1558H | 45, 61, 67, 114, 124, 174, 227 | |
VNG1559H | hypothetical protein VNG1559H | 45, 114, 124, 174, 227 | |
VNG1562H | hypothetical protein VNG1562H | 45, 114, 124, 174, 205, 227 | |
VNG1768G | eif5a | translation initiation factor IF-5A | 23, 24, 40, 59 |
VNG1793C | pyridoxal biosynthesis lyase PdxS | 19, 90 | |
VNG2099C | hypothetical protein VNG2099C | 33, 45 | |
VNG2122G | ilvE2 | branched-chain amino acid aminotransferase | 7, 19, 29, 49, 71, 75, 78 |
VNG2138G | atpB | V-type ATP synthase subunit B | 45, 67, 114, 124, 227 |
VNG2139G | atpA | V-type ATP synthase subunit A | 23, 24, 33, 39, 45, 67, 114, 124, 227 |
VNG2140G | atpF | V-type ATP synthase subunit F | 33, 39, 45, 67, 114, 124, 227 |
VNG2141G | atpC | V-type ATP synthase subunit C | 23, 39, 45, 67, 114, 124, 227 |
VNG2142G | atpE | V-type ATP synthase subunit E | 19, 24, 45, 67, 114, 227 |
VNG2143G | atpK | H+-transporting ATP synthase subunit K | 2, 19, 23, 24, 45, 67, 75, 114, 124, 227 |
VNG2144G | atpI | H+-transporting ATP synthase subunit I | 19, 23, 24, 45, 67, 75, 124, 227 |
VNG2146H | hypothetical protein VNG2146H | 2, 16, 19, 24, 45, 67, 124, 227 | |
VNG2150G | etfB | electron transfer flavoprotein subunit beta | 45, 124 |
VNG2151G | etfA | electron transfer flavoprotein subunit alpha | 33, 45, 61, 124 |
VNG2217G | pdhA2 | pyruvate dehydrogenase alpha subunit | 45, 61, 124 |
VNG2218G | pdhB | hypothetical protein VNG2218G | 45, 61, 124, 174 |
VNG2219G | dsa | branched-chain alpha-keto acid dehydrogenase subunit E2 | 45, 61, 124, 174 |
VNG2220G | lpdA | LpdA | 45, 61, 124, 174, 184 |
VNG2226G | cctA | thermosome subunit alpha | 3, 7, 12, 29, 49, 50, 52, 78, 113 |
VNG2243G | tbpE | transcription factor | 19, 24, 29, 128 |
VNG2244H | hypothetical protein VNG2244H | 24, 29 | |
VNG2251G | achY | S-adenosyl-L-homocysteine hydrolase | 24, 29, 49, 71, 79, 113 |
VNG2337C | hypothetical protein VNG2337C | 16, 29, 49, 113 | |
VNG2499G | gcdH | glutaryl-CoA dehydrogenase | 7, 24, 25, 50, 61, 78 |
VNG2539H | hypothetical protein VNG2539H | 7, 29, 78 | |
VNG2574G | can | aconitate hydratase | 23, 29 |
VNG2648G | rps10p | 30S ribosomal protein S10P | 2, 3, 16, 23, 24, 29, 40, 110 |
VNG2649G | eef1a | elongation factor 1-alpha | 2, 3, 16, 24, 29, 40, 79, 110 |
VNG2658G | rps12P | 30S ribosomal protein S12P | 23, 39, 40, 45, 98, 110, 137 |
VNG2662G | rpoC | DNA-directed RNA polymerase subunit A'' | 45, 98 |
VNG6294G | perA | peroxidase / catalase | 23, 24, 29, 52 |
VNG6312G | argS | arginine-tRNA synthetase | 24, 29 |
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.
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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".
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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.
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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.
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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)
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