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The BioPlex Network: A Systematic Exploration of the Human Interactome
Open accessAbstract
Protein interactions form a network whose structure drives cellular function and whose organization informs biological inquiry. Using high-throughput affinity-purification mass spectrometry, we identify interacting partners for 2,594 human proteins in HEK293T cells. The resulting network (BioPlex) contains 23,744 interactions among 7,668 proteins with 86% previously undocumented. BioPlex accurately depicts known complexes, attaining 80%-100% coverage for most CORUM complexes. The network readily subdivides into communities that correspond to complexes or clusters of functionally related proteins. More generally, network architecture reflects cellular localization, biological process, and molecular function, enabling functional characterization of thousands of proteins. Network structure also reveals associations among thousands of protein domains, suggesting a basis for examining structurally related proteins. Finally, BioPlex, in combination with other approaches, can be used to reveal interactions of biological or clinical significance. For example, mutations in the membrane protein VAPB implicated in familial amyotrophic lateral sclerosis perturb a defined community of interactors.
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“It comprises two sub-assemblies: Retriever composed of VPS35L, VPS26C, and VPS29; and the CCC complex which contains twelve subunits: COMMD1-COMMD10 and the coiled-coil domain-containing (CCDC) proteins CCDC22 and CCDC93.”
From Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome (2023) · cites this paper as [19]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“The CCC complex comprises twelve components, the coiled coil domain-containing proteins CCDC22 and CCDC93 and ten COMMD (copper metabolism MURR1 [Mouse U2af1-rs1 region 1) domain) family members COMMD1-COMMD10.2,16,17,18,19”
From Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome (2023) · cites this paper as [19]
Experimental — accuracy not yet measuredIn the citing paper
“The community detection approach was well illustrated in recent analyses of protein-protein interaction networks in yeast (Dutkowski et al., 2013) and human (Huttlin et al., 2015).”
From Mapping the multiscale structure of biological systems (2021) · cites this paper as Huttlin et al., 2015
In the citing paper
“In the human study, the authors first performed clique percolation to determine high-level protein communities; subsequently, they ran modularity-based clustering to further subdivide these communities into more granular subsystems, resulting in a multi-layer hierarchical structure (Figure 3A).”
From Mapping the multiscale structure of biological systems (2021) · cites this paper as Huttlin et al., 2015
In the citing paper
“several high throughput studies using robust affinity purification-mass spectrometry methodologies to elucidate protein interaction networks have revealed the interaction of ABCD1 with AT2B2 [ 167 ] and ABCD3 with AT2B2 and AT2A2 [ 168 , 169 ]”
From Peroxisomal ABC Transporters: An Update (2021) · cites this paper as [169]
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Cites
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482 · cited 1×
“This process was repeated for all domain pairs, and p values were adjusted for multiple hypothesis testing (Benjamini and Hochberg, 1995).”
Emergence of Scaling in Random Networks
Barabási, A.-L., & Albert, R. (1999) · Science · doi:10.1126/science.286.5439.509 · Cited by 36,135 · cited 1×
“…fraction of proteins observed across the range of vertex degrees follows a linear trend for degrees above 4 that is consistent with power law behavior typical of scale-free networks (Barabasi and Albert, 1999) and has been observed in protein interaction and metabolic networks (Vidal et al., 2011).”
Eng, J. K., McCormack, A. L., & Yates, J. R. (1994) · Journal of the American Society for Mass Spectrometry · doi:10.1016/1044-0305(94)80016-2 · Cited by 6,484 · cited 1×
“Using Sequest (Eng et al., 1994), spectra were searched against human protein sequences from Uniprot (Magrane and Consortium, 2011) and common contaminants.”
Pfam: the protein families database
Finn, R. D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Heger, A., Hetherington, K., Holm, L., Mistry, J., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1223 · Cited by 6,148
Fast algorithm for detecting community structure in networks
Newman, M. E. J. (2004) · Physical Review E · doi:10.1103/physreve.69.066133 · Cited by 5,415 · cited 1×
“We have employed a two-stage strategy to map BioPlex community structure, using clique percolation (Palla et al., 2005) to identify 256 communities that were further subdivided via modularity-based clustering (Newman, 2004) (legend continued on next page) subcommunities (Table S3).”
Uncovering the overlapping community structure of complex networks in nature and society
Palla, G., Derényi, I., Farkas, I., & Vicsek, T. (2005) · Nature · doi:10.1038/nature03607 · Cited by 5,373 · cited 2×
“We have employed a two-stage strategy to map BioPlex community structure, using clique percolation (Palla et al., 2005) to identify 256 communities that were further subdivided via modularity-based clustering (Newman, 2004) (legend continued on next page) subcommunities (Table S3).”
Warde-Farley, D., Donaldson, S. L., Comes, O., Zuberi, K., Badrawi, R., Chao, P., Franz, M., Grouios, C., Kazi, F., Lopes, C. T., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq537 · Cited by 4,835 · cited 6×
“To enable more extensive comparison, we compiled all human physical interactions reported in CORUM, BioGRID (Stark et al., 2011), GeneMania, STRING, and MINT (Licata et al., 2012).”
InfluentialFunctional organization of the yeast proteome by systematic analysis of protein complexes
Gavin, A., Böesche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A., Cruciat, C., et al. (2002) · Nature · doi:10.1038/415141a · Cited by 4,729 · cited 2×
“AP-MS has previously mapped a substantial fraction of yeast (Gavin et al., 2002; Ho et al., 2002; Krogan et al., 2006) and Drosophila (Guruharsha et al.”
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
Franceschini, A., Szklarczyk, D., Frankild, S., Kuhn, M., Simonovic, M., Roth, A., Lin, J., Minguez, P., Bork, P., von Mering, C., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1094 · Cited by 4,398 · cited 7×
“To enable more extensive comparison, we compiled all human physical interactions reported in CORUM, BioGRID (Stark et al., 2011), GeneMania, STRING, and MINT (Licata et al., 2012).”
InfluentialElias, J. E., & Gygi, S. P. (2007) · Nature Methods · doi:10.1038/nmeth1019 · Cited by 3,925 · cited 2×
“The target-decoy method (Elias and Gygi, 2007) was used to filter each LC-MS dataset to a preliminary 1% protein FDR.”
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Leblanc, S., & Brunet, M. A. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.10.010 · Cited by 11
“Such classifiers have previously been published to identify HCIP in large datasets [44].”
Dayer, G., Masoom, M. L., Togtema, M., & Zehbe, I. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21217980 · Cited by 8
Rozenberg, J. M., Rogovaya, O. S., Melino, G., Barlev, N. A., & Kagansky, A. (2020) · Cells · doi:10.3390/cells10010025 · Cited by 10
Tarozzi, M. E., Bartoletti‐Stella, A., Dall’Olio, D., Matteuzzi, T., Baiardi, S., Parchi, P., Castellani, G., & Capellari, S. (2022) · BMC Medical Genomics · doi:10.1186/s12920-022-01173-4 · Cited by 12
“Protein–protein interaction network (PPIn) was built by merging data from four state-of-the-art protein–protein interaction databases [35–38].”
MethodSibling rivalry among the ZBTB transcription factor family: homodimers versus heterodimers
Piepoli, S., Barakat, S., Nogay, L., Şimşek, B., Akköse, Ü., Taskiran, H., Tolay, N., Gezen, M., Yeşilada, C. Y., Tuncay, M., et al. (2022) · Life Science Alliance · doi:10.26508/lsa.202201474 · Cited by 8
“We particularly focused on four candidate pairs of ZBTB proteins (PATZ1-PATZ2, BCL6-PATZ1, MIZ1-BCL6, and LRFThPOK), which were previously reported to form heterodimers (Widom et al, 2001; Stead & Wright, 2014; Vacchio et al, 2014; Huttlin et al, 2015).”
BackgroundThe association of lipid transfer protein VPS13A with endosomes is mediated by sorting nexin SNX5
Tornero-Écija, A., Zapata-del-Baño, A., Antón-Esteban, L., Vincent, O., & Escalante, R. (2023) · Life Science Alliance · doi:10.26508/lsa.202201852 · Cited by 9
“Interestingly, a high-throughput proteomic study has shown that VPS13B coprecipitated with the sorting nexins SNX20 and SNX21 (Huttlin et al, 2015), suggesting that interaction with sorting nexins may be a general property of mammalian VPS13 proteins.”
BackgroundYu, Y., Li, Y., & Zhang, Y. (2016) · Neuroscience Bulletin · doi:10.1007/s12264-016-0021-1 · Cited by 8
Kim, E. J., Park, M. K., Kang, G.-J., Byun, H. J., Kim, H. J., Yu, L., Kim, B., Chae, H., Chin, Y., Shim, J. G., et al. (2019) · Journal of Oncology · doi:10.1155/2019/3542537 · Cited by 9
“We found that CDC16 might be a binding partner of YDJC [28].”
Ortiz-Joya, L. J., Contreras-Rodríguez, L. E., & Ramírez-Hernández, M. H. (2019) · Memórias do Instituto Oswaldo Cruz · doi:10.1590/0074-02760180506 · Cited by 10
“(14) Additionally, through the affinity capture-MS technique, the interaction of HsNMNAT1 with the ribosomal proteins L11 (RPL11) and L22 (RPL22) was identified.(19) These proteins are necessary for rRNA formation, maturation, and processing.”
MethodExtensive binding of nebulous human transcription factors to genomic dark matterPreprint
Razavi, R., Fathi, A., Yellan, I., Brechalov, A. V., Laverty, K. U., Jolma, A., Hernández-Corchado, A., Zheng, H., Yang, A. W. H., Albu, M., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.11.622123 · Cited by 9
Prabhakar, V., & Liu, K. (2023) · Archives of Clinical and Biomedical Research · doi:10.26502/acbr.50170342 · Cited by 8
James, C., Möller, U., Spillner, C., König, S., Dybkov, O., Urlaub, H., Lenz, C., & Kehlenbach, R. H. (2024) · EMBO Reports · doi:10.1038/s44319-024-00125-6 · Cited by 8
“ELYS was identi fi ed previously as a potential interacting partner of VAPs by us (James et al, 2019) and by others (Huttlin et al, 2015; Murphy and Levine, 2016).”
A ribosome-associating chaperone mediates GTP-driven vectorial folding of nascent eEF1A
Sabbarini, I. M., Reif, D., Park, K., McQuown, A. J., Nelliat, A. R., Trejtnar, C., Dötsch, V., Shakhnovich, E. I., Murray, A. W., & Denic, V. (2025) · Nature Communications · doi:10.1038/s41467-025-56489-3 · Cited by 10
Yu, C., Adavikolanu, R., Kaake, R. M., & Huang, L. (2025) · Mass Spectrometry Reviews · doi:10.1002/mas.21926 · Cited by 10
“…an enormous effort to systematically map the human interactome has led to the development of the BioPlex Network (versions 1.0, 2.0, and 3.0) (Huttlin et al. 2015, 2017, 2021) and the interactive BioPlexExplorer (Geistlinger et al. 2023), which collectively provide access to AP‐MS data…”
InfluentialUpdate on VAP, a ubiquitous signpost for the ER
Levine, T. P. (2025) · Biological Chemistry · doi:10.1515/hsz-2025-0199 · Cited by 9
“Approximately 50 % of VAPs interactors either have a sequence resembling a FFAT motif or form a tight complex with such a protein (Huttlin et al. 2015, Murphy and Levine 2016).”
Ichikawa, D. M., Corbi‐Verge, C., Shen, M. J., Snider, J. D., Wong, V., Štagljar, I., Kim, P. M., & Noyes, M. B. (2019) · ACS Synthetic Biology · doi:10.1021/acssynbio.8b00499 · Cited by 8
Deischinger, C., Harreiter, J., Leitner, K., Bancher‐Todesca, D., Baumgartner-Parzer, S. M., & Kautzky‐Willer, A. (2020) · Journal of Clinical Medicine · doi:10.3390/jcm9072277 · Cited by 8
Suo, D., Wang, L., Zeng, T., Zhang, H., Li, L., Liu, J., Yun, J., Guan, X., & Li, Y. (2020) · Oncogenesis · doi:10.1038/s41389-020-00260-4 · Cited by 9
Schor, S., Pu, S., Nicolaescu, V. I., Azari, S., Kõivomägi, M., Karim, M., Cassonnet, P., Saul, S., Neveu, G., Yueh, A., et al. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.101956 · Cited by 8
Specific gene expression signatures of low grade meningiomas
Tsitsikov, E. N., Hameed, S., Tavakol, S., Stephens, T. M., Tsytsykova, A. V., Garman, L., Bi, W. L., & Dunn, I. F. (2023) · Frontiers in Oncology · doi:10.3389/fonc.2023.1126550 · Cited by 8
“Through the WD40 domain, TRAF7 specifically interacts with a number of proteins including mitogen-activated protein kinase kinase kinase 3 (MAP3K3/ MEKK3) (64, 65), transcriptional activator MYB (c-Myb) (66), dual specificity mitogen-activated protein kinase kinase 5 (MAP2K5/MEK5) (67), Roundabout homolog 4 (ROBO4) (6…”
BackgroundZhao, S., Yang, X., Zeng, Z., Qian, P., Zhao, Z., Dai, L., Prabhu, N., Nordlund, P., & Tam, W. L. (2024) · Scientific Reports · doi:10.1038/s41598-024-51193-6 · Cited by 8
SPINK5 inhibits esophageal squamous cell carcinoma metastasis via immune activity
Chen, J., Lu, J., Chen, Z., Liu, Z., Sun, Y., He, S., Mi, Y., Gao, Y., Shen, D., & Lin, Q. (2024) · The Journal of Gene Medicine · doi:10.1002/jgm.3667 · Cited by 8
“40 Previous studies have reported that there is a certain interaction between SPINK5 and TFG. 39,40 In the present study, we explored the association between SPINK5 and the NF-κ B pathway by luciferase assays in HEK293T cells.”
BackgroundDecoding cocaine-induced proteomic adaptations in the mouse nucleus accumbens
Mews, P., Sosnick, L., Gurung, A., Sidoli, S., & Nestler, E. J. (2024) · Science Signaling · doi:10.1126/scisignal.adl4738 · Cited by 7
“Last, known protein-protein interactions were compared with the identified pool using the STRING database to test whether genetically interacting proteins were found to be coregulated in the dataset, revealing potential shared functions ( 85 , 86 ).”
MethodApproches nouvelles pour l’étude des interactions protéine-protéine
Béganton, B., Coyaud, É., Mangé, A., & Solassol, J. (2019) · médecine/sciences · doi:10.1051/medsci/2019035 · Cited by 14
Vissers, J. H. A., Dent, L., House, C. M., Kondo, S., & Harvey, K. F. (2020) · Genetics · doi:10.1534/genetics.120.303147 · Cited by 7
Khazen, G., Gyulkhandanian, A., Issa, T., & Maroun, R. C. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.09.013 · Cited by 8
Qi, H.-X., Shen, Q.-D., Zhào, H., Qi, G.-Z., & Gao, L. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab372 · Cited by 8
Nuclear Coregulatory Complexes in Tregs as Targets to Promote Anticancer Immune Responses
Christensen, L. M., & Hancock, W. W. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.909816 · Cited by 11
Sanchez-Briñas, A., Duran-Ruiz, C., Astola, A., Arroyo, M. M., Raposo, F. G., Valle, A., & Bolı́var, J. (2023) · Biology Direct · doi:10.1186/s13062-023-00384-8 · Cited by 8
“The most common strategy to study large-scale interactomes in human cell lines [22, 23] and in vivo in model organisms [24–26] relies on high-throughput proteomics technologies [27] based on affinity-purification mass spectrometry (AP-MS) approach tagging the protein of interest with specific antibodies [28] or, more…”
BackgroundMechanisms of polarity protein expression control
Ahmed, S. M., & Macara, I. G. (2016) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2016.04.002 · Cited by 8
Garrido, F., Pacheco, M., Vargas-Martínez, R., Velasco-García, R., Jorge, I., Serrano, H., Portillo, F., Vázquez, J., & Pajares, M. A. (2018) · PLoS ONE · doi:10.1371/journal.pone.0199472 · Cited by 8
The Importance of Biologic Knowledge and Gene Expression Context for Genomic Data Interpretation
Zimmermann, M. T. (2018) · Frontiers in Genetics · doi:10.3389/fgene.2018.00670 · Cited by 10
Proteomics and Precision Medicine
Ding, C., Qin, Z., Li, Y., Shi, W., Li, L., Zhan, D., & Yang, W. (2019) · Small Methods · doi:10.1002/smtd.201900075 · Cited by 9
Lawton, M. L., & Emili, A. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167318 · Cited by 8
Willing to Be Involved in Cancer
Gunn‐Moore, F. J., Tilston-Lünel, A., & Reynolds, P. A. (2016) · Genes · doi:10.3390/genes7070037 · Cited by 8
“Willin has also been suggested to interact with other junctional components such as RASSF8 however this has been observed in high throughput protein-protein interaction screens such as BioPlex (biophysical interactions of ORFeome-based complexes) performed by the Gygi laboratory and a high throughput Y2H screen perfor…”
MethodMeinnel, T. (2022) · ACS Catalysis · doi:10.1021/acscatal.2c01060 · Cited by 8
Comprehensive Overview of Bottom-up Proteomics using Mass SpectrometryPreprint
Jiang, Y., Rex, D. A. B., Schuster, D., Neely, B. A., Rosano, G. L., Volkmar, N., Momenzadeh, A., Peters-Clarke, T. M., Egbert, S., Kreimer, S. D., et al. (2023) · PubMed · doi:10.48550/arxiv.2311.07791 · Cited by 8
SPIDER: constructing cell-type-specific protein–protein interaction networks
Kupershmidt, Y., Kasif, S., & Sharan, R. (2024) · Bioinformatics Advances · doi:10.1093/bioadv/vbae130 · Cited by 7
“Protein abundance data for HEK293T and HCT116 cells were taken from the Bioplex project (Huttlin et al. 2015).”
BackgroundMethodInfluentialHyperphenylalaninemia and serotonin deficiency in Dnajc12-deficient mice
Cao, Y., Popp, O., Milani, N., Qadri, F., Kühn, R., Mertins, P., Bäder, M., & Alenina, N. V. (2024) · Communications Biology · doi:10.1038/s42003-024-07360-6 · Cited by 8
“By yeast-two-hybrid screens an interaction of DNAJC12 with TPH1, TPH2, and TH had already been suggested 13 .”
Liu, W., Lu, Y., Liu, J., Yan, Y., & Yang, H. (2025) · Acta Neuropathologica Communications · doi:10.1186/s40478-025-01949-6 · Cited by 7
“Furthermore, the interactions between α-syn and PTPIP51 are modulated by the phosphorylation of α-syn at the serine residue 129 [53].”
Chatterjee, A., Ravandi, B., Haddadi, P., Philip, N. H., Abdelmessih, M., Mowrey, W. R., Ricchiuto, P., Liang, Y., Ding, W., Mobarec, J. C., et al. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf148 · Cited by 8
“…such as gene symbols (Bruford et al. 2020), Entrez ID (Maglott et al. 2010), Ensembl ID (Martin 2022), etc., newer databases like BioPlex (Huttlin et al. 2015) report the protein IDS such as UniProt ID (Consortium 2020), PDB ID (PDB), etc. Ambiguity in gene-to-protein mapping combined…”
InfluentialStructure of the nucleosome-bound human BCL7A
Martin, F., Kazrani, A. A., Lafouge, J., Jimenez, D. M. D., Siebert, S., Fabbro-Burtschell, L., Maillard, E., Lapouge, K., Mertens, H. D. T., Sauter, C., et al. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf273 · Cited by 7
Mishra, S., Manohar, V., Chandel, S., Manoj, T., Bhattacharya, S., Hegde, N., Nath, V. R., Krishnan, H., Wendling, C., Mattia, T. D., et al. (2024) · Life Science Alliance · doi:10.26508/lsa.202302525 · Cited by 6
“But the finding most relevant to the initial premise of the study (i.e. "molecular mechanisms underlying lipid transfer protein function at membrane contact sites") is that Cert (a lipid transfer protein) and CG9205 (fly homolog of a mammalian lipid transfer protein) influence RdgB function.”
BackgroundRueter, J., Rimbach, G. H., Bilke, S., Tholey, A., & Huebbe, P. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms251910597 · Cited by 7
The gag-like gene RTL8 antagonizes PEG10-mediated virus like particles
Campodonico-Burnett, W., Mohan, H. M., Huynh, P. T., Black, H. H., Lau, C. I., Paulson, H. L., Sharkey, L. M., & Whiteley, A. M. (2024) · PLoS ONE · doi:10.1371/journal.pone.0310946 · Cited by 10
Experimental Characterization of Protein Complex Structure, Dynamics, and Assembly
Wells, J. N., & Marsh, J. A. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-7759-8_1 · Cited by 7
Varma, M., Kadoki, M., Lefkovith, A. J., Conway, K. L., Gao, K. M., Mohanan, V., Tusi, B. K., Graham, D. B., Latorre, I. J., Tolonen, A. C., et al. (2020) · The Journal of Immunology · doi:10.4049/jimmunol.1900750 · Cited by 8
“A change in topology due to genotypic perturbations was tested for in the BioPlex network (47) – an established, experimentally verified protein interaction network.”
BackgroundMethodVirus systems biology: Proteomics profiling of dynamic protein networks during infection
Klann, K., Tascher, G., & Münch, C. (2021) · Advances in virus research · doi:10.1016/bs.aivir.2020.12.001 · Cited by 7
Identification of Germinal Neurofibromin Hotspots
Lois, S., Báez-Flores, J., Isidoro‐García, M., Lacal, J., & Triviño, J. C. (2022) · Biomedicines · doi:10.3390/biomedicines10082044 · Cited by 7
“Neurofibromin functional domains were obtained from Uniprot database [47], P21359; UniProt, as well as from Interpro [48], Prosite [49], and previous published papers [50,51].”
MethodVPS13 Forum Proceedings: XK, XK-Related and VPS13 Proteins in Membrane Lipid Dynamics
Peikert, K., & Danek, A. (2023) · Contact · doi:10.1177/25152564231156994 · Cited by 7
“With respect to the corresponding XK binding site, Neiman referred to its novel topology (Figure 1) and noted that its second intracellular loop is highly conserved in XK and XKr2, the latter known to interact with VPS13A (Huttlin et al., 2015; Suzuki et al., 2014).”
BackgroundStauber, M., Boldt, K., Wrede, C., Weidemann, M., Kellner, M., Schuster-Gossler, K., Kühnel, M., Hegermann, J., Ueffing, M., & Gossler, A. (2017) · Developmental Biology · doi:10.1016/j.ydbio.2017.06.027 · Cited by 7
Perspective on architecture and assembly of membrane contact sites
Hoffmann, P. C., & Kukulski, W. (2017) · Biology of the Cell · doi:10.1111/boc.201700031 · Cited by 7
Altered expression of telomere‐associated genes in leukocytes among BRCA1 and BRCA2 carriers
Tanaka, H., Phipps, E. A., Wei, T., Wu, X., Goswami, C. P., Liu, Y., Sledge, G. W., Mina, L. A., & Herbert, B. (2017) · Molecular Carcinogenesis · doi:10.1002/mc.22773 · Cited by 7
“The PPP2CB gene encodes a component of PP2A, one of four major serine/threonine phosphatases.(36,37) Because PP2A regulates autophosphorylation of ATM,(38) altered gene expression of PP2A subunits could affect the telomere damage signaling pathway.”
The effect of QTL-rich region polymorphisms identified by targeted DNA-seq on pig production traits
Stuczyńska, A., Piórkowska, K., Tyra, M., & Żukowski, K. (2018) · Molecular Biology Reports · doi:10.1007/s11033-018-4170-3 · Cited by 7
“[17] postulated that PECR interacts with actin alpha 2 (ACTA2), which is involved in actin cytoskeleton and calcium signalling pathways, among others.”
Selective profiling of ribosomes associated with yeast Upf proteins
Ganesan, R., Leszyk, J., & Jacobson, A. (2018) · Methods · doi:10.1016/j.ymeth.2018.12.008 · Cited by 6
Birla, S., Vijayakumar, P., Sehgal, S., Bhatnagar, S., Pallavi, K., & Sharma, A. (2019) · Hormone and Metabolic Research · doi:10.1055/a-0867-1026 · Cited by 7
“The wild type (wt) POU1F1 expression vector (HsCD00461922) consists of the human POU1F1 cDNA sub cloned into a mammalian expression vector pPHAGE C-Tap (obtained from Harvard PlasmID Database, Harvard Medical School, USA) [10].”
MethodInteraction between NSMCE4A and GPS1 links the SMC5/6 complex to the COP9 signalosome
Horváth, A., Róna, G., Pagano, M., & Jordan, P. W. (2020) · BMC Molecular and Cell Biology · doi:10.1186/s12860-020-00278-x · Cited by 8
Frauenstein, A., Ebner, S., Hansen, F. M., Sinha, A., Phulphagar, K. M., Swatek, K. N., Hornburg, D., Mann, M., & Meissner, F. (2021) · Molecular Systems Biology · doi:10.15252/msb.202010125 · Cited by 6
Network-Based Analysis for Biological Discovery
Tripathi, L. P., Chen, Y. A., Mizuguchi, K., & Murakami, Y. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.20674-2 · Cited by 7
Mapping the Human Cell Surface Interactome: A Key to Decode Cell-to-Cell Communication
Shilts, J., & Wright, G. J. (2024) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-102523-103821 · Cited by 7
Evaluating sequence and structural similarity metrics for predicting shared paralog functions
Dennler, O., & Ryan, C. J. (2025) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqaf051 · Cited by 6
“For the PPI features, we made use of systematically generated PPI networks (Bioplex for humans; social interactome for yeast) [ 36 , 37 ] to avoid the ascertainment bias associated with networks that aggregate interactions from multiple sources [ 54 ].”
InfluentialJang, S. H., Song, H. G., Joo, S. Y., Kim, J. A., Kim, S. J., Choi, J. Y., Jung, J., & Gee, H. Y. (2025) · Molecular Therapy · doi:10.1016/j.ymthe.2025.10.005 · Cited by 6
“As MPZL2 has been reported to interact with tight junction proteins, such as ZO1 and occludin, 8,26 we evaluated the integrity of reticular tight junctions in the organ of Corti and found that the structure of the reticular lamina remained intact in Mpzl2 Q74 * /Q74 * mice up to 24 weeks (Figure…”
Jeong, H., Kim, Y., Jung, Y.-S., Kang, D. R., & Cho, Y. (2021) · Entropy · doi:10.3390/e23101271 · Cited by 6
“The BioPlex network [19] consists of PPIs obtained using high-throughput affinity-purification mass spectrometry.”
MethodGassaway, B. M., Huttlin, E. L., Huntsman, E. M., Yaron-Barir, T. M., Johnson, J. L., Kurmi, K., Cantley, L. C., Paulo, J. A., Ringel, A. E., Gygi, S. P., et al. (2024) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2024.100801 · Cited by 6
“This observation correlates with the BioPlex protein-protein interaction network of this complex (35 – 37), in that there is some distance between the two core subnetworks (containing the PolA-Primase complex and the PolD complex) and PCNA, suggesting that even though PCNA is a member of the…”
Finding New Ways How to Control BACE1
Nahálková, J. (2022) · The Journal of Membrane Biology · doi:10.1007/s00232-022-00225-1 · Cited by 6
Genome-wide CRISPR screening identifies new regulators of glycoprotein secretion
Popa, S. J., Villeneuve, J., Stewart, S., Garcia, E. P., Harrison, A. P., & Moreau, K. (2019) · Wellcome Open Research · doi:10.12688/wellcomeopenres.15232.2 · Cited by 6
Almutairi, B. O., Almutairi, M. H., Alrefaei, A. F., Alkahtani, S. H., & Alarifi, S. A. (2023) · Medicina · doi:10.3390/medicina59050996 · Cited by 6
“In contrast, HSPB1 has the strongest physical interaction with HSPB6 [57,58].”
BackgroundBen‐Mahmoud, A., Kishikawa, S., Gupta, V. R., Leach, N. T., Shen, Y., Moldovan, O., Goel, H., Hopper, B., Ranguin, K., Gruchy, N., et al. (2023) · Scientific Reports · doi:10.1038/s41598-023-40037-4 · Cited by 5
Celik, A., Beyer, I., & Fiedler, D. (2024) · Journal of the American Chemical Society · doi:10.1021/jacs.4c03069 · Cited by 5
Kasztura, M., Śnieżewski, Ł., Łaszkiewicz, A., Majkowski, M., Kobak, K. A., Peczek, K., Janik, S., Kapusniak, V., Miążek, A., Cebrat, M., et al. (2015) · Archivum Immunologiae et Therapiae Experimentalis · doi:10.1007/s00005-015-0379-1 · Cited by 6
“Moreover, it is important to note that IFT-43, IFT-122 and IFT-144 proteins were also found to interact with human homolog of NWC protein, encoded by c11orf74 gene (Chatr-Aryamontri et al. 2015; Huttlin et al. 2015).”
Uversky, V., Landau, K. S., Na, I., & Schenck, R. O. (2016) · Asian Journal of Andrology · doi:10.4103/1008-682x.184999 · Cited by 7
Fluorescence ImmunoPrecipitation (FLIP): a Novel Assay for High-Throughput IP
Mita, P., Lhakhang, T. W., Li, D., Eichinger, D. J., Fenyö, D., & Boeke, J. D. (2016) · Biological Procedures Online · doi:10.1186/s12575-016-0046-x · Cited by 6
“An essential tool for the study of the function and interaction of proteins is the immunopurification of the protein of interest with or without its interacting partners and molecules [3, 4].”
MethodKim, E. J., Park, M. K., Byun, H. J., Kang, G.-J., Yu, L., Kim, H. J., Shim, J. G., Lee, H., & Lee, C. H. (2018) · Oncotarget · doi:10.18632/oncotarget.25145 · Cited by 6
“Furthermore, CDC16 has been proposed as a binding partner of YDJC in breast cancer cells [26].”
BackgroundWrobel, J. A., Xie, L., Wang, L., Liu, C., Rashid, N. U., Gallagher, K. K., Xiong, Y., Konze, K. D., Jin, J. J., Gatza, M. L., et al. (2019) · iScience · doi:10.1016/j.isci.2019.07.001 · Cited by 6
Wang, W., Wang, S., Chu, X., Liu, H., & Xiang, M. (2019) · Journal of Computational Biology · doi:10.1089/cmb.2019.0138 · Cited by 6
“The protein-protein interaction (PPI) data sets InBio version 2016_05_31 (https://www.intomics.com/ inbio/map/#home) (Li et al., 2017) and BioPlex 2.0 (http://bioplex.hms.harvard.edu/index.php) (Huttlin et al., 2015) were collected and integrated.”
InfluentialNeural expression of sorting nexin 25 and its regulation of tyrosine receptor kinase B trafficking
Takemura, S., Isonishi, A., Tanaka, T., Okuda, H., Tatsumi, K., Yamano, M., & Wanaka, A. (2020) · Brain Structure and Function · doi:10.1007/s00429-020-02144-0 · Cited by 6
Sequestosome 1 Is Part of the Interaction Network of VAPB
James, C., Lenz, C., Urlaub, H., & Kehlenbach, R. H. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222413271 · Cited by 6
“In the past few years, several proteomic screens have established the interaction network of VAPB, with more than 200 potential binding partners [1,11,16,17].”
BackgroundSay, Y., Sio, Y. Y., Heng, A. H. S., Ng, Y. T., Matta, S. A., Pang, S. L., Teh, K. F., Wong, Y. R., Shah, S. M. R., Reginald, K., et al. (2022) · Experimental Dermatology · doi:10.1111/exd.14575 · Cited by 6
dbBIP: a comprehensive bipolar disorder database for genetic research
Li, X., Ma, S., Yan, W., Wu, Y. Q., Kong, H., Zhang, M., Luo, X., & Xia, J. (2022) · Database · doi:10.1093/database/baac049 · Cited by 7
“Proteins are essential for biological processes, and those implicated in the same disease often show strong associations or interactions (67, 68).”
BackgroundAnalysis of context-specific KRAS–effector (sub)complexes in Caco-2 cells
Ternet, C., Junk, P., Sevrin, T., Catozzi, S., Wåhlén, E., Heldin, J., Oliviero, G., Wynne, K. J., & Kiel, C. (2023) · Life Science Alliance · doi:10.26508/lsa.202201670 · Cited by 8
“Together with initiatives such as the Human Protein Atlas (Uhl´en et al, 2015) and the large-scale interactome (AP-MS – based) BioPlex database (Huttlin et al, 2015, 2017), analyzing human PPI and the conditions in which they occur will be essential for the creation of a context-dependent human…”
Prediction of Protein-Protein Interactions: Looking Through the Kaleidoscope
Laddach, A., Chung, S. S., & Fraternali, F. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.20470-6 · Cited by 6
Interaction between VPS13A and the XK scramblase is required to prevent VPS13A disease in humansPreprint
Park, J.-S., Hu, Y., Hollingsworth, N. M., Miltenberger-Miltényi, G., & Neiman, A. M. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.05.09.491223 · Cited by 6
“XKR2 encodes the most closely related paralog of XK in human cells and co-precipitated with VPS13A in a proteomic study (Huttlin et al., 2015; Suzuki et al., 2014).”
BackgroundPerspectives in computational mass spectrometry: recent developments and key challenges
Sachsenberg, T., Pino, L. K., Brunet, M., Bludau, I., Kohlbacher, O., Vizcaino, J. A., & Bittremieux, W. (2024) · Bioinformatics Advances · doi:10.1093/bioadv/vbaf301 · Cited by 6
“…lies in integrating MS-based measurements with other imaging modalities, for example combining protein–protein interaction data from BioPlex (Huttlin et al. 2015, 2017) with fluorescence-based localization data from the Human Protein Atlas (Uhlen et al. 2010) to uncover new molecular…”
Ambrose, A., Bahl, S., Sharma, S., Zhang, D., Hung, C. H.-L., Jain‐Ghai, S., Chan, A. K. J., & Mercimek‐Andrews, S. (2024) · Orphanet Journal of Rare Diseases · doi:10.1186/s13023-024-03437-x · Cited by 7
Wang, S., Shen, M., Pang, B., Zhou, B., Yuan, Y., Lü, M., Deng, X., Yang, M. S., Liu, S., Wang, Q., et al. (2025) · Orphanet Journal of Rare Diseases · doi:10.1186/s13023-025-03580-z · Cited by 5
Escors, D., Chocarro, L., Echaide, M., Rodriguez-Neira, C., Vilaplana‐Martí, B., & Kochan, G. T. (2025) · Cancers · doi:10.3390/cancers17101635 · Cited by 5
“We continued with a follow-up study taking advantage of the fact that the human interactome had been published [128].”
Deng, I. B., Follett, J., Fox, J. D., Wall, S. C., & Farrer, M. J. (2025) · npj Parkinson s Disease · doi:10.1038/s41531-025-00991-4 · Cited by 5
Shahzaib, M., Aprile, D., Squillaro, T., Alessio, N., Peluso, G., Bernardo, G. D., & Galderisi, U. (2025) · Ageing Research Reviews · doi:10.1016/j.arr.2025.102916 · Cited by 6
Ayon, N. J. (2025) · AppliedChem · doi:10.3390/appliedchem5040035 · Cited by 6
“These tagged proteins are used as baits to capture interacting proteins from complex biological samples to study protein–protein interaction, as reported by the BioPlex study, which identified 56,533 interactions with 10,961 proteins in HEK233T cells [119,120].”
Autism mutations rewire protein interaction networks to drive neurodevelopmental pathology
Wang, B., Vartak, R. S., Hennick, K. M., Zaltsman, Y., Naing, Z. Z. C., Polacco, B. J., Bashir, A., Eckhardt, M., Bouhaddou, M., Xu, J., et al. (2026) · Science · doi:10.1126/science.ady4523 · Cited by 6
Izquierdo, I., Mirra, S., Manso, Y., Parcerisas, A., Rubio, J. A., del Valle, J., Gil-Bea, F. J., Ulloa, F., Herrero‐Lorenzo, M., Verdaguer, E., et al. (2024) · Science Signaling · doi:10.1126/scisignal.abq1007 · Cited by 6
“Alex3 also interacts with guanine nucleotide binding protein subunit alpha S (GNAS) and guanine nucleotide binding protein subunit alpha T2 (GNAT2) (G α s and G α t proteins) ( 57 , 58 ).”
BackgroundThe nucleolar phase of signal recognition particle assembly
Issa, A., Schlotter, F., Flayac, J., Chen, J., Wacheul, L., Philippe, M., Sardini, L., Mostefa, L., Vandermoere, F., Bertrand, É., et al. (2024) · Life Science Alliance · doi:10.26508/lsa.202402614 · Cited by 5
“…and were described in high-throughput screens (Hayano et al, 2003; Ewing et al, 2007; Todd & Picketts, 2012; Marcon et al, 2014; Hein et al, 2015; Huttlin et al, 2015, 2017, 2021; K¨arblane et al, 2015;…”
Neutrophil-specific interactome of ARHGAP25 reveals novel partners and regulatory insights
Sasvári, P., Pettkó‐Szandtner, A., Wisniewski, É., & Csépányi‐Kömi, R. (2024) · Scientific Reports · doi:10.1038/s41598-024-71002-4 · Cited by 5
“With the emergence of high-throughput protein–protein interaction (PPI) research, ARHGAP25 has been implicated in several binary interactions 20–22 .”
Adapting to change: resolving the dynamic and dual roles of NCK1 and NCK2
Teyssier, V., Williamson, C. R., Shata, E., Rosen, S. P., Jones, N., & Bisson, N. (2024) · Biochemical Journal · doi:10.1042/bcj20230232 · Cited by 5
Lazarewicz, N., Dez, G. L., Cerjani, R., Runeshaw, L., Meurer, M., Knop, M., Wysocki, R., & Rabut, G. E. E. (2024) · Cell Reports Methods · doi:10.1016/j.crmeth.2024.100880 · Cited by 5
Takemon, Y., Pleasance, E., Gagliardi, A., Hughes, C. S., Csizmók, V., Wee, K., Trinh, D. L. N., Huff, R. D., Mungall, A. J. J., Moore, R. A., et al. (2024) · Genome Medicine · doi:10.1186/s13073-024-01401-9 · Cited by 7
“Gene functions have been inferred from their co-essential genes and protein interactors [5, 100].”
Matsuhisa, K., Sato, S., & Kaneko, M. (2025) · Biomedicines · doi:10.3390/biomedicines13040854 · Cited by 4
“BioID2 is a promiscuous mutant of a biotin ligase derived from A. aeolicus , with a smaller size (233 amino acids) than BioID (321 amino acids) [114]. candidates with Nup43 has been shown by other methods [126,127].”
GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets
Marino, G. B., Olaiya, S., Evangelista, J. E., Clarke, D. J. B., & Ma’ayan, A. (2025) · GigaScience · doi:10.1093/gigascience/giaf025 · Cited by 8
“T he PPIs in Genes2Networks are assembled from BioGRID ( RRID:SCR _ 007393 ) [ 22 ], BioPlex ( RRID:SCR _ 016144 ) [ 23 ], IntAct ( RRID:SCR _ 006944 ) [ 24 ], MINT ( RRID:SCR _ 001523 ) [ 25 ], PPID [ 26 ], iRefWeb ( RRID:SCR _ 008118 ) [ 27 ], Stelzl et al. [ 28 ], and a few other PPI resour ces.”
Rueter, J., Rimbach, G. H., Treitz, C., Schloesser, A., Lüersen, K., Tholey, A., & Huebbe, P. (2023) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-023-04706-x · Cited by 5
Zinc deficiency is associated with the development of ovarian endometrial cysts.
Onuma, T., Mizutani, T., Fujita, Y., Ohgami, N., Ohnuma, S., Kato, M., & Yoshida, Y. (2023) · PubMed Central · Cited by 5
Metadata
- Authors
- Huttlin, E. L., Ting, L., Bruckner, R. J., Gebreab, F., Gygi, M. P., Szpyt, J., Tam, S., Zarraga, G., Colby, G., Baltier, K., Dong, R., Guarani, V., Vaites, L. P., Ordureau, A., Rad, R., Erickson, B. K., Wühr, M., Chick, J., Zhai, B., Kolippakkam, D., Mintseris, J., Obar, R. A., Harris, T., Artavanis-Tsakonas, S., Sowa, M. E., De Camilli, P., Paulo, J. A., Harper, J. W., & Gygi, S. P.
- Affiliations
- Harvard University (US)
- Howard Hughes Medical Institute (US)
- Biogen (United States) (US)
- Corresponding author
- Harper, J. Wade
- Gygi, Steven P.
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2015-07
- Volume
- 162
- Issue
- 2
- Pages
- 425-440
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC4617211
- OpenAlex
- W1611787727
- Cited by
- 1,425
- References
- 41
- Citations by year
- 2026: 46 · 2025: 82 · 2024: 116 · 2023: 105 · 2022: 98 · 2021: 162 · 2020: 159 · 2019: 197 · 2018: 171 · 2017: 147 · 2016: 122 · 2015: 18
- FWCI
- 66.47
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- Damon Runyon Cancer Research Foundation
- Biogen
- Charles A. King Trust
- National Institutes of Health (HG006673)
- National Human Genome Research Institute (U41HG006673)
- National Institute of Diabetes and Digestive and Kidney Diseases (K01DK098285)
- National Institute of Neurological Disorders and Stroke (R37NS036251)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Biotin and Related Studies
- Keywords
- BioPlex, human interactome, protein-protein interaction, protein complexes, protein domain interactions, community structure, HEK293T cells, VAPB, amyotrophic lateral sclerosis
- MeSH terms
- Amyotrophic Lateral Sclerosis, Humans, Proteins, Mass Spectrometry, Protein Interaction Mapping, Proteomics, Protein Interaction Maps
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