{"id":"https://openalex.org/W7202136014","doi":"https://doi.org/10.64898/2026.08.09.743737","title":"Sample-specific protein-protein interaction networks inferred from transcriptomics and proteomics show high similarities","display_name":"Sample-specific protein-protein interaction networks inferred from transcriptomics and proteomics show high similarities","publication_year":2026,"publication_date":"2026-08-10","ids":{"openalex":"https://openalex.org/W7202136014","doi":"https://doi.org/10.64898/2026.08.09.743737"},"language":"en","primary_location":{"id":"doi:10.64898/2026.08.09.743737","doi":"https://doi.org/10.64898/2026.08.09.743737","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.09.743737","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/10/2026.08.09.743737.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/10/2026.08.09.743737.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010327116","display_name":"Enik\u0151 Zakar\u2010Poly\u00e1k","orcid":"https://orcid.org/0000-0001-5655-4940","observed_orcids":["https://orcid.org/0000-0001-5655-4940"]},"institutions":[{"id":"https://openalex.org/I106118109","display_name":"E\u00f6tv\u00f6s Lor\u00e1nd University","ror":"https://ror.org/01jsq2704","country_code":"HU","type":"education","lineage":["https://openalex.org/I106118109"]},{"id":"https://openalex.org/I4210117195","display_name":"HUN-REN Institute for Computer Science and Control","ror":"https://ror.org/0249v7n71","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4210117195","https://openalex.org/I4387152226"]},{"id":"https://openalex.org/I4387152226","display_name":"Hungarian Research Network","ror":"https://ror.org/04w6pnc49","country_code":"HU","type":"other","lineage":["https://openalex.org/I4387152226"]}],"countries":["HU"],"is_corresponding":true,"raw_author_name":"Enik\u0151 Zakar-Poly\u00e1k","raw_affiliation_strings":["Doctoral School of Informatics, E\u00f6tv\u00f6s Lor\u00e1nd University, Budapest, Hungary","HUN-REN Institute for Computer Science and Control (SZTAKI), Budapest, Hungary","HUN-REN-SZTAKI-SU Rejuvenation Research Group, HUN-REN Office for Supported Research Groups (TKI), Hungarian Research Network (HUN-REN), Budapest, Hungary"],"raw_orcid":"https://orcid.org/0000-0001-5655-4940","affiliations":[{"raw_affiliation_string":"Doctoral School of Informatics, E\u00f6tv\u00f6s Lor\u00e1nd University, Budapest, Hungary","institution_ids":["https://openalex.org/I106118109"]},{"raw_affiliation_string":"HUN-REN Institute for Computer Science and Control (SZTAKI), Budapest, Hungary","institution_ids":["https://openalex.org/I4210117195"]},{"raw_affiliation_string":"HUN-REN-SZTAKI-SU Rejuvenation Research Group, HUN-REN Office for Supported Research Groups (TKI), Hungarian Research Network (HUN-REN), Budapest, Hungary","institution_ids":["https://openalex.org/I4210117195","https://openalex.org/I4387152226"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033755056","display_name":"Csaba Kerepesi","orcid":"https://orcid.org/0000-0001-9541-246X","observed_orcids":["https://orcid.org/0000-0001-9541-246X"]},"institutions":[{"id":"https://openalex.org/I4210117195","display_name":"HUN-REN Institute for Computer Science and Control","ror":"https://ror.org/0249v7n71","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4210117195","https://openalex.org/I4387152226"]},{"id":"https://openalex.org/I4387152226","display_name":"Hungarian Research Network","ror":"https://ror.org/04w6pnc49","country_code":"HU","type":"other","lineage":["https://openalex.org/I4387152226"]}],"countries":["HU"],"is_corresponding":true,"raw_author_name":"Csaba Kerepesi","raw_affiliation_strings":["HUN-REN Institute for Computer Science and Control (SZTAKI), Budapest, Hungary","HUN-REN-SZTAKI-SU Rejuvenation Research Group, HUN-REN Office for Supported Research Groups (TKI), Hungarian Research Network (HUN-REN), Budapest, Hungary"],"raw_orcid":"https://orcid.org/0000-0001-9541-246X","affiliations":[{"raw_affiliation_string":"HUN-REN Institute for Computer Science and Control (SZTAKI), Budapest, Hungary","institution_ids":["https://openalex.org/I4210117195"]},{"raw_affiliation_string":"HUN-REN-SZTAKI-SU Rejuvenation Research Group, HUN-REN Office for Supported Research Groups (TKI), Hungarian Research Network (HUN-REN), Budapest, Hungary","institution_ids":["https://openalex.org/I4210117195","https://openalex.org/I4387152226"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5010327116","https://openalex.org/A5033755056"],"corresponding_institution_ids":["https://openalex.org/I106118109","https://openalex.org/I4210117195","https://openalex.org/I4387152226"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":1.0,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":1.0,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.0,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.0,"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/protein-protein-interaction-network","display_name":"protein-protein interaction network","score":0.9900000095367432},{"id":"https://openalex.org/keywords/transcriptomics","display_name":"transcriptomics","score":0.8619999885559082},{"id":"https://openalex.org/keywords/proteomics","display_name":"proteomics","score":0.9990000128746033},{"id":"https://openalex.org/keywords/network-dynamics","display_name":"network dynamics","score":0.7440000176429749}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5692999958992004},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5584999918937683},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.5231000185012817},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.49709999561309814},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4959000051021576},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.4677000045776367},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.4562999904155731},{"id":"https://openalex.org/C2909613950","wikidata":"https://www.wikidata.org/wiki/Q158695","display_name":"Protein Interaction Networks","level":3,"score":0.4523000121116638},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.4309000074863434},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4156000018119812},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.40959998965263367},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.38440001010894775},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.34790000319480896},{"id":"https://openalex.org/C2988224531","wikidata":"https://www.wikidata.org/wiki/Q20830730","display_name":"Network structure","level":2,"score":0.33880001306533813},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.3224000036716461},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.3172000050544739},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.3077000081539154},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.3075999915599823},{"id":"https://openalex.org/C2778334786","wikidata":"https://www.wikidata.org/wiki/Q1586270","display_name":"Variation (astronomy)","level":2,"score":0.30709999799728394},{"id":"https://openalex.org/C117220453","wikidata":"https://www.wikidata.org/wiki/Q5172842","display_name":"Correlation","level":2,"score":0.3025999963283539},{"id":"https://openalex.org/C2992929089","wikidata":"https://www.wikidata.org/wiki/Q748695","display_name":"Genetic similarity","level":4,"score":0.2831000089645386},{"id":"https://openalex.org/C104122410","wikidata":"https://www.wikidata.org/wiki/Q1416406","display_name":"Network model","level":2,"score":0.28290000557899475},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.27880001068115234},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.27469998598098755},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.26269999146461487},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.26010000705718994},{"id":"https://openalex.org/C3020318244","wikidata":"https://www.wikidata.org/wiki/Q4812187","display_name":"Large sample","level":2,"score":0.2529999911785126}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.08.09.743737","doi":"https://doi.org/10.64898/2026.08.09.743737","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.09.743737","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/10/2026.08.09.743737.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.08.09.743737","doi":"https://doi.org/10.64898/2026.08.09.743737","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.09.743737","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/10/2026.08.09.743737.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1041794956","display_name":null,"funder_award_id":"TKCS-2024/37","funder_id":"https://openalex.org/F2608926379","funder_display_name":"Hungarian Research Network"},{"id":"https://openalex.org/G5471440219","display_name":null,"funder_award_id":"FK-146113","funder_id":"https://openalex.org/F4320336675","funder_display_name":"National Research, Development and Innovation Office"},{"id":"https://openalex.org/G8885186033","display_name":null,"funder_award_id":"146113","funder_id":"https://openalex.org/F4320326762","funder_display_name":"Nemzeti Kutat\u00e1si Fejleszt\u00e9si \u00e9s Innov\u00e1ci\u00f3s Hivatal"},{"id":"https://openalex.org/G9000380496","display_name":null,"funder_award_id":"FK-146113","funder_id":"https://openalex.org/F4320326762","funder_display_name":"Nemzeti Kutat\u00e1si Fejleszt\u00e9si \u00e9s Innov\u00e1ci\u00f3s Hivatal"}],"funders":[{"id":"https://openalex.org/F2608926379","display_name":"Hungarian Research Network","ror":"https://ror.org/04w6pnc49"},{"id":"https://openalex.org/F4320322192","display_name":"Magyar Tudom\u00e1nyos Akad\u00e9mia","ror":"https://ror.org/02ks8qq67"},{"id":"https://openalex.org/F4320326762","display_name":"Nemzeti Kutat\u00e1si Fejleszt\u00e9si \u00e9s Innov\u00e1ci\u00f3s Hivatal","ror":null},{"id":"https://openalex.org/F4320336675","display_name":"National Research, Development and Innovation Office","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7202136014.pdf","grobid_xml":"https://content.openalex.org/works/W7202136014.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1963856668","https://openalex.org/W1977186059","https://openalex.org/W1989635088","https://openalex.org/W1993153599","https://openalex.org/W2006837755","https://openalex.org/W2013759403","https://openalex.org/W2040956707","https://openalex.org/W2048839385","https://openalex.org/W2049719481","https://openalex.org/W2052357007","https://openalex.org/W2057498577","https://openalex.org/W2084619201","https://openalex.org/W2091567346","https://openalex.org/W2126693856","https://openalex.org/W2127087491","https://openalex.org/W2129793061","https://openalex.org/W2161174387","https://openalex.org/W2163480486","https://openalex.org/W2165867280","https://openalex.org/W2604856406","https://openalex.org/W2901411431","https://openalex.org/W2974281011","https://openalex.org/W2983909687","https://openalex.org/W2997594760","https://openalex.org/W3036344983","https://openalex.org/W3093053585","https://openalex.org/W3112963616","https://openalex.org/W3174549668","https://openalex.org/W4206540351","https://openalex.org/W4282929997","https://openalex.org/W4308634875","https://openalex.org/W4308834893","https://openalex.org/W4323042987","https://openalex.org/W4377294382","https://openalex.org/W4384154439","https://openalex.org/W4386694140","https://openalex.org/W4387297029","https://openalex.org/W4403781707","https://openalex.org/W4406297545","https://openalex.org/W4407391537","https://openalex.org/W4409351113","https://openalex.org/W4410042582","https://openalex.org/W4410773163","https://openalex.org/W4414594146"],"related_works":["https://openalex.org/W2949329134","https://openalex.org/W2023754289","https://openalex.org/W1987258236","https://openalex.org/W2147043524","https://openalex.org/W2084685373","https://openalex.org/W3197477793","https://openalex.org/W7155058851","https://openalex.org/W3158181125","https://openalex.org/W2599029890","https://openalex.org/W2073738984"],"abstract_inverted_index":{"Abstract":[0],"Contextualized":[1],"protein-protein":[2,29],"interaction":[3],"networks":[4,128,189,225],"provide":[5],"crucial":[6],"insight":[7],"into":[8],"diseases":[9],"and":[10,22,73,76,106,142,159,230,253],"other":[11],"biological":[12],"processes,":[13],"but":[14,115,207,237],"for":[15,156],"a":[16,46,51,137,154,157,172],"profound":[17],"understanding":[18],"of":[19,45,54,86,97,103,120,125,140,162,185,196,210,217,224,235,249],"such":[20],"processes":[21],"their":[23],"distinct":[24],"effects":[25],"on":[26,175,246],"individuals,":[27],"the":[28,42,58,64,83,87,98,113,118,121,126,163,182,186,193,205,208,211,218,247],"interactions":[30],"within":[31],"individual":[32],"samples":[33],"must":[34],"be":[35],"investigated.":[36],"A":[37],"straightforward":[38],"approach":[39],"to":[40,49,57,148],"estimate":[41],"PPI":[43,127,145,250],"network":[44,53,146,177,251],"sample":[47],"is":[48,90,129,202],"restrict":[50],"general":[52],"known":[55],"PPIs":[56],"proteins":[59],"that":[60,181],"are":[61,69,190],"found":[62,180],"in":[63,112,167,221,256],"sample.":[65],"Although":[66],"proteomics":[67],"methods":[68],"becoming":[70],"more":[71],"accessible":[72],"precise,":[74],"large-scale":[75],"single-cell":[77],"studies":[78],"still":[79,130],"mainly":[80],"target":[81],"characterizing":[82],"transcriptomics":[84],"profile":[85],"samples,":[88],"which":[89],"then":[91],"often":[92,204,231],"used":[93],"as":[94],"an":[95],"approximation":[96],"protein":[99,107],"activities.":[100],"The":[101,215],"correlation":[102],"gene":[104],"expression":[105],"abundance":[108],"has":[109],"been":[110],"addressed":[111],"past,":[114],"information":[116],"about":[117],"deviations":[119],"different":[122,187,232],"omics-based":[123,188],"estimates":[124,147],"lacking.":[131],"In":[132],"this":[133,150,238],"study,":[134],"we":[135],"performed":[136],"comparative":[138],"analysis":[139],"transcriptomic-based":[141],"proteomic-based":[143],"sample-specific":[144],"fill":[149],"gap.":[151],"We":[152,179],"created":[153],"framework":[155],"comprehensive":[158],"transparent":[160],"comparison":[161],"two":[164,168],"omics":[165],"levels":[166],"independent":[169],"datasets,":[170],"with":[171,200],"special":[173],"focus":[174],"time-related":[176,233],"dynamics.":[178],"size-adjusted":[183],"characteristics":[184,216],"very":[191],"similar;":[192],"overall":[194],"trend":[195],"how":[197],"they":[198],"change":[199],"time":[201],"also":[203,226],"same,":[206],"rate":[209],"changes":[212],"typically":[213],"differs.":[214],"nodes":[219],"present":[220],"both":[222],"types":[223],"show":[227],"high":[228],"similarity":[229],"rates":[234],"change,":[236],"varies":[239],"among":[240],"metrics.":[241],"These":[242],"results":[243],"shed":[244],"light":[245],"properties":[248],"estimations":[252],"advise":[254],"caution":[255],"interpreting":[257],"them":[258],"appropriately.":[259]},"counts_by_year":[],"updated_date":"2026-10-29T09:56:32.521200","created_date":"2026-08-11T00:00:00"}