PMC:7111504 / 13142-13805 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7111504","sourcedb":"PMC","sourceid":"7111504","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7111504","text":"Here, we scanned all 9-mers from the 2019-nCoV proteome (9613 peptides) with Binding, Activating and Killing Position Weight Matrices (PWM, see the method section) and associated each peptide with the geometric mean of these three assays as a measure of immunogenicity (Data Table 4 4). The distributions of binding, activation and killing scores along with their multiplicative score and geometric mean are illustrated in Figure 4. Based on geometric mean, we observed 20 2019-nCoV peptides with a score \u003e 0.8 and 516 peptides \u003e 0.7. The 9-mer peptides with geometric mean \u003e 0.7 and positive HLA-A*02:01 binding prediction by NetMHCpan 4.0 are listed in Table 4.","tracks":[{"project":"LitCovid-PubTator","denotations":[{"id":"203","span":{"begin":593,"end":598},"obj":"Gene"},{"id":"204","span":{"begin":37,"end":46},"obj":"Species"},{"id":"205","span":{"begin":473,"end":482},"obj":"Species"},{"id":"206","span":{"begin":519,"end":527},"obj":"Chemical"},{"id":"207","span":{"begin":627,"end":636},"obj":"Chemical"}],"attributes":[{"id":"A203","pred":"tao:has_database_id","subj":"203","obj":"Gene:3105"},{"id":"A204","pred":"tao:has_database_id","subj":"204","obj":"Tax:2697049"},{"id":"A205","pred":"tao:has_database_id","subj":"205","obj":"Tax:2697049"},{"id":"A206","pred":"tao:has_database_id","subj":"206","obj":"MESH:D010455"},{"subj":"203","pred":"source","obj":"LitCovid-PubTator"},{"subj":"204","pred":"source","obj":"LitCovid-PubTator"},{"subj":"205","pred":"source","obj":"LitCovid-PubTator"},{"subj":"206","pred":"source","obj":"LitCovid-PubTator"},{"subj":"207","pred":"source","obj":"LitCovid-PubTator"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}]},{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T159","span":{"begin":23,"end":27},"obj":"SP_9"},{"id":"T160","span":{"begin":37,"end":46},"obj":"SP_7"},{"id":"T161","span":{"begin":254,"end":268},"obj":"BV_15"},{"id":"T162","span":{"begin":473,"end":482},"obj":"SP_7"},{"id":"T163","span":{"begin":593,"end":598},"obj":"PR:000002009"},{"id":"T99554","span":{"begin":23,"end":27},"obj":"SP_9"},{"id":"T68802","span":{"begin":37,"end":46},"obj":"SP_7"},{"id":"T66664","span":{"begin":254,"end":268},"obj":"BV_15"},{"id":"T22144","span":{"begin":473,"end":482},"obj":"SP_7"},{"id":"T48296","span":{"begin":593,"end":598},"obj":"PR:000002009"}],"attributes":[{"subj":"T159","pred":"source","obj":"LitCovid-PMC-OGER-BB"},{"subj":"T160","pred":"source","obj":"LitCovid-PMC-OGER-BB"},{"subj":"T161","pred":"source","obj":"LitCovid-PMC-OGER-BB"},{"subj":"T162","pred":"source","obj":"LitCovid-PMC-OGER-BB"},{"subj":"T163","pred":"source","obj":"LitCovid-PMC-OGER-BB"},{"subj":"T99554","pred":"source","obj":"LitCovid-PMC-OGER-BB"},{"subj":"T68802","pred":"source","obj":"LitCovid-PMC-OGER-BB"},{"subj":"T66664","pred":"source","obj":"LitCovid-PMC-OGER-BB"},{"subj":"T22144","pred":"source","obj":"LitCovid-PMC-OGER-BB"},{"subj":"T48296","pred":"source","obj":"LitCovid-PMC-OGER-BB"}]},{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T83","span":{"begin":593,"end":596},"obj":"Body_part"}],"attributes":[{"id":"A83","pred":"fma_id","subj":"T83","obj":"http://purl.org/sig/ont/fma/fma84795"},{"subj":"T83","pred":"source","obj":"LitCovid-PD-FMA-UBERON"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T182","span":{"begin":62,"end":70},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T183","span":{"begin":86,"end":96},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T184","span":{"begin":184,"end":191},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T185","span":{"begin":241,"end":242},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T186","span":{"begin":317,"end":327},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T187","span":{"begin":483,"end":491},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T188","span":{"begin":497,"end":498},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T189","span":{"begin":519,"end":527},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T190","span":{"begin":545,"end":553},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T191","span":{"begin":597,"end":598},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"attributes":[{"subj":"T182","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T183","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T184","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T185","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T186","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T187","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T188","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T189","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T190","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T191","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T91","span":{"begin":62,"end":70},"obj":"Chemical"},{"id":"T92","span":{"begin":184,"end":191},"obj":"Chemical"},{"id":"T93","span":{"begin":483,"end":491},"obj":"Chemical"},{"id":"T94","span":{"begin":519,"end":527},"obj":"Chemical"},{"id":"T95","span":{"begin":545,"end":553},"obj":"Chemical"}],"attributes":[{"id":"A91","pred":"chebi_id","subj":"T91","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A92","pred":"chebi_id","subj":"T92","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A93","pred":"chebi_id","subj":"T93","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A94","pred":"chebi_id","subj":"T94","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A95","pred":"chebi_id","subj":"T95","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"subj":"T91","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T92","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T93","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T94","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T95","pred":"source","obj":"LitCovid-PD-CHEBI"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T149","span":{"begin":0,"end":286},"obj":"Sentence"},{"id":"T150","span":{"begin":287,"end":432},"obj":"Sentence"},{"id":"T151","span":{"begin":433,"end":534},"obj":"Sentence"},{"id":"T152","span":{"begin":535,"end":663},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T149","pred":"source","obj":"LitCovid-sentences"},{"subj":"T150","pred":"source","obj":"LitCovid-sentences"},{"subj":"T151","pred":"source","obj":"LitCovid-sentences"},{"subj":"T152","pred":"source","obj":"LitCovid-sentences"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PubTator","color":"#eccd93","default":true},{"id":"LitCovid-PMC-OGER-BB","color":"#b393ec"},{"id":"LitCovid-PD-FMA-UBERON","color":"#93ec99"},{"id":"LitCovid-PD-CLO","color":"#ec93a6"},{"id":"LitCovid-PD-CHEBI","color":"#93c0ec"},{"id":"LitCovid-sentences","color":"#daec93"}]}]}}