Organism : Halobacterium salinarum NRC-1 | Module List :
VNG2122G ilvE2
branched-chain amino acid aminotransferase
Functional Annotations (9)
Function | System |
---|---|
Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase | cog/ cog |
branched-chain-amino-acid transaminase activity | go/ molecular_function |
branched chain family amino acid metabolic process | go/ biological_process |
Valine leucine and isoleucine degradation | kegg/ kegg pathway |
Valine leucine and isoleucine biosynthesis | kegg/ kegg pathway |
Pantothenate and CoA biosynthesis | kegg/ kegg pathway |
Metabolic pathways | kegg/ kegg pathway |
Biosynthesis of secondary metabolites | kegg/ kegg pathway |
ilvE_I | tigr/ tigrfam |
Regulation information for VNG2122G
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
VNG0258H | 19 | tf |
VNG0458G VNG0258H |
19 | combiner |
VNG0703H | 19 | tf |
VNG1029C | 19 | tf |
VNG1617H | 19 | tf |
VNG2661G VNG1029C |
19 | combiner |
VNG0194H | 29 | tf |
VNG0258H | 29 | tf |
VNG2661G VNG1029C |
29 | combiner |
VNG0458G VNG1029C |
75 | combiner |
VNG0536G VNG0258H |
75 | combiner |
VNG1836G VNG0458G |
75 | combiner |
VNG0194H | 78 | tf |
VNG0258H | 78 | tf |
VNG0536G VNG0258H |
78 | combiner |
VNG1836G | 78 | tf |
VNG1836G VNG1899G |
78 | combiner |
VNG1836G VNG2441G |
78 | combiner |
VNG0194H | 49 | tf |
VNG0254G | 49 | tf |
VNG0293H VNG0703H |
49 | combiner |
VNG0734G VNG2641H |
49 | combiner |
VNG1029C | 49 | tf |
VNG1123G | 49 | tf |
VNG1464G VNG1029C |
49 | combiner |
VNG1496G VNG0320H |
49 | combiner |
VNG2163H | 49 | tf |
VNG2243G | 49 | tf |
VNG0254G | 7 | tf |
VNG0536G VNG0258H |
7 | combiner |
VNG1836G VNG1899G |
7 | combiner |
VNG1899G VNG0258H |
7 | combiner |
VNG5028G VNG0258H |
7 | combiner |
VNG0258H | 71 | tf |
VNG0703H VNG2641H |
71 | combiner |
VNG1029C | 71 | tf |
VNG1123G VNG0194H |
71 | combiner |
VNG1464G VNG1029C |
71 | combiner |
VNG2163H | 71 | tf |
Motif information (de novo identified motifs for modules)
There are 14 motifs predicted.
Motif Id | e-value | Consensus | Motif Logo |
---|---|---|---|
993 | 1.30e+01 | ttggtGataaTcgat | |
994 | 7.70e+02 | GAtAat..tCaactGTt.gtaA | |
1017 | 1.70e+01 | AATtaacct.TatcA | |
1018 | 1.60e+03 | acgtgGTTT.A | |
1035 | 1.80e+00 | Cag.AaTtaacgTttataa | |
1036 | 3.80e+02 | tTTAtaacCgt | |
1075 | 7.90e-01 | aGAaAAttgtTga | |
1076 | 7.90e+00 | gaAtcgaacggaAagcaTtaAgT | |
1117 | 1.20e-04 | AtaT.TgtttT.TGttagcaaat | |
1118 | 3.40e+03 | tTtTcgGg | |
1125 | 7.80e+00 | agct.Taatg.t.GtT.a | |
1126 | 3.60e+02 | ATAAtTcA | |
1131 | 2.00e-04 | aTTtTc.Gtga | |
1132 | 3.90e+00 | TtcgAgtacATcA |
Functional Enrichment for VNG2122G
Function | System |
---|---|
Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase | cog/ cog |
branched-chain-amino-acid transaminase activity | go/ molecular_function |
branched chain family amino acid metabolic process | go/ biological_process |
Valine leucine and isoleucine degradation | kegg/ kegg pathway |
Valine leucine and isoleucine biosynthesis | kegg/ kegg pathway |
Pantothenate and CoA biosynthesis | kegg/ kegg pathway |
Metabolic pathways | kegg/ kegg pathway |
Biosynthesis of secondary metabolites | kegg/ kegg pathway |
ilvE_I | tigr/ tigrfam |
Module neighborhood information for VNG2122G
Gene | Common Name | Description | Module membership |
---|---|---|---|
VNG0162G | alkK | AlkK | 3, 12, 49, 113, 123 |
VNG0192G | ftsZ2 | cell division protein FtsZ | 2, 3, 7, 12, 16, 49, 50, 71, 78, 79, 123 |
VNG0194H | hypothetical protein VNG0194H | 3, 7, 12, 16, 50, 79, 123 | |
VNG0207H | hypothetical protein VNG0207H | 2, 3, 7, 12, 16, 49, 67, 71, 78, 79, 113, 123 | |
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 | |
VNG0258H | hypothetical protein VNG0258H | 3, 12, 16, 49, 79, 100, 109, 150 | |
VNG0259G | ipp | inorganic pyrophosphatase | 7, 12, 16, 79, 109 |
VNG0261H | hypothetical protein VNG0261H | 7, 12, 16, 25, 49, 50, 55, 79, 109, 113 | |
VNG0262C | hypothetical protein VNG0262C | 12, 25, 49, 50, 55, 79, 109, 113 | |
VNG0303G | lon | ATP-dependent protease Lon | 78 |
VNG0321G | ids | Ids | 7, 25, 50, 55 |
VNG0524G | yurY | ABC transporter ATP-binding protein | 2, 3, 7, 12, 16, 71, 113, 225 |
VNG0525C | hypothetical protein VNG0525C | 7, 12, 71, 78, 113, 225 | |
VNG0527C | hypothetical protein VNG0527C | 2, 3, 7, 12, 16, 71, 78, 79, 113, 123, 225 | |
VNG0579H | hypothetical protein VNG0579H | 49, 79, 123, 187 | |
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 |
VNG0768H | hypothetical protein VNG0768H | 71, 283 | |
VNG0796G | cgs | cystathionine gamma synthase/lyase | 7, 50 |
VNG0801C | hypothetical protein VNG0801C | 12, 49, 71, 79, 113, 187 | |
VNG0880G | psmA | proteasome subunit alpha | 12, 49, 71, 79, 109 |
VNG0906H | hypothetical protein VNG0906H | 71, 79 | |
VNG0940Gm | ACS3 | Acetyl-CoA synthetase | 7, 19, 24, 25, 29, 49 |
VNG0946G | minD1 | cell division inhibitor | 7 |
VNG0949G | gspE3 | type II secretion system protein | 7 |
VNG0954C | hypothetical protein VNG0954C | 7, 278, 283 | |
VNG0955G | fapE | flagella-like protein E | 7, 16, 25, 50, 100, 291 |
VNG0960G | flaB1 | flagellin B1 | 2, 3, 7, 12, 16, 49, 78, 79, 100, 113, 123 |
VNG0961G | flaB2 | flagellin B2 | 2, 3, 7, 12, 16, 49, 78, 79, 100, 113, 123, 291 |
VNG0962G | flaB3 | flagellin B3 | 2, 3, 7, 12, 16, 49, 78, 100, 113, 123 |
VNG0964C | hypothetical protein VNG0964C | 12, 24, 49, 100, 109 | |
VNG0974G | cheY | hypothetical protein VNG0974G | 7, 55, 61, 184 |
VNG0976G | cheW1 | chemotaxis protein | 7, 55 |
VNG1002H | hypothetical protein VNG1002H | 49, 242 | |
VNG1008G | flaA1a | flagellin A1 | 78, 81 |
VNG1092C | hypothetical protein VNG1092C | 71, 187 | |
VNG1093C | hypothetical protein VNG1093C | 71, 79, 187 | |
VNG1125G | korB | KorB | 7, 12, 24, 29 |
VNG1128G | korA | KorA | 3, 7, 12, 24, 29, 49, 71, 78, 113 |
VNG1190G | sod1 | superoxide dismutase | 78, 283 |
VNG1261H | hypothetical protein VNG1261H | 49, 113 | |
VNG1306G | sdhA | hypothetical protein VNG1306G | 2, 3, 12, 16, 78, 79, 90, 100 |
VNG1376H | hypothetical protein VNG1376H | 71 | |
VNG1412H | hypothetical protein VNG1412H | 3, 12, 49, 71, 79, 113 | |
VNG1793C | pyridoxal biosynthesis lyase PdxS | 19, 90 | |
VNG1801G | hsp1 | Hsp1 | 75 |
VNG1802H | hypothetical protein VNG1802H | 75, 242 | |
VNG1804G | noxA | NADH oxidase | 75 |
VNG1836G | cspD2 | cold shock protein | 3, 12, 49, 71, 79 |
VNG1933G | ftsZ3 | cell division protein | 7, 25, 61, 227 |
VNG2008H | hypothetical protein VNG2008H | 9, 49, 79, 113, 170, 187 | |
VNG2081H | hypothetical protein VNG2081H | 49, 50, 123, 175, 187 | |
VNG2093G | glnA | hypothetical protein VNG2093G | 75, 76, 163, 174 |
VNG2122G | ilvE2 | branched-chain amino acid aminotransferase | 7, 19, 29, 49, 71, 75, 78 |
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 | |
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 | |
VNG2443G | dpsA | starvation induced DNA-binding protein | 3, 12, 49, 71, 79, 113, 123, 187 |
VNG2499G | gcdH | glutaryl-CoA dehydrogenase | 7, 24, 25, 50, 61, 78 |
VNG2539H | hypothetical protein VNG2539H | 7, 29, 78 | |
VNG2543C | hypothetical protein VNG2543C | 3, 12, 49, 71, 78, 113, 156 | |
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 |
VNG6201G | hsp5 | heat shock protease protein | 3, 49, 71, 79, 98, 100, 113, 187, 240 |
VNG6294G | perA | peroxidase / catalase | 23, 24, 29, 52 |
VNG6312G | argS | arginine-tRNA synthetase | 24, 29 |
VNG7027 | gvpN | gas vesicle protein GvpN | 78 |
VNG7101 | hypothetical protein VNG7101 | 49, 71, 113 |
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.
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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
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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)
- 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
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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.