{"id":"https://openalex.org/W2104724027","doi":"https://doi.org/10.1093/bioinformatics/btv118","title":"Guidance for RNA-seq co-expression network construction and analysis: safety in numbers","display_name":"Guidance for RNA-seq co-expression network construction and analysis: safety in numbers","publication_year":2015,"publication_date":"2015-02-26","ids":{"openalex":"https://openalex.org/W2104724027","doi":"https://doi.org/10.1093/bioinformatics/btv118","mag":"2104724027","pmid":"https://pubmed.ncbi.nlm.nih.gov/25717192"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv118","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv118","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/13/2123/17122526/btv118.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/13/2123/17122526/btv118.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091633064","display_name":"Sara Ballouz","orcid":"https://orcid.org/0000-0003-4701-3020"},"institutions":[{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"S. Ballouz","raw_affiliation_strings":["Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 500 Sunnyside Boulevard Woodbury, NY 11797, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 500 Sunnyside Boulevard Woodbury, NY 11797, USA","institution_ids":["https://openalex.org/I2750212522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034038625","display_name":"Wim Verleyen","orcid":null},"institutions":[{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"W. Verleyen","raw_affiliation_strings":["Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 500 Sunnyside Boulevard Woodbury, NY 11797, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 500 Sunnyside Boulevard Woodbury, NY 11797, USA","institution_ids":["https://openalex.org/I2750212522"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021003479","display_name":"Jesse Gillis","orcid":"https://orcid.org/0000-0002-0936-9774"},"institutions":[{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"J. Gillis","raw_affiliation_strings":["Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 500 Sunnyside Boulevard Woodbury, NY 11797, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 500 Sunnyside Boulevard Woodbury, NY 11797, USA","institution_ids":["https://openalex.org/I2750212522"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5021003479","https://openalex.org/A5091633064"],"corresponding_institution_ids":["https://openalex.org/I2750212522"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":11.6755,"has_fulltext":false,"cited_by_count":239,"citation_normalized_percentile":{"value":0.99048155,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"31","issue":"13","first_page":"2123","last_page":"2130"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.867900013923645,"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":0.867900013923645,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.06639999896287918,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.00860000029206276,"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/rna-seq","display_name":"RNA-Seq","score":0.6681018471717834},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.6542788743972778},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.6244131922721863},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.6122215986251831},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5661986470222473},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4822691082954407},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4814431071281433},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.416428804397583},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39823615550994873},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.367716521024704},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.31380775570869446},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.29013556241989136}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.6681018471717834},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.6542788743972778},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.6244131922721863},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6122215986251831},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5661986470222473},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4822691082954407},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4814431071281433},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.416428804397583},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39823615550994873},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.367716521024704},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31380775570869446},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.29013556241989136},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btv118","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv118","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/13/2123/17122526/btv118.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25717192","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25717192","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:repository.cshl.edu:31255","is_oa":false,"landing_page_url":"https://repository.cshl.edu/id/eprint/31255/","pdf_url":null,"source":{"id":"https://openalex.org/S4306402288","display_name":"Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Paper"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:31/13/2123","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/13/2123","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv118","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv118","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/13/2123/17122526/btv118.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.49000000953674316}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W1777871578","https://openalex.org/W1995070233","https://openalex.org/W1995647101","https://openalex.org/W1996984681","https://openalex.org/W1999574084","https://openalex.org/W2028133290","https://openalex.org/W2030677229","https://openalex.org/W2033579591","https://openalex.org/W2034784092","https://openalex.org/W2044525257","https://openalex.org/W2060705109","https://openalex.org/W2064397275","https://openalex.org/W2071598557","https://openalex.org/W2081098333","https://openalex.org/W2091825929","https://openalex.org/W2095932050","https://openalex.org/W2096465161","https://openalex.org/W2100239923","https://openalex.org/W2101986518","https://openalex.org/W2103017472","https://openalex.org/W2105187843","https://openalex.org/W2106142493","https://openalex.org/W2116041602","https://openalex.org/W2118585731","https://openalex.org/W2124649441","https://openalex.org/W2127372456","https://openalex.org/W2128962304","https://openalex.org/W2138453085","https://openalex.org/W2141458291","https://openalex.org/W2147461734","https://openalex.org/W2148606196","https://openalex.org/W2150429594","https://openalex.org/W2150926065","https://openalex.org/W2154053567","https://openalex.org/W2154431984","https://openalex.org/W2158261276","https://openalex.org/W2159482845","https://openalex.org/W2160218441","https://openalex.org/W2163296115","https://openalex.org/W2170551349","https://openalex.org/W2770983033","https://openalex.org/W2911964244","https://openalex.org/W3009009611","https://openalex.org/W3099289621","https://openalex.org/W4294216483","https://openalex.org/W6677656871","https://openalex.org/W6683584131"],"related_works":["https://openalex.org/W4200033037","https://openalex.org/W106077234","https://openalex.org/W2041374557","https://openalex.org/W2081929287","https://openalex.org/W3002447856","https://openalex.org/W2144348650","https://openalex.org/W2132561013","https://openalex.org/W1994852842","https://openalex.org/W4246178523","https://openalex.org/W1902990570"],"abstract_inverted_index":{"MOTIVATION:":[0],"RNA-seq":[1,19,36,42,130],"co-expression":[2,31,37,57,133],"analysis":[3],"is":[4,105],"in":[5,30,48,111,134,149],"its":[6],"infancy":[7],"and":[8,28,131,169],"reasonable":[9],"practices":[10],"remain":[11],"poorly":[12],"defined.":[13],"We":[14,34,123],"assessed":[15,52],"a":[16,45,125],"variety":[17],"of":[18,56,102,115,137,152],"expression":[20,153],"data":[21,38,171],"to":[22,58,65,108,119,147],"determine":[23],"factors":[24],"affecting":[25],"functional":[26],"connectivity":[27],"topology":[29],"networks.":[32],"RESULTS:":[33],"examine":[35],"generated":[39],"from":[40,143],"1970":[41],"samples":[43,74,116],"using":[44],"Guilt-By-Association":[46],"framework,":[47],"which":[49],"genes":[50,142],"are":[51,117,165,172],"for":[53],"the":[54,83,92,98,135,150],"tendency":[55],"reflect":[59],"shared":[60],"function.":[61],"Minimal":[62],"experimental":[63],"criteria":[64],"obtain":[66,120],"performance":[67,89],"on":[68,100],"par":[69],"with":[70,75],"microarrays":[71],"were":[72],">20":[73],"read":[76],"depth":[77],">10":[78],"M":[79],"per":[80],"sample.":[81],"While":[82],"aggregate":[84],"network":[85,145],"constructed":[86],"shows":[87],"good":[88],"(area":[90],"under":[91],"receiver":[93],"operator":[94],"characteristic":[95],"curve":[96],"\u223c0.71),":[97],"dependency":[99],"number":[101],"experiments":[103],"used":[104],"nearly":[106],"identical":[107],"that":[109],"present":[110],"microarrays,":[112],"suggesting":[113],"thousands":[114],"required":[118],"'gold-standard'":[121],"co-expression.":[122],"find":[124],"major":[126],"topological":[127],"difference":[128],"between":[129,140],"microarray":[132],"form":[136],"low":[138],"overlaps":[139],"hub-like":[141],"each":[144,156],"due":[146],"changes":[148],"correlation":[151],"noise":[154],"within":[155],"technology.":[157],"CONTACT:":[158],"jgillis@cshl.edu":[159],"or":[160],"sballouz@cshl.edu":[161],"SUPPLEMENTARY":[162],"INFORMATION:":[163],"Networks":[164],"available":[166,173],"at:":[167],"http://gillislab.labsites.cshl.edu/supplements/rna-seq-networks/":[168],"supplementary":[170],"at":[174],"Bioinformatics":[175],"online.":[176]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":19},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":23},{"year":2022,"cited_by_count":15},{"year":2021,"cited_by_count":36},{"year":2020,"cited_by_count":28},{"year":2019,"cited_by_count":23},{"year":2018,"cited_by_count":23},{"year":2017,"cited_by_count":26},{"year":2016,"cited_by_count":23},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":1}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}