PubMed:32224844 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PubMed/sourceid/32224844","sourcedb":"PubMed","sourceid":"32224844","source_url":"https://www.ncbi.nlm.nih.gov/pubmed/32224844","text":"HisCoM-PCA: software for hierarchical structural component analysis for pathway analysis based using principal component analysis.\nIn genome-wide association studies, pathway-based analysis has been widely performed to enhance interpretation of single-nucleotide polymorphism association results. We proposed a novel method of hierarchical structural component model (HisCoM) for pathway analysis of common variants (HisCoM for pathway analysis of common variants [HisCoM-PCA]) which was used to identify pathways associated with traits. HisCoM-PCA is based on principal component analysis (PCA) for dimensional reduction of single nucleotide polymorphisms in each gene, and the HisCoM for pathway analysis. In this study, we developed a HisCoM-PCA software for the hierarchical pathway analysis of common variants. HisCoM-PCA software has several features. Various principle component scores selection criteria in PCA step can be specified by users who want to summarize common variants at each gene-level by different threshold values. In addition, multiple public pathway databases and customized pathway information can be used to perform pathway analysis. We expect that HisCoM-PCA software will be useful for users to perform powerful pathway analysis.","tracks":[{"project":"week10","denotations":[{"id":"T2","span":{"begin":7,"end":10},"obj":"P00299"},{"id":"T5","span":{"begin":7,"end":10},"obj":"UBERON:0001628"},{"id":"T1","span":{"begin":7,"end":10},"obj":"C562643"},{"id":"T3","span":{"begin":7,"end":10},"obj":"CHEBI:62248"},{"id":"T4","span":{"begin":7,"end":10},"obj":"CHEBI:36751"},{"id":"T6","span":{"begin":134,"end":140},"obj":"SO:0001026"},{"id":"T8","span":{"begin":245,"end":275},"obj":"SO:0000694"},{"id":"T9","span":{"begin":252,"end":262},"obj":"CHEBI:7656"},{"id":"T10","span":{"begin":252,"end":262},"obj":"CHEBI:36976"},{"id":"T12","span":{"begin":472,"end":475},"obj":"P00299"},{"id":"T15","span":{"begin":472,"end":475},"obj":"UBERON:0001628"},{"id":"T11","span":{"begin":472,"end":475},"obj":"C562643"},{"id":"T13","span":{"begin":472,"end":475},"obj":"CHEBI:62248"},{"id":"T14","span":{"begin":472,"end":475},"obj":"CHEBI:36751"},{"id":"T16","span":{"begin":530,"end":536},"obj":"PR:Q811X5"},{"id":"T17","span":{"begin":530,"end":536},"obj":"PR:000006862"},{"id":"T18","span":{"begin":530,"end":536},"obj":"PR:Q96CJ1"},{"id":"T19","span":{"begin":530,"end":536},"obj":"PR:Q91ZD6"},{"id":"T21","span":{"begin":545,"end":548},"obj":"P00299"},{"id":"T24","span":{"begin":545,"end":548},"obj":"UBERON:0001628"},{"id":"T20","span":{"begin":545,"end":548},"obj":"C562643"},{"id":"T22","span":{"begin":545,"end":548},"obj":"CHEBI:62248"},{"id":"T23","span":{"begin":545,"end":548},"obj":"CHEBI:36751"},{"id":"T26","span":{"begin":591,"end":594},"obj":"P00299"},{"id":"T29","span":{"begin":591,"end":594},"obj":"UBERON:0001628"},{"id":"T25","span":{"begin":591,"end":594},"obj":"C562643"},{"id":"T27","span":{"begin":591,"end":594},"obj":"CHEBI:62248"},{"id":"T28","span":{"begin":591,"end":594},"obj":"CHEBI:36751"},{"id":"T30","span":{"begin":612,"end":621},"obj":"MOP:0000569"},{"id":"T31","span":{"begin":625,"end":631},"obj":"SO:0000984"},{"id":"T32","span":{"begin":632,"end":642},"obj":"CHEBI:7656"},{"id":"T33","span":{"begin":632,"end":642},"obj":"CHEBI:36976"},{"id":"T34","span":{"begin":665,"end":669},"obj":"SO:0000704"},{"id":"T36","span":{"begin":745,"end":748},"obj":"P00299"},{"id":"T39","span":{"begin":745,"end":748},"obj":"UBERON:0001628"},{"id":"T35","span":{"begin":745,"end":748},"obj":"C562643"},{"id":"T37","span":{"begin":745,"end":748},"obj":"CHEBI:62248"},{"id":"T38","span":{"begin":745,"end":748},"obj":"CHEBI:36751"},{"id":"T41","span":{"begin":823,"end":826},"obj":"P00299"},{"id":"T44","span":{"begin":823,"end":826},"obj":"UBERON:0001628"},{"id":"T40","span":{"begin":823,"end":826},"obj":"C562643"},{"id":"T42","span":{"begin":823,"end":826},"obj":"CHEBI:62248"},{"id":"T43","span":{"begin":823,"end":826},"obj":"CHEBI:36751"},{"id":"T46","span":{"begin":915,"end":918},"obj":"P00299"},{"id":"T49","span":{"begin":915,"end":918},"obj":"UBERON:0001628"},{"id":"T45","span":{"begin":915,"end":918},"obj":"C562643"},{"id":"T47","span":{"begin":915,"end":918},"obj":"CHEBI:62248"},{"id":"T48","span":{"begin":915,"end":918},"obj":"CHEBI:36751"},{"id":"T50","span":{"begin":924,"end":927},"obj":"PR:000034449"},{"id":"T51","span":{"begin":950,"end":953},"obj":"PR:O01367"},{"id":"T52","span":{"begin":996,"end":1000},"obj":"SO:0000704"},{"id":"T53","span":{"begin":1120,"end":1123},"obj":"PR:000034449"},{"id":"T55","span":{"begin":1183,"end":1186},"obj":"P00299"},{"id":"T58","span":{"begin":1183,"end":1186},"obj":"UBERON:0001628"},{"id":"T54","span":{"begin":1183,"end":1186},"obj":"C562643"},{"id":"T56","span":{"begin":1183,"end":1186},"obj":"CHEBI:62248"},{"id":"T57","span":{"begin":1183,"end":1186},"obj":"CHEBI:36751"}],"attributes":[{"subj":"T2","pred":"source","obj":"week10"},{"subj":"T5","pred":"source","obj":"week10"},{"subj":"T1","pred":"source","obj":"week10"},{"subj":"T3","pred":"source","obj":"week10"},{"subj":"T4","pred":"source","obj":"week10"},{"subj":"T6","pred":"source","obj":"week10"},{"subj":"T8","pred":"source","obj":"week10"},{"subj":"T9","pred":"source","obj":"week10"},{"subj":"T10","pred":"source","obj":"week10"},{"subj":"T12","pred":"source","obj":"week10"},{"subj":"T15","pred":"source","obj":"week10"},{"subj":"T11","pred":"source","obj":"week10"},{"subj":"T13","pred":"source","obj":"week10"},{"subj":"T14","pred":"source","obj":"week10"},{"subj":"T16","pred":"source","obj":"week10"},{"subj":"T17","pred":"source","obj":"week10"},{"subj":"T18","pred":"source","obj":"week10"},{"subj":"T19","pred":"source","obj":"week10"},{"subj":"T21","pred":"source","obj":"week10"},{"subj":"T24","pred":"source","obj":"week10"},{"subj":"T20","pred":"source","obj":"week10"},{"subj":"T22","pred":"source","obj":"week10"},{"subj":"T23","pred":"source","obj":"week10"},{"subj":"T26","pred":"source","obj":"week10"},{"subj":"T29","pred":"source","obj":"week10"},{"subj":"T25","pred":"source","obj":"week10"},{"subj":"T27","pred":"source","obj":"week10"},{"subj":"T28","pred":"source","obj":"week10"},{"subj":"T30","pred":"source","obj":"week10"},{"subj":"T31","pred":"source","obj":"week10"},{"subj":"T32","pred":"source","obj":"week10"},{"subj":"T33","pred":"source","obj":"week10"},{"subj":"T34","pred":"source","obj":"week10"},{"subj":"T36","pred":"source","obj":"week10"},{"subj":"T39","pred":"source","obj":"week10"},{"subj":"T35","pred":"source","obj":"week10"},{"subj":"T37","pred":"source","obj":"week10"},{"subj":"T38","pred":"source","obj":"week10"},{"subj":"T41","pred":"source","obj":"week10"},{"subj":"T44","pred":"source","obj":"week10"},{"subj":"T40","pred":"source","obj":"week10"},{"subj":"T42","pred":"source","obj":"week10"},{"subj":"T43","pred":"source","obj":"week10"},{"subj":"T46","pred":"source","obj":"week10"},{"subj":"T49","pred":"source","obj":"week10"},{"subj":"T45","pred":"source","obj":"week10"},{"subj":"T47","pred":"source","obj":"week10"},{"subj":"T48","pred":"source","obj":"week10"},{"subj":"T50","pred":"source","obj":"week10"},{"subj":"T51","pred":"source","obj":"week10"},{"subj":"T52","pred":"source","obj":"week10"},{"subj":"T53","pred":"source","obj":"week10"},{"subj":"T55","pred":"source","obj":"week10"},{"subj":"T58","pred":"source","obj":"week10"},{"subj":"T54","pred":"source","obj":"week10"},{"subj":"T56","pred":"source","obj":"week10"},{"subj":"T57","pred":"source","obj":"week10"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"week10","color":"#ec93d3","default":true}]}]}}