{"id":"https://openalex.org/W2062422541","doi":"https://doi.org/10.1186/1471-2105-10-170","title":"A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling","display_name":"A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling","publication_year":2009,"publication_date":"2009-06-06","ids":{"openalex":"https://openalex.org/W2062422541","doi":"https://doi.org/10.1186/1471-2105-10-170","mag":"2062422541","pmid":"https://pubmed.ncbi.nlm.nih.gov/19500384"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-170","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-170","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-170","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-170","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050097835","display_name":"Daniel Guariz Pinheiro","orcid":"https://orcid.org/0000-0001-7062-5936"},"institutions":[{"id":"https://openalex.org/I1331278255","display_name":"Universidade de Ribeir\u00e3o Preto","ror":"https://ror.org/00ey54k21","country_code":"BR","type":"education","lineage":["https://openalex.org/I1331278255"]},{"id":"https://openalex.org/I17974374","display_name":"Universidade de S\u00e3o Paulo","ror":"https://ror.org/036rp1748","country_code":"BR","type":"education","lineage":["https://openalex.org/I17974374"]},{"id":"https://openalex.org/I4210140912","display_name":"Funda\u00e7\u00e3o Hemopa","ror":"https://ror.org/04e080j72","country_code":"BR","type":"nonprofit","lineage":["https://openalex.org/I4210140912"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Daniel G Pinheiro","raw_affiliation_strings":["Departamento de Gen\u00e9tica, Faculdade de Medicina de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Preto, SP, Brazil. dgpinheiro@usp.br","Centro de Terapia Celular, Hemocentro de Ribeir\u00e3o Preto, Ribeir\u00e3o Preto, Brazil","Departamento de Gen\u00e9tica, Faculdade de Medicina de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Preto, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Gen\u00e9tica, Faculdade de Medicina de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Preto, SP, Brazil. dgpinheiro@usp.br","institution_ids":["https://openalex.org/I1331278255"]},{"raw_affiliation_string":"Centro de Terapia Celular, Hemocentro de Ribeir\u00e3o Preto, Ribeir\u00e3o Preto, Brazil","institution_ids":["https://openalex.org/I4210140912"]},{"raw_affiliation_string":"Departamento de Gen\u00e9tica, Faculdade de Medicina de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Preto, Brazil","institution_ids":["https://openalex.org/I1331278255","https://openalex.org/I17974374"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067274615","display_name":"Pedro A. F. Galante","orcid":"https://orcid.org/0000-0002-4820-4155"},"institutions":[{"id":"https://openalex.org/I1283280774","display_name":"Brigham and Women's Hospital","ror":"https://ror.org/04b6nzv94","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1283280774","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I196064397","display_name":"Ludwig Cancer Research","ror":"https://ror.org/05923xh51","country_code":"BE","type":"nonprofit","lineage":["https://openalex.org/I196064397","https://openalex.org/I4210150094"]},{"id":"https://openalex.org/I4210130541","display_name":"Instituto Paulo Gontijo","ror":"https://ror.org/03h8wyx14","country_code":"BR","type":"nonprofit","lineage":["https://openalex.org/I4210130541"]},{"id":"https://openalex.org/I4210143601","display_name":"Decision Systems (United States)","ror":"https://ror.org/0434dpa13","country_code":"US","type":"company","lineage":["https://openalex.org/I4210143601"]}],"countries":["BE","BR","US"],"is_corresponding":false,"raw_author_name":"Pedro AF Galante","raw_affiliation_strings":["Decision Systems Group, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA","Ludwig Institute for Cancer Research, So Paulo, SP, Brazil and","Decision Systems Group, Brigham and Women's Hospital, Harvard Medical School, Boston, USA","Ludwig Institute for Cancer Research, S\u00e3o Paulo, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Decision Systems Group, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I1283280774","https://openalex.org/I4210143601"]},{"raw_affiliation_string":"Ludwig Institute for Cancer Research, So Paulo, SP, Brazil and","institution_ids":["https://openalex.org/I196064397"]},{"raw_affiliation_string":"Decision Systems Group, Brigham and Women's Hospital, Harvard Medical School, Boston, USA","institution_ids":["https://openalex.org/I1283280774","https://openalex.org/I4210143601"]},{"raw_affiliation_string":"Ludwig Institute for Cancer Research, S\u00e3o Paulo, Brazil","institution_ids":["https://openalex.org/I4210130541"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035667949","display_name":"Sandro J. de Souza","orcid":"https://orcid.org/0000-0002-1012-3237"},"institutions":[{"id":"https://openalex.org/I4210130541","display_name":"Instituto Paulo Gontijo","ror":"https://ror.org/03h8wyx14","country_code":"BR","type":"nonprofit","lineage":["https://openalex.org/I4210130541"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Sandro J de Souza","raw_affiliation_strings":["Ludwig Institute for Cancer Research, S\u00e3o Paulo, SP, Brazil","Ludwig Institute for Cancer Research, S\u00e3o Paulo, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ludwig Institute for Cancer Research, S\u00e3o Paulo, SP, Brazil","institution_ids":["https://openalex.org/I4210130541"]},{"raw_affiliation_string":"Ludwig Institute for Cancer Research, S\u00e3o Paulo, Brazil","institution_ids":["https://openalex.org/I4210130541"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010187682","display_name":"Marco A. Zago","orcid":"https://orcid.org/0000-0002-2840-0650"},"institutions":[{"id":"https://openalex.org/I1331278255","display_name":"Universidade de Ribeir\u00e3o Preto","ror":"https://ror.org/00ey54k21","country_code":"BR","type":"education","lineage":["https://openalex.org/I1331278255"]},{"id":"https://openalex.org/I17974374","display_name":"Universidade de S\u00e3o Paulo","ror":"https://ror.org/036rp1748","country_code":"BR","type":"education","lineage":["https://openalex.org/I17974374"]},{"id":"https://openalex.org/I4210140912","display_name":"Funda\u00e7\u00e3o Hemopa","ror":"https://ror.org/04e080j72","country_code":"BR","type":"nonprofit","lineage":["https://openalex.org/I4210140912"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Marco A Zago","raw_affiliation_strings":["Centro de Terapia Celular, Hemocentro de Ribeir\u00e3o Preto, Ribeir\u00e3o Preto, SP, Brazil","Departamento de Cl\u00ednica M\u00e9dica, Faculdade de Medicina de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Preto, SP, Brazil","Centro de Terapia Celular, Hemocentro de Ribeir\u00e3o Preto, Ribeir\u00e3o Preto, Brazil","Departamento de Cl\u00ednica M\u00e9dica, Faculdade de Medicina de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Preto, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro de Terapia Celular, Hemocentro de Ribeir\u00e3o Preto, Ribeir\u00e3o Preto, SP, Brazil","institution_ids":["https://openalex.org/I1331278255","https://openalex.org/I4210140912"]},{"raw_affiliation_string":"Departamento de Cl\u00ednica M\u00e9dica, Faculdade de Medicina de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Preto, SP, Brazil","institution_ids":["https://openalex.org/I1331278255","https://openalex.org/I17974374"]},{"raw_affiliation_string":"Centro de Terapia Celular, Hemocentro de Ribeir\u00e3o Preto, Ribeir\u00e3o Preto, Brazil","institution_ids":["https://openalex.org/I4210140912"]},{"raw_affiliation_string":"Departamento de Cl\u00ednica M\u00e9dica, Faculdade de Medicina de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Preto, Brazil","institution_ids":["https://openalex.org/I1331278255","https://openalex.org/I17974374"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072335040","display_name":"Wilson A. Silva","orcid":"https://orcid.org/0000-0001-9364-2886"},"institutions":[{"id":"https://openalex.org/I1331278255","display_name":"Universidade de Ribeir\u00e3o Preto","ror":"https://ror.org/00ey54k21","country_code":"BR","type":"education","lineage":["https://openalex.org/I1331278255"]},{"id":"https://openalex.org/I17974374","display_name":"Universidade de S\u00e3o Paulo","ror":"https://ror.org/036rp1748","country_code":"BR","type":"education","lineage":["https://openalex.org/I17974374"]},{"id":"https://openalex.org/I4210140912","display_name":"Funda\u00e7\u00e3o Hemopa","ror":"https://ror.org/04e080j72","country_code":"BR","type":"nonprofit","lineage":["https://openalex.org/I4210140912"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Wilson A Silva","raw_affiliation_strings":["Centro de Terapia Celular, Hemocentro de Ribeir\u00e3o Preto, Ribeir\u00e3o Preto, SP, Brazil","Departamento de Gen\u00e9tica, Faculdade de Medicina de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Preto, SP, Brazil","Centro de Terapia Celular, Hemocentro de Ribeir\u00e3o Preto, Ribeir\u00e3o Preto, Brazil","Departamento de Gen\u00e9tica, Faculdade de Medicina de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Preto, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro de Terapia Celular, Hemocentro de Ribeir\u00e3o Preto, Ribeir\u00e3o Preto, SP, Brazil","institution_ids":["https://openalex.org/I1331278255","https://openalex.org/I4210140912"]},{"raw_affiliation_string":"Departamento de Gen\u00e9tica, Faculdade de Medicina de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Preto, SP, Brazil","institution_ids":["https://openalex.org/I1331278255","https://openalex.org/I17974374"]},{"raw_affiliation_string":"Centro de Terapia Celular, Hemocentro de Ribeir\u00e3o Preto, Ribeir\u00e3o Preto, Brazil","institution_ids":["https://openalex.org/I4210140912"]},{"raw_affiliation_string":"Departamento de Gen\u00e9tica, Faculdade de Medicina de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Preto, Brazil","institution_ids":["https://openalex.org/I1331278255","https://openalex.org/I17974374"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5050097835","https://openalex.org/A5072335040"],"corresponding_institution_ids":["https://openalex.org/I1331278255","https://openalex.org/I17974374","https://openalex.org/I4210140912"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.126,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.5205433,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"10","issue":"1","first_page":"170","last_page":"170"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9269000291824341,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9269000291824341,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.018300000578165054,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.011599999852478504,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5851927995681763},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.569381058216095},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.5507708787918091},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5460255146026611},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.5247369408607483},{"id":"https://openalex.org/keywords/serial-analysis-of-gene-expression","display_name":"Serial analysis of gene expression","score":0.5182830691337585},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.49133196473121643},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4780716896057129},{"id":"https://openalex.org/keywords/sequence-analysis","display_name":"Sequence analysis","score":0.4354243874549866},{"id":"https://openalex.org/keywords/hierarchical-clustering","display_name":"Hierarchical clustering","score":0.41432690620422363},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.413818359375},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3898218870162964},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.30725085735321045},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.28550732135772705},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15396809577941895}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5851927995681763},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.569381058216095},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.5507708787918091},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5460255146026611},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.5247369408607483},{"id":"https://openalex.org/C20032557","wikidata":"https://www.wikidata.org/wiki/Q286721","display_name":"Serial analysis of gene expression","level":5,"score":0.5182830691337585},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.49133196473121643},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4780716896057129},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.4354243874549866},{"id":"https://openalex.org/C92835128","wikidata":"https://www.wikidata.org/wiki/Q1277447","display_name":"Hierarchical clustering","level":3,"score":0.41432690620422363},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.413818359375},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3898218870162964},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.30725085735321045},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.28550732135772705},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15396809577941895},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003110","descriptor_name":"Colonic Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003110","descriptor_name":"Colonic Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003110","descriptor_name":"Colonic Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003110","descriptor_name":"Colonic Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003110","descriptor_name":"Colonic Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003110","descriptor_name":"Colonic Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-10-170","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-170","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-170","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19500384","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19500384","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:www.producao.usp.br:BDPI/15299","is_oa":false,"landing_page_url":"http://producao.usp.br/handle/BDPI/15299","pdf_url":null,"source":{"id":"https://openalex.org/S4306402433","display_name":"Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"reponame:Reposit\u00f3rio Institucional da USP","raw_type":"publishedVersion"},{"id":"pmh:oai:www.producao.usp.br:BDPI/47438","is_oa":false,"landing_page_url":"http://doi.org/10.1186/1471-2105-10-170","pdf_url":null,"source":{"id":"https://openalex.org/S4306402433","display_name":"Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"reponame:Reposit\u00f3rio Institucional da USP","raw_type":"publishedVersion"},{"id":"pmh:oai:doaj.org/article:bd3b4d9514534721887c847850db0476","is_oa":false,"landing_page_url":"https://doaj.org/article/bd3b4d9514534721887c847850db0476","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 10, Iss 1, p 170 (2009)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2701951","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2701951","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-10-170","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-170","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-170","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","score":0.49000000953674316,"id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G658818914","display_name":null,"funder_award_id":"D43 TW007015","funder_id":"https://openalex.org/F4320337356","funder_display_name":"Fogarty International Center"},{"id":"https://openalex.org/G660123638","display_name":null,"funder_award_id":"5D43TW007015-02","funder_id":"https://openalex.org/F4320337356","funder_display_name":"Fogarty International Center"}],"funders":[{"id":"https://openalex.org/F4320320997","display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","ror":"https://ror.org/02ddkpn78"},{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337356","display_name":"Fogarty International Center","ror":"https://ror.org/02xey9a22"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2062422541.pdf","grobid_xml":"https://content.openalex.org/works/W2062422541.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W938539187","https://openalex.org/W1518838580","https://openalex.org/W1966366355","https://openalex.org/W1984539096","https://openalex.org/W2002982210","https://openalex.org/W2006074076","https://openalex.org/W2010888033","https://openalex.org/W2015255374","https://openalex.org/W2050163545","https://openalex.org/W2054804828","https://openalex.org/W2059797405","https://openalex.org/W2063001117","https://openalex.org/W2073883677","https://openalex.org/W2097794038","https://openalex.org/W2101800045","https://openalex.org/W2107363136","https://openalex.org/W2122872071","https://openalex.org/W2125558666","https://openalex.org/W2128114769","https://openalex.org/W2138586080","https://openalex.org/W2140897574","https://openalex.org/W2142187732","https://openalex.org/W2150815784","https://openalex.org/W2150926065","https://openalex.org/W2151238743","https://openalex.org/W2153562609","https://openalex.org/W2161260747","https://openalex.org/W2164527179","https://openalex.org/W2165270659","https://openalex.org/W2166359901","https://openalex.org/W2172052253","https://openalex.org/W4213387068","https://openalex.org/W4230607658","https://openalex.org/W4249877820"],"related_works":["https://openalex.org/W1982027298","https://openalex.org/W2069695727","https://openalex.org/W1974145978","https://openalex.org/W1996185163","https://openalex.org/W4233500668","https://openalex.org/W2084813257","https://openalex.org/W2055306123","https://openalex.org/W2771731734","https://openalex.org/W2045929470","https://openalex.org/W2320712057"],"abstract_inverted_index":{"BACKGROUND:":[0],"High-throughput":[1],"molecular":[2],"approaches":[3],"for":[4,82,117,199],"gene":[5,119,203],"expression":[6,57,120,204],"profiling,":[7],"such":[8],"as":[9],"Serial":[10],"Analysis":[11],"of":[12,32,38,41,100,112,153,201],"Gene":[13],"Expression":[14],"(SAGE),":[15],"Massively":[16],"Parallel":[17],"Signature":[18],"Sequencing":[19],"(MPSS)":[20],"or":[21],"Sequencing-by-Synthesis":[22],"(SBS)":[23],"represent":[24],"powerful":[25],"techniques":[26,47],"that":[27,168],"provide":[28,165],"global":[29,202],"transcription":[30],"profiles":[31,58],"different":[33],"cell":[34],"types":[35],"through":[36,97],"sequencing":[37],"short":[39],"fragments":[40],"transcripts,":[42],"denominated":[43],"sequence":[44],"tags.":[45],"These":[46,183],"have":[48],"improved":[49],"our":[50],"understanding":[51],"about":[52],"the":[53,110,150,186,226],"relationships":[54],"between":[55],"these":[56,160],"and":[59,138,219],"cellular":[60],"phenotypes.":[61],"Despite":[62],"this,":[63],"more":[64,115,174,191],"reliable":[65,116,192],"datasets":[66,220],"are":[67],"still":[68],"necessary.":[69],"In":[70,132],"this":[71],"work,":[72],"we":[73],"present":[74],"a":[75,98,104,128,141,196],"web-based":[76],"tool":[77],"named":[78],"S3T:":[79],"Score":[80],"System":[81],"Sequence":[83],"Tags,":[84],"to":[85,127,134,172,189],"index":[86],"sequenced":[87],"tags":[88],"in":[89,147,155],"accordance":[90],"with":[91,209],"their":[92],"reliability.":[93],"This":[94,123,194],"is":[95,170,195,211],"made":[96],"series":[99],"evaluations":[101],"based":[102],"on":[103],"defined":[105],"rule":[106],"set.":[107],"S3T":[108,179,210,216],"allows":[109],"identification/selection":[111],"tags,":[113],"considered":[114],"further":[118],"analysis.":[121],"RESULTS:":[122],"methodology":[124],"was":[125,145],"applied":[126],"public":[129],"SAGE":[130],"dataset.":[131],"order":[133],"compare":[135],"data":[136],"before":[137],"after":[139,177],"filtering,":[140],"hierarchical":[142],"clustering":[143],"analysis":[144,208],"performed":[146],"samples":[148],"from":[149,225],"same":[151],"type":[152],"tissue,":[154],"distinct":[156],"biological":[157],"conditions,":[158],"using":[159,178],"two":[161],"datasets.":[162],"Our":[163],"results":[164,184],"evidences":[166],"suggesting":[167],"it":[169],"possible":[171],"find":[173],"congruous":[175],"clusters":[176],"scoring":[180],"system.":[181],"CONCLUSION:":[182],"substantiate":[185],"proposed":[187],"application":[188],"generate":[190],"data.":[193],"significant":[197],"contribution":[198],"determination":[200],"profiles.":[205],"The":[206],"library":[207],"freely":[212],"available":[213],"at":[214],"http://gdm.fmrp.usp.br/s3t/.":[215],"source":[217],"code":[218],"can":[221],"also":[222],"be":[223],"downloaded":[224],"aforementioned":[227],"website.":[228]},"counts_by_year":[{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
