{"id":"https://openalex.org/W2080549727","doi":"https://doi.org/10.1186/1752-0509-5-108","title":"An organogenesis network-based comparative transcriptome analysis for understanding early human development in vivo and in vitro","display_name":"An organogenesis network-based comparative transcriptome analysis for understanding early human development in vivo and in vitro","publication_year":2011,"publication_date":"2011-07-06","ids":{"openalex":"https://openalex.org/W2080549727","doi":"https://doi.org/10.1186/1752-0509-5-108","mag":"2080549727","pmid":"https://pubmed.ncbi.nlm.nih.gov/21733158"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-5-108","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-5-108","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-5-108","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-5-108","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015356302","display_name":"Hai Fang","orcid":"https://orcid.org/0000-0003-3961-8572"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I2801556517","display_name":"Ruijin Hospital","ror":"https://ror.org/01hv94n30","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2801556517"]},{"id":"https://openalex.org/I36234482","display_name":"University of Bristol","ror":"https://ror.org/0524sp257","country_code":"GB","type":"education","lineage":["https://openalex.org/I36234482"]},{"id":"https://openalex.org/I4210106477","display_name":"Shanghai Institutes for Biological Sciences","ror":"https://ror.org/011rf9d86","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210106477"]}],"countries":["CN","GB"],"is_corresponding":false,"raw_author_name":"Hai Fang","raw_affiliation_strings":["State Key Laboratory of Medical Genomics, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Ruijin Rd, II, Shanghai 200025, China","Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and SJTU-SM, 225 South Chongqing Road, Shanghai, 200025, China","State Key Laboratory of Medical Genomics, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine (SJTU-SM), Ruijin Rd. II, Shanghai, 200025, China","Department of Computer Science, University of Bristol, Woodland Road, Bristol, BS8 1UB, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Medical Genomics, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Ruijin Rd, II, Shanghai 200025, China","institution_ids":["https://openalex.org/I2801556517"]},{"raw_affiliation_string":"Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and SJTU-SM, 225 South Chongqing Road, Shanghai, 200025, China","institution_ids":["https://openalex.org/I4210106477","https://openalex.org/I19820366"]},{"raw_affiliation_string":"State Key Laboratory of Medical Genomics, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine (SJTU-SM), Ruijin Rd. II, Shanghai, 200025, China","institution_ids":["https://openalex.org/I2801556517","https://openalex.org/I183067930"]},{"raw_affiliation_string":"Department of Computer Science, University of Bristol, Woodland Road, Bristol, BS8 1UB, UK","institution_ids":["https://openalex.org/I36234482"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049511371","display_name":"Wen Jin","orcid":"https://orcid.org/0000-0002-5084-2076"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I2801556517","display_name":"Ruijin Hospital","ror":"https://ror.org/01hv94n30","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2801556517"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wen Jin","raw_affiliation_strings":["State Key Laboratory of Medical Genomics, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine (SJTU-SM), Ruijin Rd. II, Shanghai, 200025, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Medical Genomics, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine (SJTU-SM), Ruijin Rd. II, Shanghai, 200025, China","institution_ids":["https://openalex.org/I2801556517","https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044641119","display_name":"Ying Yang","orcid":"https://orcid.org/0000-0002-8104-5985"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210106477","display_name":"Shanghai Institutes for Biological Sciences","ror":"https://ror.org/011rf9d86","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210106477"]},{"id":"https://openalex.org/I4210156766","display_name":"Shanghai Cell Therapy Research Institute","ror":"https://ror.org/044ef5h76","country_code":"CN","type":"nonprofit","lineage":["https://openalex.org/I4210156766"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ying Yang","raw_affiliation_strings":["Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and SJTU-SM, 225 South Chongqing Road, Shanghai, 200025, China","Shanghai Stem Cell Institute, 225 South Chongqing Road, Shanghai, 200025, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and SJTU-SM, 225 South Chongqing Road, Shanghai, 200025, China","institution_ids":["https://openalex.org/I4210106477","https://openalex.org/I19820366"]},{"raw_affiliation_string":"Shanghai Stem Cell Institute, 225 South Chongqing Road, Shanghai, 200025, China","institution_ids":["https://openalex.org/I4210156766"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108578677","display_name":"Ying Jin","orcid":"https://orcid.org/0000-0003-0070-2048"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210106477","display_name":"Shanghai Institutes for Biological Sciences","ror":"https://ror.org/011rf9d86","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210106477"]},{"id":"https://openalex.org/I4210156766","display_name":"Shanghai Cell Therapy Research Institute","ror":"https://ror.org/044ef5h76","country_code":"CN","type":"nonprofit","lineage":["https://openalex.org/I4210156766"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ying Jin","raw_affiliation_strings":["Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and SJTU-SM, 225 South Chongqing Road, Shanghai, 200025, China","Shanghai Stem Cell Institute, 225 South Chongqing Road, Shanghai, 200025, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and SJTU-SM, 225 South Chongqing Road, Shanghai, 200025, China","institution_ids":["https://openalex.org/I4210106477","https://openalex.org/I19820366"]},{"raw_affiliation_string":"Shanghai Stem Cell Institute, 225 South Chongqing Road, Shanghai, 200025, China","institution_ids":["https://openalex.org/I4210156766"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100329253","display_name":"Ji Zhang","orcid":"https://orcid.org/0000-0001-9649-9608"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I2801556517","display_name":"Ruijin Hospital","ror":"https://ror.org/01hv94n30","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2801556517"]},{"id":"https://openalex.org/I4210106477","display_name":"Shanghai Institutes for Biological Sciences","ror":"https://ror.org/011rf9d86","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210106477"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Ji Zhang","raw_affiliation_strings":["Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and SJTU-SM, 225 South Chongqing Road, Shanghai, 200025, China","State Key Laboratory of Medical Genomics, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine (SJTU-SM), Ruijin Rd. II, Shanghai, 200025, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and SJTU-SM, 225 South Chongqing Road, Shanghai, 200025, China","institution_ids":["https://openalex.org/I4210106477","https://openalex.org/I19820366"]},{"raw_affiliation_string":"State Key Laboratory of Medical Genomics, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine (SJTU-SM), Ruijin Rd. II, Shanghai, 200025, China","institution_ids":["https://openalex.org/I2801556517","https://openalex.org/I183067930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103260031","display_name":"Kankan Wang","orcid":"https://orcid.org/0000-0001-7198-2134"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I2801556517","display_name":"Ruijin Hospital","ror":"https://ror.org/01hv94n30","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2801556517"]},{"id":"https://openalex.org/I4210106477","display_name":"Shanghai Institutes for Biological Sciences","ror":"https://ror.org/011rf9d86","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210106477"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Kankan Wang","raw_affiliation_strings":["Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and SJTU-SM, 225 South Chongqing Road, Shanghai, 200025, China","State Key Laboratory of Medical Genomics, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine (SJTU-SM), Ruijin Rd. II, Shanghai, 200025, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and SJTU-SM, 225 South Chongqing Road, Shanghai, 200025, China","institution_ids":["https://openalex.org/I4210106477","https://openalex.org/I19820366"]},{"raw_affiliation_string":"State Key Laboratory of Medical Genomics, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine (SJTU-SM), Ruijin Rd. II, Shanghai, 200025, China","institution_ids":["https://openalex.org/I2801556517","https://openalex.org/I183067930"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5100329253","https://openalex.org/A5103260031"],"corresponding_institution_ids":["https://openalex.org/I183067930","https://openalex.org/I19820366","https://openalex.org/I2801556517","https://openalex.org/I4210106477"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.11553237,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"5","issue":"1","first_page":"108","last_page":"108"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.660099983215332,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.660099983215332,"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/T10505","display_name":"Pluripotent Stem Cells Research","score":0.211899995803833,"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/T10885","display_name":"Gene expression and cancer classification","score":0.026799999177455902,"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/organogenesis","display_name":"Organogenesis","score":0.7882471680641174},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7817975878715515},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.7250885367393494},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5730982422828674},{"id":"https://openalex.org/keywords/induced-pluripotent-stem-cell","display_name":"Induced pluripotent stem cell","score":0.5720612406730652},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5607929825782776},{"id":"https://openalex.org/keywords/cellular-differentiation","display_name":"Cellular differentiation","score":0.5524467825889587},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5398058891296387},{"id":"https://openalex.org/keywords/embryoid-body","display_name":"Embryoid body","score":0.5384502410888672},{"id":"https://openalex.org/keywords/stem-cell","display_name":"Stem cell","score":0.46322134137153625},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.459555983543396},{"id":"https://openalex.org/keywords/developmental-biology","display_name":"Developmental biology","score":0.4582156538963318},{"id":"https://openalex.org/keywords/embryonic-stem-cell","display_name":"Embryonic stem cell","score":0.36076194047927856},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.34842967987060547},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2992745637893677},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21909379959106445},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19330528378486633}],"concepts":[{"id":"https://openalex.org/C30503417","wikidata":"https://www.wikidata.org/wiki/Q958938","display_name":"Organogenesis","level":3,"score":0.7882471680641174},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7817975878715515},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.7250885367393494},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5730982422828674},{"id":"https://openalex.org/C107459253","wikidata":"https://www.wikidata.org/wiki/Q674925","display_name":"Induced pluripotent stem cell","level":4,"score":0.5720612406730652},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5607929825782776},{"id":"https://openalex.org/C148738053","wikidata":"https://www.wikidata.org/wiki/Q210861","display_name":"Cellular differentiation","level":3,"score":0.5524467825889587},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5398058891296387},{"id":"https://openalex.org/C143948831","wikidata":"https://www.wikidata.org/wiki/Q3384920","display_name":"Embryoid body","level":5,"score":0.5384502410888672},{"id":"https://openalex.org/C28328180","wikidata":"https://www.wikidata.org/wiki/Q48196","display_name":"Stem cell","level":2,"score":0.46322134137153625},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.459555983543396},{"id":"https://openalex.org/C183074962","wikidata":"https://www.wikidata.org/wiki/Q213713","display_name":"Developmental biology","level":2,"score":0.4582156538963318},{"id":"https://openalex.org/C145103041","wikidata":"https://www.wikidata.org/wiki/Q1151519","display_name":"Embryonic stem cell","level":3,"score":0.36076194047927856},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.34842967987060547},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2992745637893677},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21909379959106445},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19330528378486633},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","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":"D006803","descriptor_name":"Human Development","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006803","descriptor_name":"Human Development","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006803","descriptor_name":"Human Development","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018507","descriptor_name":"Gene Expression Regulation, Developmental","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018507","descriptor_name":"Gene Expression Regulation, Developmental","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018507","descriptor_name":"Gene Expression Regulation, Developmental","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"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":"D038081","descriptor_name":"Organogenesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D038081","descriptor_name":"Organogenesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D038081","descriptor_name":"Organogenesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D039904","descriptor_name":"Pluripotent Stem Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D039904","descriptor_name":"Pluripotent Stem Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D039904","descriptor_name":"Pluripotent Stem Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D058732","descriptor_name":"Embryoid Bodies","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D058732","descriptor_name":"Embryoid Bodies","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D058732","descriptor_name":"Embryoid Bodies","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D058732","descriptor_name":"Embryoid Bodies","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D058732","descriptor_name":"Embryoid Bodies","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D058732","descriptor_name":"Embryoid Bodies","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1752-0509-5-108","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-5-108","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-5-108","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},{"id":"pmid:21733158","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21733158","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 systems biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:c55b1bfb9f624362b4b2d7d141a77f1b","is_oa":false,"landing_page_url":"https://doaj.org/article/c55b1bfb9f624362b4b2d7d141a77f1b","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 Systems Biology, Vol 5, Iss 1, p 108 (2011)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3141417","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3141417","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 Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-5-108","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-5-108","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-5-108","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.5199999809265137}],"awards":[{"id":"https://openalex.org/G3034210637","display_name":null,"funder_award_id":"KSCX1-YW-22","funder_id":"https://openalex.org/F4320321133","funder_display_name":"Chinese Academy of Sciences"},{"id":"https://openalex.org/G3746065520","display_name":null,"funder_award_id":"KSCX1-YW-22-01","funder_id":"https://openalex.org/F4320321133","funder_display_name":"Chinese Academy of Sciences"},{"id":"https://openalex.org/G4886387037","display_name":null,"funder_award_id":"90919059","funder_id":"https://openalex.org/F4320321133","funder_display_name":"Chinese Academy of Sciences"}],"funders":[{"id":"https://openalex.org/F4320321133","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35"},{"id":"https://openalex.org/F4320321543","display_name":"China Postdoctoral Science Foundation","ror":"https://ror.org/0426zh255"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2080549727.pdf","grobid_xml":"https://content.openalex.org/works/W2080549727.grobid-xml"},"referenced_works_count":61,"referenced_works":["https://openalex.org/W1509900513","https://openalex.org/W1534454035","https://openalex.org/W1591423336","https://openalex.org/W1876024155","https://openalex.org/W1916533195","https://openalex.org/W1948275303","https://openalex.org/W1969202196","https://openalex.org/W1970779075","https://openalex.org/W1971445167","https://openalex.org/W1976386441","https://openalex.org/W1985397068","https://openalex.org/W1987774343","https://openalex.org/W2002179012","https://openalex.org/W2007674596","https://openalex.org/W2014426141","https://openalex.org/W2020999791","https://openalex.org/W2026034241","https://openalex.org/W2027703497","https://openalex.org/W2035530476","https://openalex.org/W2036956532","https://openalex.org/W2049598074","https://openalex.org/W2050570489","https://openalex.org/W2054340912","https://openalex.org/W2056827131","https://openalex.org/W2062533676","https://openalex.org/W2065751798","https://openalex.org/W2080343832","https://openalex.org/W2081098333","https://openalex.org/W2084487156","https://openalex.org/W2086943348","https://openalex.org/W2091015733","https://openalex.org/W2095151940","https://openalex.org/W2095180064","https://openalex.org/W2095436466","https://openalex.org/W2097698606","https://openalex.org/W2102545006","https://openalex.org/W2103486350","https://openalex.org/W2107575419","https://openalex.org/W2108794048","https://openalex.org/W2110065044","https://openalex.org/W2111198796","https://openalex.org/W2112811019","https://openalex.org/W2119854708","https://openalex.org/W2123280311","https://openalex.org/W2125987139","https://openalex.org/W2130410032","https://openalex.org/W2130687290","https://openalex.org/W2134582937","https://openalex.org/W2135805255","https://openalex.org/W2137531873","https://openalex.org/W2138977668","https://openalex.org/W2142046859","https://openalex.org/W2146767125","https://openalex.org/W2147714160","https://openalex.org/W2153156148","https://openalex.org/W2154222972","https://openalex.org/W2166468869","https://openalex.org/W2168546553","https://openalex.org/W2168755415","https://openalex.org/W2171860665","https://openalex.org/W2916288174"],"related_works":["https://openalex.org/W3130211295","https://openalex.org/W2069048331","https://openalex.org/W2038214754","https://openalex.org/W2322635330","https://openalex.org/W2949927938","https://openalex.org/W2029387041","https://openalex.org/W2135896045","https://openalex.org/W1973268559","https://openalex.org/W2117395648","https://openalex.org/W2884256268"],"abstract_inverted_index":{"BACKGROUND:":[0],"Integrated":[1],"networks":[2],"hold":[3],"great":[4],"promise":[5],"in":[6,70,73,185,209,241,263,271,303,313,326],"a":[7,12,24,91,118,139,177,222],"variety":[8,92],"of":[9,65,93,121,138,142,165,168,187,200,213,216,228,280,289],"contexts.":[10],"In":[11,191],"recent":[13],"study,":[14],"we":[15,81,112],"have":[16],"combined":[17],"expression":[18],"and":[19,39,72,99,106,153,232,257],"interaction":[20],"data":[21,89,335],"to":[22,46,61,206,267,269,301,323,346],"identify":[23],"putative":[25],"network":[26,55,98,347],"underlying":[27],"early":[28,66,130,233,307],"human":[29,67,131,308,329],"organogenesis":[30,309],"that":[31,173,180,260],"contains":[32],"two":[33,101,230,282],"modules,":[34],"the":[35,40,86,97,114,122,126,133,136,143,149,174,193,210,247,254,258,278,296,302],"stemness-relevant":[36],"module":[37,42],"(hStemModule)":[38],"differentiation-relevant":[41],"(hDiffModule).":[43],"However,":[44],"owing":[45],"its":[47,100],"hypothetical":[48],"nature,":[49],"it":[50],"remains":[51],"unclear":[52],"whether":[53],"this":[54,78],"allows":[56],"for":[57,158],"comparative":[58,318],"transcriptome":[59,88,319,334],"analysis":[60,320],"advance":[62],"our":[63],"understanding":[64],"development,":[68],"both":[69],"vivo":[71,272,304],"vitro.":[74],"RESULTS:":[75],"Based":[76],"on":[77],"integrated":[79],"network,":[80],"here":[82],"report":[83],"comparisons":[84,249,297],"with":[85],"context-dependent":[87],"from":[90],"sources.":[94],"By":[95],"viewing":[96],"modules":[102,231,283],"as":[103,117,240],"gene":[104,108],"sets":[105],"conducting":[107],"set":[109],"enrichment":[110],"analysis,":[111],"demonstrate":[113],"network's":[115],"utility":[116],"quantitative":[119],"monitor":[120],"stem":[123,144,189],"potential":[124,152,212],"versus":[125],"differentiation":[127,151,211,243,315],"potential.":[128,145,190],"During":[129],"organogenesis,":[132],"hStemModule":[134,175],"reflects":[135],"generality":[137],"gradual":[140],"loss":[141],"The":[146],"hDiffModule":[147,194],"indicates":[148],"stage-specific":[150],"is":[154,176,204],"therefore":[155],"not":[156],"suitable":[157],"depicting":[159],"an":[160,311,324,343],"extended":[161],"developmental":[162],"window.":[163],"Processing":[164],"cultured":[166,262],"cells":[167,199,215],"different":[169,182,201,217,290],"types":[170,184,202,288],"further":[171],"revealed":[172],"general":[178],"indicator":[179],"distinguishes":[181],"cell":[183,287],"terms":[186],"their":[188],"contrast,":[192],"cannot":[195],"distinguish":[196],"between":[197,226,253],"differentiated":[198],"but":[203],"able":[205],"predict":[207],"differences":[208,252],"pluripotent":[214,286],"origins.":[218],"We":[219,275],"also":[220],"observed":[221],"significant":[223],"positive":[224],"correlation":[225],"each":[227],"these":[229,281],"embryoid":[234],"bodies":[235],"(EBs),":[236],"which":[237],"are":[238,292,299,336],"used":[239],"vitro":[242,264,314],"models.":[244],"Despite":[245],"this,":[246],"network-oriented":[248],"showed":[250],"considerable":[251],"developing":[255],"embryos":[256,305],"EBs":[259],"were":[261],"over":[265],"time":[266],"try":[268],"mimic":[270],"processes.":[273],"CONCLUSIONS:":[274],"strongly":[276],"recommend":[277],"use":[279],"either":[284],"when":[285,295,332],"origins":[291],"involved":[293],"or":[294],"made":[298],"constrained":[300],"during":[306],"(and":[310],"equivalent":[312],"models).":[316],"Network-based":[317],"will":[321,341],"contribute":[322],"increase":[325],"knowledge":[327],"about":[328],"embryogenesis,":[330],"particularly":[331],"only":[333],"currently":[337],"available.":[338],"These":[339],"advances":[340],"add":[342],"extra":[344],"dimension":[345],"applications.":[348]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
