Organism : Halobacterium salinarum NRC-1 | Module List :
VNG2616G cxp
putative carboxypeptidase
Functional Annotations (3)
Function | System |
---|---|
Zn-dependent carboxypeptidase | cog/ cog |
metallocarboxypeptidase activity | go/ molecular_function |
proteolysis | go/ biological_process |
Regulation information for VNG2616G
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
VNG0530G VNG0654C |
163 | combiner |
VNG1377G VNG1816G |
163 | combiner |
VNG1405C | 163 | tf |
VNG1899G VNG2094G |
163 | combiner |
VNG1899G VNG2476C |
163 | combiner |
VNG2441G VNG2094G |
163 | combiner |
VNG2476C | 163 | tf |
VNG5028G VNG1899G |
163 | combiner |
VNG5182G VNG2094G |
163 | combiner |
VNG1405C | 174 | tf |
VNG1899G | 174 | tf |
VNG2441G | 174 | tf |
VNG2441G VNG2094G |
174 | combiner |
VNG0458G VNG1922G |
77 | combiner |
VNG0458G VNG2476C |
77 | combiner |
VNG1483C | 77 | tf |
VNG1899G VNG0536G |
77 | combiner |
VNG1899G VNG2094G |
77 | combiner |
VNG2441G VNG0751C |
77 | combiner |
VNG5028G VNG1899G |
77 | combiner |
Motif information (de novo identified motifs for modules)
There are 6 motifs predicted.
Motif Id | e-value | Consensus | Motif Logo |
---|---|---|---|
1129 | 3.60e-01 | TG.gA.cAaacCCcaTaaTaaTaT | |
1130 | 7.40e+02 | AcAccccacAc | |
1287 | 9.20e-04 | AtataaatTtcgac | |
1288 | 5.60e-01 | tAtTAtAAa | |
1307 | 7.10e-04 | attagata.a.cTaAattTctaTt | |
1308 | 7.90e+01 | GGgT.GAAttAtacA |
Functional Enrichment for VNG2616G
Function | System |
---|---|
Zn-dependent carboxypeptidase | cog/ cog |
metallocarboxypeptidase activity | go/ molecular_function |
proteolysis | go/ biological_process |
Module neighborhood information for VNG2616G
Gene | Common Name | Description | Module membership |
---|---|---|---|
VNG0451G | phoU | hypothetical protein VNG0451G | 6, 76, 124, 163, 174, 205, 226 |
VNG0452G | pstB2 | phosphate ABC transporter ATP-binding protein | 6, 76, 124, 163, 174, 205, 226 |
VNG0453G | pstA2 | phosphate ABC transporter permease | 6, 76, 124, 163, 174, 205, 226 |
VNG0455G | pstC2 | phosphate ABC transporter permease | 6, 76, 124, 163, 174, 205, 226 |
VNG0457G | phoX | phosphate ABC transporter periplasmic phosphate-binding protein | 6, 76, 124, 163, 174, 205, 226 |
VNG0458G | prp1 | phosphate regulatory protein-like protein | 6, 76, 124, 163, 174, 205, 226 |
VNG0535C | hypothetical protein VNG0535C | 76, 163, 174, 226 | |
VNG0536G | sirR | transcription repressor | 163, 174 |
VNG0745G | spoVR | hypothetical protein VNG0745G | 77 |
VNG0746C | hypothetical protein VNG0746C | 77 | |
VNG0748G | prkA | hypothetical protein VNG0748G | 77 |
VNG0749G | prk | serine protein kinase | 77 |
VNG0750C | hypothetical protein VNG0750C | 77, 284 | |
VNG1018G | adh3 | alcohol dehydrogenase | 77 |
VNG1021C | GTP cyclohydrolase III | 77 | |
VNG1023C | hypothetical protein VNG1023C | 77 | |
VNG1024C | hypothetical protein VNG1024C | 77 | |
VNG1025H | hypothetical protein VNG1025H | 77 | |
VNG1295H | hypothetical protein VNG1295H | 6, 77, 163, 205, 226 | |
VNG1543G | zim | CTAG modification methylase | 114, 124, 174, 184 |
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 | |
VNG1564H | hypothetical protein VNG1564H | 114, 124, 174, 205, 226, 227 | |
VNG1632G | cbiQ | hypothetical protein VNG1632G | 76, 114, 163, 174, 205, 226, 227 |
VNG1635G | cbiM | cobalt transport protein CbiM | 76, 163, 205, 226, 227 |
VNG1644G | nrdB2 | ribonucleoside reductase large chain | 174 |
VNG1760G | htr5 | Htr5 | 77 |
VNG1821G | adh4 | alcohol dehydrogenase | 77 |
VNG1925H | hypothetical protein VNG1925H | 77 | |
VNG2093G | glnA | hypothetical protein VNG2093G | 75, 76, 163, 174 |
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 |
VNG2302G | yuxL | acylaminoacyl-peptidase | 76, 174, 184 |
VNG2343G | ykfD | oligopeptide ABC transporter ATP-binding protein | 174 |
VNG2344G | oppD2 | oligopeptide ABC transporter | 163 |
VNG2358G | appA | oligopeptide binding protein | 6, 76, 77 |
VNG2359G | appB | oligopeptide ABC permease | 6, 76, 77 |
VNG2361G | appC | oligopeptide transport permease | 6, 76, 77 |
VNG2363Gm | oppD1 | oligopeptide ABC transporter ATP-binding protein | 6, 77, 226 |
VNG2365G | appF | oligopeptide ABC transporter ATP-binding protein | 6, 76, 77 |
VNG2430G | thrC1 | threonine synthase | 61, 77 |
VNG2436G | argH | argininosuccinate lyase | 77 |
VNG2437G | argG | argininosuccinate synthase | 77 |
VNG2477H | hypothetical protein VNG2477H | 6, 77, 163, 205, 226 | |
VNG2480Hm | hypothetical protein VNG2480Hm | 6, 163, 205 | |
VNG2482G | pstB1 | phosphate ABC transporter ATP-binding protein | 6, 76, 77, 163, 174, 205, 226 |
VNG2483G | pstA1 | phosphate ABC transporter permease | 6, 76, 77, 163, 174, 205 |
VNG2484G | pstC1 | phosphate transporter permease | 6, 76, 77, 163, 205 |
VNG2486G | yqgG | phosphate ABC transporter binding protein | 6, 76, 77, 163 |
VNG2527G | dppD | hypothetical protein VNG2527G | 77 |
VNG2529G | dppB2 | hypothetical protein VNG2529G | 6, 76, 77, 163, 205, 226 |
VNG2531G | dppC1 | dipeptide ABC transporter permease | 6, 76, 77, 163, 174, 205, 226 |
VNG2532H | hypothetical protein VNG2532H | 6, 76, 77 | |
VNG2546G | pepB3 | aminopeptidase-like protein | 174 |
VNG2615C | ATPase | 174 | |
VNG2616G | cxp | putative carboxypeptidase | 77, 163, 174 |
VNG6262G | zurM | ABC transporter permease | 6, 76, 163, 174, 205, 226, 249 |
VNG6264G | zurA | ABC transporter ATP-binding protein | 6, 76, 163, 205, 226, 249 |
VNG6265G | ycdH | adhesion protein | 6, 76, 163, 174, 205, 226, 249 |
VNG6277G | ugpB | glycerol-3-phosphate-binding protein | 6, 76, 163, 205 |
VNG6279G | ugpA | sn-glycerol-3-phosphate transport system permease | 6, 76, 163, 205, 226 |
VNG6280G | ugpE | sn-glycerol-3-phosphate transport system permease | 6, 76, 163, 205, 226 |
VNG6281G | ugpC | sn-glycerol-3-phosphate transport system ATP-binding protein | 6, 76, 163, 205 |
VNG6301G | aph | alkaline phosphatase | 6, 77, 163, 205, 226 |
VNG6311G | pyrI | aspartate carbamoyltransferase regulatory subunit | 174 |
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.