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glinks [2015/01/27 14:07]
gaou
glinks [2015/11/03 16:42] (current)
cory [Versions]
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     * Java script to get related information about hsa:128 and RECA_ECOLI in TSV format.     * Java script to get related information about hsa:128 and RECA_ECOLI in TSV format.
    
 +==== Example of programatic access ====
  
 +One of the strength of G-Links is its programmatic access. For example, GO slim classification of all genes of E.coli for GO:Process ontology can be retrieved from the following URL:
 +  * http://​link.g-language.org/​NC_000913/​extract=GOslim_process ​
 +This result is shown as a formatted HTML page when viewed in a browser, but when it is accessed from the command line or from programs, the result is automatically returned as TSV file. Using this, simple combination of UNIX commands can produce a classification summary of all genes in E.coli with GOslim:​Process terms. Here is an example:
 +
 +<​code>​
 +$ curl -v http://​link.g-language.org/​NC_000913/​extract=GOslim_process ​ |grep \# |cut -f 2,3 |grep GO: |sort |uniq -c |sort -rn
 +</​code>​
 +
 +Here, G-Links is accessed from the command line, producing the result to standard output via "curl -v", and the sections containing GO terms and its descriptions are extracted ("​|grep \# |cut -f 2,3 |grep GO:). Then, the terms are sorted and counted ("​|sort |uniq -c"), and printed in a descending order ("​|sort -rn").
 +
 +Following is the output of the above line of commands:
 +
 +<​code>​
 +1056 GO:​0009058 biosynthetic process
 +1032 GO:​0008150 biological_process
 + 860 GO:​0034641 cellular nitrogen compound metabolic process
 + 636 GO:​0044281 small molecule metabolic process
 + 526 GO:​0006810 transport
 + 484 GO:​0006950 response to stress
 + 381 GO:​0005975 carbohydrate metabolic process
 + 374 GO:​0009056 catabolic process
 + 285 GO:​0055085 transmembrane transport
 + 273 GO:​0006259 DNA metabolic process
 + 257 GO:​0006520 cellular amino acid metabolic process
 + 190 GO:​0051186 cofactor metabolic process
 + 169 GO:​0006629 lipid metabolic process
 + 127 GO:​0006464 cellular protein modification process
 + 127 GO:​0006091 generation of precursor metabolites and energy
 +  98 GO:​0006790 sulfur compound metabolic process
 +  96 GO:​0042592 homeostatic process
 +  92 GO:​0032196 transposition
 +  84 GO:​0006399 tRNA metabolic process
 +  79 GO:​0007165 signal transduction
 +  76 GO:​0071554 cell wall organization or biogenesis
 +  72 GO:​0022607 cellular component assembly
 +  63 GO:​0006412 translation
 +  52 GO:​0034655 nucleobase-containing compound catabolic process
 +  50 GO:​0051301 cell division
 +  50 GO:​0007155 cell adhesion
 +  50 GO:​0006457 protein folding
 +  45 GO:​0048870 cell motility
 +  43 GO:​0006461 protein complex assembly
 +  39 GO:​0007049 cell cycle
 +  37 GO:​0040011 locomotion
 +  32 GO:​0051604 protein maturation
 +  31 GO:​0071941 nitrogen cycle metabolic process
 +  31 GO:​0051276 chromosome organization
 +  21 GO:​0061024 membrane organization
 +  19 GO:​0019748 secondary metabolic process
 +  18 GO:​0044403 symbiosis,​ encompassing mutualism through parasitism
 +  17 GO:​0000003 reproduction
 +  15 GO:​0022618 ribonucleoprotein complex assembly
 +  14 GO:​0007059 chromosome segregation
 +  14 GO:​0002376 immune system process
 +   9 GO:​0006605 protein targeting
 +   7 GO:​0008219 cell death
 +   5 GO:​0042254 ribosome biogenesis
 +   4 GO:​0006397 mRNA processing
 +   3 GO:​0000902 cell morphogenesis
 +   2 GO:​0048646 anatomical structure formation involved in morphogenesis
 +   2 GO:​0030198 extracellular matrix organization
 +   2 GO:​0030154 cell differentiation
 +   1 GO:​0065003 macromolecular complex assembly
 +   1 GO:​0015979 photosynthesis
 +   1 GO:​0007267 cell-cell signaling
 +   1 GO:​0007010 cytoskeleton organization
 +</​code>​
 +
 +If you have a specific set of genes, such as RECA_ECOLI,​RUVB_ECOLI,​LEXA_ECOLI,​UMUD_ECOLI,​ that may be over represented in a microarray experiment, running the same routine with this list of genes can produce the Gene Ontology classification of these genes of interest.
 +
 +<​code>​
 +$ curl -v http://​link.g-language.org/​RECA_ECOLI,​RUVB_ECOLI,​LEXA_ECOLI,​UMUD_ECOLI/​extract=GOslim_process ​ |grep \# |cut -f 2,3 |grep GO: |sort |uniq -c |sort -rn
 +</​code>​
 +
 +This will produce:
 +
 +<​code>​
 +   4 GO:​0006950 response to stress
 +   4 GO:​0006259 DNA metabolic process
 +   3 GO:​0008150 biological_process
 +   2 GO:​0009058 biosynthetic process
 +   1 GO:​0051276 chromosome organization
 +   1 GO:​0048870 cell motility
 +   1 GO:​0034641 cellular nitrogen compound metabolic process
 +</​code>​
 +
 +Now these values are readily used to test its enrichment by Fisher'​s exact test, for example, to calculate Gene Ontology enrichment scores.
 +
 +If alternative classification is desirable, simply change the extracting term from GOslim_process to, for example, KEGG BRITE hierarchy.
 +
 +<​code>​
 +$ curl -v http://​link.g-language.org/​NC_000913/​extract=KEGG_Brite ​ |grep \# |cut -f 2,3 |grep ko |sort |uniq -c |sort -rn
 +</​code>​
 +
 +This will produce: ​
 +
 +<​code>​
 +1452 ko00001 KEGG Orthology (KO)
 +1017 ko01000 Enzymes
 + 838 ko00002 KEGG pathway modules
 + 358 ko01000 Enzymes
 + 282 ko02000 Transporters
 + 197 ko02000 Transporters
 + 129 ko03000 Transcription factors
 +  89 ko03400 DNA repair and recombination proteins
 +  84 ko03016 Transfer RNA biogenesis
 +  65 ko01002 Peptidases
 +  61 ko02035 Bacterial motility proteins
 +  58 ko02022 Two-component system
 +  57 ko03011 Ribosome
 +  56 ko03011 M00178 ​ Ribosome, bacteria
 +  52 ko02044 Secretion system
 +  49 ko03009 Ribosome biogenesis
 +  45 ko01007 Amino acid related enzymes
 +  44 ko00002 KEGG pathway modules
 +  39 ko01005 Lipopolysaccharide biosynthesis proteins
 +  33 ko01001 Protein kinases
 +  31 ko03011 M00179 ​ Ribosome, archaea
 +  28 ko03036 Chromosome
 +  27 ko03110 Chaperones and folding catalysts
 +  27 ko01003 Glycosyltransferases
 +  26 ko03036 Chromosome
 +  26 ko03032 DNA replication proteins
 +  25 ko02044 Secretion system
 +  20 ko03110 Chaperones and folding catalysts
 +  20 ko01004 Lipid biosynthesis proteins
 +  19 ko03009 Ribosome biogenesis
 +  15 ko03012 Translation factors
 +  13 ko02044 M00331 ​ Type II general secretion system
 +  12 ko02044 M00335 ​ Sec (secretion) system
 +  11 ko02000 M00240 ​ Iron complex transport system
 +  11 ko01002 Peptidases
 +  10 ko03021 Transcription machinery
 +  10 ko03021 Transcription machinery
 +  10 ko02035 Bacterial motility proteins
 +  10 ko02000 M00324 ​ Dipeptide transport system
 +   9 ko03400 M00260 ​ DNA polymerase III complex, bacteria
 +   9 ko03032 M00260 ​ DNA polymerase III complex, bacteria
 +   9 ko02000 M00306 ​ PTS system, fructose-specific II-like component
 +   8 ko03400 DNA repair and recombination proteins
 +   8 ko03032 DNA replication proteins
 +   8 ko03000 Transcription factors
 +   8 ko00194 Photosynthesis proteins
 +   7 ko02000 M00221 ​ Putative simple sugar transport system
 +   7 ko01006 Prenyltransferases
 +   6 ko02000 M00439 ​ Oligopeptide transport system
 +   6 ko02000 M00239 ​ Peptides/​nickel transport system
 +   6 ko02000 M00237 ​ Branched-chain amino acid transport system
 +   6 ko01005 Lipopolysaccharide biosynthesis proteins
 +   5 ko03016 Transfer RNA biogenesis
 +   5 ko03012 Translation factors
 +   5 ko02000 M00440 ​ Nickel transport system
 +   5 ko02000 M00279 ​ PTS system, galactitol-specific II component
 +   5 ko02000 M00229 ​ Arginine transport system
 +   5 ko02000 M00185 ​ Sulfate transport system
 +   4 ko03400 M00183 ​ RNA polymerase, bacteria
 +   4 ko03021 M00183 ​ RNA polymerase, bacteria
 +   4 ko02044 M00336 ​ Twin-arginine translocation (Tat) system
 +   4 ko02022 Two-component system
 +   4 ko02000 M00349 ​ Microcin C transport system
 +   4 ko02000 M00348 ​ Glutathione transport system
 +   4 ko02000 M00300 ​ Putrescine transport system
 +   4 ko02000 M00299 ​ Spermidine/​putrescine transport system
 +   4 ko02000 M00283 ​ PTS system, ascorbate-specific II component
 +   4 ko02000 M00238 ​ D-Methionine transport system
 +   4 ko02000 M00230 ​ Glutamate/​aspartate transport system
 +   4 ko02000 M00226 ​ Histidine transport system
 +   4 ko02000 M00225 ​ Lysine/​arginine/​ornithine transport system
 +   4 ko02000 M00222 ​ Phosphate transport system
 +   4 ko02000 M00219 ​ AI-2 transport system
 +   4 ko02000 M00209 ​ Osmoprotectant transport system
 +   4 ko02000 M00198 ​ Putative sn-glycerol-phosphate transport system
 +   4 ko02000 M00197 ​ Putative fructooligosaccharide transport system
 +   4 ko02000 M00194 ​ Maltose/​maltodextrin transport system
 +   4 ko02000 M00193 ​ Putative spermidine/​putrescine transport system
 +   4 ko02000 M00189 ​ Molybdate transport system
 +   3 ko04812 Cytoskeleton proteins
 +   3 ko02035 M00506 ​ CheA-CheYBV (chemotaxis) two-component regulatory system
 +   3 ko02030 M00506 ​ CheA-CheYBV (chemotaxis) two-component regulatory system
 +   3 ko02022 M00506 ​ CheA-CheYBV (chemotaxis) two-component regulatory system
 +   3 ko02022 M00474 ​ RcsC-RcsD-RcsB (capsule synthesis) two-component regulatory system
 +   3 ko02001 Solute carrier family
 +   3 ko02000 M00436 ​ Sulfonate transport system
 +   3 ko02000 M00435 ​ Taurine transport system
 +   3 ko02000 M00320 ​ Lipopolysaccharide export system
 +   3 ko02000 M00287 ​ PTS system, galactosamine-specific II component
 +   3 ko02000 M00280 ​ PTS system, glucitol/​sorbitol-specific II component
 +   3 ko02000 M00276 ​ PTS system, mannose-specific II component
 +   3 ko02000 M00275 ​ PTS system, cellobiose-specific II component
 +   3 ko02000 M00274 ​ PTS system, mannitol-specific II component
 +   3 ko02000 M00259 ​ Heme transport system
 +   3 ko02000 M00255 ​ Lipoprotein-releasing system
 +   3 ko02000 M00254 ​ ABC-2 type transport system
 +   3 ko02000 M00248 ​ Putative antibiotic transport system
 +   3 ko02000 M00242 ​ Zinc transport system
 +   3 ko02000 M00241 ​ Vitamin B12 transport system
 +   3 ko02000 M00234 ​ Cystine transport system
 +   3 ko02000 M00232 ​ General L-amino acid transport system
 +   3 ko02000 M00227 ​ Glutamine transport system
 +   3 ko02000 M00217 ​ D-Allose transport system
 +   3 ko02000 M00215 ​ D-Xylose transport system
 +   3 ko02000 M00214 ​ Methyl-galactoside transport system
 +   3 ko02000 M00213 ​ L-Arabinose transport system
 +   3 ko02000 M00212 ​ Ribose transport system
 +   3 ko02000 M00210 ​ Putative ABC transport system
 +   3 ko02000 M00208 ​ Glycine betaine/​proline transport system
 +   3 ko02000 M00207 ​ Putative multiple sugar transport system
 +   3 ko02000 M00192 ​ Putative thiamine transport system
 +   3 ko02000 M00191 ​ Thiamine transport system
 +   3 ko01008 Polyketide biosynthesis proteins
 +   2 ko04040 Ion channels
 +   2 ko02044 M00429 ​ Competence-related DNA transformation transporter
 +   2 ko02042 Bacterial toxins
 +   2 ko02022 M00502 ​ GlrK-GlrR (amino sugar metabolism) two-component regulatory system
 +   2 ko02022 M00500 ​ AtoS-AtoC (complexed poly-(R)-3-hydroxybutyrate biosynthesis) two-component regulatory system
 +   2 ko02022 M00499 ​ HydH-HydG (metal tolerance) two-component regulatory system
 +   2 ko02022 M00497 ​ GlnL-GlnG (nitrogen regulation) two-component regulatory system
 +   2 ko02022 M00488 ​ DcuS-DcuR (aerobic C4-dicarboxylate metabolism) two-component regulatory system
 +   2 ko02022 M00486 ​ CitA-CitB (citrate fermentation) two-component regulatory system
 +   2 ko02022 M00477 ​ EvgS-EvgA (acid and drug tolerance) two-component regulatory system
 +   2 ko02022 M00475 ​ BarA-UvrY (central carbon metabolism) two-component regulatory system
 +   2 ko02022 M00473 ​ UhpB-UhpA (hexose phosphates uptake) two-component regulatory system
 +   2 ko02022 M00472 ​ NarQ-NarP (nitrate respiration) two-component regulatory system
 +   2 ko02022 M00471 ​ NarX-NarL (nitrate respiration) two-component regulatory system
 +   2 ko02022 M00456 ​ ArcB-ArcA (anoxic redox control) two-component regulatory system
 +   2 ko02022 M00455 ​ TorS-TorR (trimethylamine N-oxide respiration) two-component regulatory system
 +   2 ko02022 M00454 ​ KdpD-KdpE (potassium transport) two-component regulatory system
 +   2 ko02022 M00453 ​ QseC-QseB (quorum sensing) two-component regulatory system
 +   2 ko02022 M00452 ​ CusS-CusR (copper tolerance) two-component regulatory system
 +   2 ko02022 M00451 ​ BasS-BasR (antimicrobial peptide resistance) two-component regulatory system
 +   2 ko02022 M00450 ​ BaeS-BaeR (envelope stress response) two-component regulatory system
 +   2 ko02022 M00449 ​ CreC-CreB (phosphate regulation) two-component regulatory system
 +   2 ko02022 M00447 ​ CpxA-CpxR (envelope stress response) two-component regulatory system
 +   2 ko02022 M00446 ​ RstB-RstA two-component regulatory system
 +   2 ko02022 M00445 ​ EnvZ-OmpR (osmotic stress response) two-component regulatory system
 +   2 ko02022 M00444 ​ PhoQ-PhoP (magnesium transport) two-component regulatory system
 +   2 ko02022 M00434 ​ PhoR-PhoB (phosphate starvation response) two-component regulatory system
 +   2 ko02000 M00303 ​ PTS system, N-acetylmuramic acid-specific II component
 +   2 ko02000 M00272 ​ PTS system, arbutin-, cellobiose-,​ and salicin-specific II component
 +   2 ko02000 M00270 ​ PTS system, trehalose-specific II component
 +   2 ko02000 M00266 ​ PTS system, maltose and glucose-specific II component
 +   2 ko02000 M00265 ​ PTS system, glucose-specific II component
 +   2 ko02000 M00258 ​ Putative ABC transport system
 +   2 ko02000 M00256 ​ Cell division transport system
 +   2 ko02000 M00224 ​ Putative phosphonate transport system
 +   2 ko02000 M00223 ​ Phosphonate transport system
 +   2 ko02000 M00211 ​ Putative ABC transport system
 +   1 ko04121 Ubiquitin system
 +   1 ko04090 Cellular antigens
 +   1 ko03051 Proteasome
 +   1 ko02044 M00571 ​ AlgE-type Mannuronan C-5-Epimerase transport system
 +   1 ko02044 M00339 ​ RaxAB-RaxC type I secretion system
 +   1 ko02044 M00326 ​ RTX toxin transport system
 +   1 ko02000 M00491 ​ Putative arabinogalactan oligomer transport system
 +   1 ko02000 M00325 ​ alpha-Hemolysin/​cyclolysin transport system
 +   1 ko02000 M00305 ​ PTS system, 2-O-A-mannosyl-D-glycerate-specific II component
 +   1 ko02000 M00277 ​ PTS system, N-acetylgalactosamine-specific II component
 +   1 ko02000 M00273 ​ PTS system, fructose-specific II component
 +   1 ko02000 M00271 ​ PTS system, beta-glucosides-specific II component
 +   1 ko02000 M00268 ​ PTS system, arbutin-like II component
 +   1 ko02000 M00267 ​ PTS system, N-acetylglucosamine-specific II component
 +   1 ko02000 M00190 ​ Iron(III) transport system
 +   1 ko00194 Photosynthesis proteins
 +</​code>​
 + 
 +===== Versions =====
 +G-Links database is updated once every six month. Next update is Feb 2016.
 +
 +  * UniProt : 2015_10
 +    * idmapping, Swiss-Prot, TrEMBL, taxnomic_divisions
 +  * GEO : 2015_10
 +    * GeoDb_blob82
 +  * Enzyme : 16-Sep-2015
 +  * PharmGKB : 2015-10-04
 +    * Genes, RSID mapping
 +  * PID : 2012-9-18 (latest)
 +  * BIOGRID : 3.4.129
 +  * Gene Ontology : 2015-09-24
 +
 +===== License =====
 +  * Data and images from UniProt: [[http://​www.uniprot.org/​help/​license|Creative Commons Attribution-NoDerivs]]
 +  * Data and images from Coxpresdb: [[http://​coxpresdb.jp/​license.shtml|Creative Commons Attribution 2.1]]
 +  * Data and images from PDB: [[http://​www.rcsb.org/​pdb/​static.do?​p=general_information/​about_pdb/​policies_references.html|Free of all copyright restrictions]]
 +  * Data and images from STRING API: [[http://​string-db.org/​help/​index.jsp?​topic=/​org.string-db.docs/​api.html|N.A. for individual items]]
 +  * Data and images from KEGG: [[http://​www.kegg.jp/​kegg/​legal.html|Commercial users should obtain a license]]
  
 ===== Reference ===== ===== Reference =====
   * [[http://​www.g-language.org/​data/​cory/​glinks_poster.pdf|Poster (BMB2012)]]   * [[http://​www.g-language.org/​data/​cory/​glinks_poster.pdf|Poster (BMB2012)]]
glinks.1422367662.txt.gz ยท Last modified: 2015/01/27 14:07 by gaou