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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]
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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
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Myeloid-derived growth factor is a resident endoplasmic reticulum protein
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A Hippo-like Signaling Pathway Controls Tracheal Morphogenesis in Drosophila melanogaster
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ResultMitochondria-associated endoplasmic reticulum membranes in the heart
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BackgroundZaman, M., Fu, Y., Chen, P., Sun, H., Yang, S., Wu, Z., Wang, Z., Poudel, S., Serrano, G. E., Beach, T. G., et al. (2023) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2023.100608 · Cited by 29
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“1) is supported by independent studies that used highthroughput affinity purifications coupled toMS in human cells (42), as well as analysis of protein–protein interactions in Drosophila using high-throughput two-hybrid screening (28).”
MASS SPECTROMETRY IN VIROLOGICAL SCIENCES
Milewska, A., Ner‐Kluza, J., Dąbrowska, A., Bodzoń‐Kułakowska, A., Pyrć, K., & Suder, P. (2019) · Mass Spectrometry Reviews · doi:10.1002/mas.21617 · Cited by 33
“So far, several maps have been published: BioPlex (Huttlin et al., 2015), Qubic (Hein et al., 2015), CoFrac‐15 (Wan et al., 2015), HI_11_14 and novel generation HI‐III‐19 (Rolland et al., 2014) and HuRi (The Human Reference Protein Interactome Mapping Project).”
BackgroundMirzaei, M., Gupta, V., Chitranshi, N., Deng, L., Pushpitha, K., Abbasi, M., Chick, J. M., Rajput, R., Wu, Y., McKay, M. J., et al. (2020) · Journal of Cellular Biochemistry · doi:10.1002/jcb.29822 · Cited by 30
“Peptide fragmentation was performed using the SPS‐MS3 method described previously.22 2.5 | Database searching/quantification and statistical analysis Charge state and monoisotopic m/z values were corrected using a method previously detailed by Huttlin et al.23 Spectra were searched against an indexed Rattus norvegicus…”
MethodInfluentialA lysosomal enigma CLN5 and its significance in understanding neuronal ceroid lipofuscinosis
Basak, I., Wicky, H. E., McDonald, K. O., Xu, J. B., Palmer, J. E., Best, H. L., Lefrancois, S., Lee, S. Y., Schoderboeck, L., & Hughes, S. M. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-03813-x · Cited by 32
“studies [81, 82], while all other interactors were only identified in one study each.”
BackgroundThe titin N2B and N2A regions: biomechanical and metabolic signaling hubs in cross-striated muscles
van der Pijl, R. J., Domenighetti, A. A., Sheikh, F., Ehler, E., Ottenheijm, C. A. C., & Lange, S. (2021) · Biophysical Reviews · doi:10.1007/s12551-021-00836-3 · Cited by 31
“FHL2 has been suggested to tether phosphofructokinase, adenylate kinase and muscle creatine kinase to the sarcomeric I-band in cardiomyocytes (Lange et al. 2002), and to bind to pyruvate dehydrogenase (Pdhb) (Huttlin et al. 2015).”
BackgroundPaquin, N., Murata, Y., Froehlich, A. C., Omura, D. T., Ailion, M., Pender, C. L., Constantine‐Paton, M., & Horvitz, H. R. (2016) · Current Biology · doi:10.1016/j.cub.2016.01.049 · Cited by 29
“Interestingly, recent studies have shown that fly and human VPS50 can associate with components of the Golgi-associated retrograde protein (GARP) complex, which functions in retrograde transport from endosomes to the trans-Golgi, suggesting that vps-50 might act in protein sorting [32–35].”
Protein Complex Affinity Capture from Cryomilled Mammalian Cells
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Kafková, L., Debler, E., Fisk, J. C., Jain, K., Clarke, S. G., & Read, L. K. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m116.757112 · Cited by 29
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“Previously reported protein–protein interaction data indicate that PP1 interacts with PP1 and PP1 in human cells (35,36).”
BackgroundHou, Y., Zhou, Y., Gack, M. U., Lathia, J. D., Kallianpur, A. R., Mehra, R., Chan, T. A.-T., Jung, J. U., Jehi, L. E., Eng, C., et al. (2021) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-021-00709-x · Cited by 32
“0.(74) The final human protein–protein interactome used in this study included 351,444 unique PPIs (edges or links) connecting 17,706 proteins (nodes).”
MethodRecent Advances in Molecular and Cellular Functions of S100A10
Okura, G. C., Bharadwaj, A. G., & Waisman, D. M. (2023) · Biomolecules · doi:10.3390/biom13101450 · Cited by 30
Yang, Y., Chen, Q., Fan, S., Lu, Y., Huang, Q., Liu, X., & Peng, X. (2024) · Redox Report · doi:10.1080/13510002.2024.2312320 · Cited by 31
“Notably, in proteomic studies, HSP60 has been identi fi ed as a potential target protein of SIRT4 [46 – 48 , To address this, we generated SIRT4-knockdown liver cells to investigate whether SIRT4 contributes to the reduction of mitochondrial protein misfolding mediated by glutamine.”
BackgroundGenetic Factors Conferring Metastasis In Osteosarcoma
Maximov, V. V., & Aqeilan, R. I. (2016) · Future Oncology · doi:10.2217/fon-2016-0014 · Cited by 30
Recent advances in large-scale protein interactome mapping
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The exomic landscape of t(14;18)‐negative diffuse follicular lymphoma with 1p36 deletion
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20 Years of Secretagogin: Exocytosis and Beyond
Maj, M. A., Wagner, L., & Tretter, V. E. (2019) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2019.00029 · Cited by 30
ANKRD9 is a metabolically-controlled regulator of IMPDH2 abundance and macro-assembly
Hayward, D., Kouznetsova, V. L., Pierson, H. E., Hasan, N. M., Guzman, E. R., Tsigelny, I. F., & Lutsenko, S. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.ra119.008231 · Cited by 30
“In a large MS screen of human interactome, ANKRD9 was copurified with inosine monophosphate dehydrogenase 2 (IMPDH2) (14), the rate-limiting enzyme in the GTP biosynthetic pathway.”
BackgroundBeasley, H. K., Rodman, T. A., Collins, G. V., Hinton, A. O., Jr., & Exil, V. J. (2021) · Cells · doi:10.3390/cells10071750 · Cited by 29
Rapid Profiling of Protein Complex Reorganization in Perturbed Systems
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“5), and (3) a good average sibling peptide correlation (>= 0.”
BackgroundPeng, M., Hu, Y., Song, W., Duan, S., Xu, Q., Ding, Y., Geng, J., & Zhou, J. (2017) · Scientific Reports · doi:10.1038/s41598-017-11374-y · Cited by 30
Biomimetic Virulomics for Capture and Identification of Cell-Type Specific Effector Proteins
Lapek, J. D., Fang, R. H., Wei, X., Li, P., Wang, B., Zhang, L., & Gonzalez, D. J. (2017) · ACS Nano · doi:10.1021/acsnano.7b02650 · Cited by 30
Zanini, I. M. Y., Soneson, C., Lorenzi, L. E., & Azzalin, C. M. (2017) · Journal of Cell Science · doi:10.1242/jcs.194068 · Cited by 29
“Notably, DHX8 was previously found to interact with cactin in a high-throughput study (Huttlin et al., 2015), and MOG-5, the C. elegans ortholog of DHX8, was previously isolated as a component of the CACN-1 interactome (Doherty et al., 2014).”
Hartwig, C. L., Monis, W. J., Chen, X., Dickman, D. K., Pazour, G. J., & Faúndez, V. (2017) · Developmental Neurobiology · doi:10.1002/dneu.22542 · Cited by 29
“4A) (Camargo et al., 2007, Huttlin et al., 2015; Wang et al., 2011; Havugimana et al., 2012; Wan et al., 2015; Monis et al., 2017).”
Pathway perturbations in signaling networks: Linking genotype to phenotype
Li, Y., McGrail, D. J., Latysheva, N. S., Yi, S. S., Babu, M. M., & Sahni, N. (2018) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2018.05.001 · Cited by 30
“Huttlin EL, Ting L, Bruckner RJ, Gebreab F, Gygi MP, Szpyt J, Tam S, Zarraga G, Colby G, Baltier K, Dong R, Guarani V, Vaites LP, Ordureau A, Rad R, Erickson BK, Wuhr M, Chick J, Zhai B, Kolippakkam D, Mintseris J, Obar RA, Harris T, Artavanis-Tsakonas S, Sowa ME, De Camilli P, Paulo JA, Harper JW, Gygi SP, The BioPle…”
MethodArabidopsis RIBOSOMAL RNA PROCESSING7 Is Required for 18S rRNA Maturation
Micol‐Ponce, R., Sarmiento‐Mañús, R., Ruiz-Bayón, A., Montacié, C., Sáez‐Vasquez, J., & Ponce, M. R. (2018) · The Plant Cell · doi:10.1105/tpc.18.00245 · Cited by 29
“However, a role for NTD in such dimerization is yet to be demonstrated (Huttlin et al., 2015).”
BackgroundCK2-mediated CCDC106 phosphorylation is required for p53 degradation in cancer progression
Ning, Y., Wang, C., Liu, X., Du, Y., Liu, S., Liu, K., Zhou, J., & Zhou, C. (2019) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-019-1137-8 · Cited by 29
Mid-Gestation lethality of Atxn2l-Ablated Mice
Key, J., Harter, P. N., Şen, N.-E., Gradhand, E., Auburger, G. W. J., & Gispert, S. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21145124 · Cited by 30
“This reprogramming of nutrient metabolism is accompanied by an important influence on the mitochondrial breakdown of fatty acids and amino acids, as well as glucose utilization [16–19], probably mediated by the direct protein interaction of ATXN2 with the cytosolic enzyme BCAT1 [20] as the rate-limiting factor in the…”
BackgroundDOORS syndrome and a recurrent truncating ATP6V1B2 variant
Beauregard‐Lacroix, É., Pacheco-Cuellar, G., Ajeawung, N. F., Tardif, J., Dieterich, K. D., Dabir, T. A., Vind-Kezunovic, D., White, S. M., Zádori, D., Claudia Castiglioni, T., et al. (2020) · Genetics in Medicine · doi:10.1038/s41436-020-00950-9 · Cited by 29
Molecular architecture of postsynaptic Interactomes
Wilkinson, B., & Coba, M. P. (2020) · Cellular Signalling · doi:10.1016/j.cellsig.2020.109782 · Cited by 25
Xie, Y., Chen, S., Li, Q., Sheng, Y., Alvarez, M. R., Reyes, J. M., Xu, G., Solakyildirim, K., & Lebrilla, C. B. (2021) · Chemical Science · doi:10.1039/d1sc00814e · Cited by 29
Functional diversity of apolipoprotein E: from subcellular localization to mitochondrial function
Rueter, J., Rimbach, G. H., & Huebbe, P. (2022) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-022-04516-7 · Cited by 32
The origin and evolution of human glutaminases and their atypical C-terminal ankyrin repeats
Pasquali, C. C., Islam, Z., Adamóski, D., Ferreira, I. M., RIGHETTO, R. D., Bettini, J., Portugal, R. V., Yue, W. W., Gonzalez, A. M., Dias, S. M. G., et al. (2017) · Journal of Biological Chemistry · doi:10.1074/jbc.m117.787291 · Cited by 29
“Considering the long list of partners that were shown to interact with glutaminases using mass spectrometrybased approaches (51), further investigations are required to confirm the mechanism by which the ANK repeats in glutaminases mediate protein-protein interactions.”
BackgroundPhylogenetic and Molecular Evolutionary Analysis of Mitophagy Receptors under Hypoxic Conditions
Wu, X., Wu, F.-H., Wu, Q.-R., Zhang, S., Chen, S., & Sima, M. W. (2017) · Frontiers in Physiology · doi:10.3389/fphys.2017.00539 · Cited by 30
“…cells remains poorly understood, although several high-throughput experiments (Stelzl et al., 2005; Castello et al., 2012; Hein et al., 2015; Huttlin et al., 2015) determined that the interacting proteins of human FUNDC2 are involved in mitophagy (FUNDC1), apoptosis and transport between…”
Banks, C. A. S., Thornton, J. L., Kempf, C. G., Adams, M. K., Miah, S., Boanca, G., Liu, X., Katt, M. L., Parmely, T. J., Florens, L. A., et al. (2018) · Molecular & Cellular Proteomics · doi:10.1074/mcp.tir118.000661 · Cited by 29
“identified the interaction partners for 2594 HA-tagged human proteins expressed in HEK293T cells (2).”
BackgroundThe role of prostate tumor overexpressed 1 in cancer progression
Cánovas, V., LLeonart, M. E., Moróte, J., & Paciucci, R. (2016) · Oncotarget · doi:10.18632/oncotarget.14104 · Cited by 29
“KLHDC2 Affinity capture-MS [136] Kelch domain containing 2.”
BackgroundThe Role of Calcium and Iron Homeostasis in Parkinson’s Disease
Wang, J., Zhao, J., Zhao, K., Wu, S., Chen, X., & Hu, W. (2024) · Brain Sciences · doi:10.3390/brainsci14010088 · Cited by 27
“…membrane protein-associated protein B)—PTPIP51 (mitochondrial outer membrane protein, protein tyrosine phosphatase interacting protein 51) tethers affected ER-mitochondrial association, thereby affecting calcium signaling between mitochondria and endoplasmic reticulum and ATP production [65–67].”
BackgroundCORUM in 2024: protein complexes as drug targets
Steinkamp, R., Tsitsiridis, G., Brauner, B., Montrone, C., Fobo, G., Frishman, G., Avram, S. I., Oprea, T. I., & Ruepp, A. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1033 · Cited by 28
Understanding molecular mechanisms of disease through spatial proteomics
Pankow, S., Martínez‐Bartolomé, S., Bamberger, C., & Yates, J. R. (2018) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2018.09.016 · Cited by 28
“A very large-scale study of the human interactome has been conducted and is known as Bioplex [27,28].”
BackgroundInteractome of the Autoimmune Risk Protein ANKRD55
Ugidos-Damboriena, N., Mena, J., Baquero, S., Alloza, I., Azkargorta, M., Elortza, F., & Vandenbroeck, K. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.02067 · Cited by 28
“0 dataset (42, 43), which has been deposited into the BioGRID database, described thirteen ANKRD55-interacting partners; seven were included in at least two out of three replicates from our interactome analysis (YWHAE, YWHAQ, IFT52, IFT74, MIB1, YWHAZ, and YWHAG).”
MethodLY6D as a Chemoresistance Marker Gene and Therapeutic Target for Laryngeal Squamous Cell Carcinoma
Wang, J., Fan, J., Gao, W., Wu, Y., Zhao, Q., Chen, B., Ding, Y., Wen, S., Nan, X., & Wang, B. (2020) · Stem Cells and Development · doi:10.1089/scd.2019.0210 · Cited by 28
“Huttlin et al. [16,17] reported that LY6D interacts with CTNNAIL , which affects cell adhesion.”
Laddach, A., Ng, J. C.-F., & Fraternali, F. (2021) · PLoS Biology · doi:10.1371/journal.pbio.3001207 · Cited by 26
“Genomic positions were mapped against protein sequence data from UniProt [64] and Ensembl [65], protein structural data from the Protein Data Bank (biounit database, downloaded 28/04/2017), and protein interaction data from a large nonredundant protein–protein interaction network (UniPPIN) [66], which incorporates var…”
Recent advances in induced proximity modalities
Ng, C. S. C., & Banik, S. M. (2022) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2021.102107 · Cited by 27
Integer Linear Programming in Computational and Systems Biology
Gusfield, D. (2019) · Cambridge University Press eBooks · doi:10.1017/9781108377737 · Cited by 26
Stable preparations of tyrosine hydroxylase provide the solution structure of the full-length enzyme
Bezem, M. T., Baumann, A., Skjærven, L., Meyer, R., Kursula, P., Martı́nez, A., & Flydal, M. I. (2016) · Scientific Reports · doi:10.1038/srep30390 · Cited by 28
Human PDCD2L Is an Export Substrate of CRM1 That Associates with 40S Ribosomal Subunit Precursors
Landry-Voyer, A.-M., Bilodeau, S., Bergeron, D., Dionne, K. L., Port, S. A., Rouleau, C., Boisvert, F., Kehlenbach, R. H., & Bachand, F. (2016) · Molecular and Cellular Biology · doi:10.1128/mcb.00303-16 · Cited by 28
“Consistent with our results, data from a recent study using high-throughput affinity purification coupled to mass spectrometry detection also support the existence of a stable PRMT3-RPS2-PDCD2L complex in human cells (53).”
ResultAn Integrative Framework Reveals Signaling-to-Transcription Events in Toll-like Receptor Signaling
Mertins, P., Przybylski, D., Yosef, N., Qiao, J., Clauser, K. R., Raychowdhury, R., Eisenhaure, T., Maritzen, T., Haucke, V., Satoh, T., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.06.016 · Cited by 28
“Interest-ingly, physical interactions between SAMHD1 and TLR pathway proteins havebeenreportedpreviously, suchasthe TLR4adaptor protein TIRAP (Li et al., 2011), and also with CCNA2 and CDK2, which can be activated by TLR4 signaling (Hasan et al., 2007; Huttlin et al., 2015).”
BackgroundDynamic scaffolds for neuronal signaling: in silico analysis of the TANC protein family
Gasparini, A., Tosatto, S. C. E., Murgia, A., & Leonardi, E. (2017) · Scientific Reports · doi:10.1038/s41598-017-05748-5 · Cited by 27
Li, N., Yang, Y., Liang, C., Qiu, Q., Pan, C., Li, M., Yang, S., Chen, L., Zhu, X., & Hu, Y. (2018) · American Journal Of Pathology · doi:10.1016/j.ajpath.2018.02.015 · Cited by 27
Systems-level analysis of risk genes reveals the modular nature of schizophrenia
Liu, J., Li, M., Luo, X., & Su, B. (2018) · Schizophrenia Research · doi:10.1016/j.schres.2018.05.015 · Cited by 28
Functional Annotation of Bacterial Signal Transduction Systems: Progress and Challenges
Martín‐Mora, D., Fernández, M., Velando, F., Ortega, Á., Gavira, J. A., Matilla, M. A., & Krell, T. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19123755 · Cited by 28
“Approaches for large scale characterization of protein-protein interactions include yeast two-hybrid screening [106], co-immunoprecipitation [107], affinity purification-mass spectrometry [108], in vitro cross linking-mass spectrometry [109], phage display [110], yeast display [111] or reprogramming yeast mating [112].”
MethodShaheen, R., Jiang, N., Alzahrani, F., Ewida, N., Al‐Sheddi, T., Alobeid, E., Musaev, D., Stanley, V., Hashem, M., Ibrahim, N., et al. (2019) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2019.02.018 · Cited by 31
“While the function of FAM149B1 is unknown, we were intrigued by the findings of Huttlin and colleagues who used high-throughput affinity-purification mass spectrometry to identify interacting partners of 2,594 human proteins in HEK293T cells.(20) The resulting database showed experimental evidence of FAM149B1 interact…”
BackgroundRainer, J., Meraviglia, V., Blankenburg, H., Piubelli, C., Pramstaller, P. P., Paolin, A., Cogliati, E., Pompilio, G., Sommariva, E., Domingues, F. S., et al. (2018) · BMC Genomics · doi:10.1186/s12864-018-4876-6 · Cited by 29
“Huttlin EL, Ting L, Bruckner RJ, Gebreab F, Gygi MP, Szpyt J, et al. The BioPlex network: a systematic exploration of the human Interactome.”
MethodInfluentialTong, M., Yu, C., Zhan, D., Zhang, M., Zhen, B., Zhu, W., Wang, Y. N., Wu, C., He, F., Qin, J., et al. (2018) · EBioMedicine · doi:10.1016/j.ebiom.2018.12.039 · Cited by 27
“Those candidate substrates were further filtered by the known protein-protein interactions downloaded from eight public protein databases: BioGrid [27], PioPlex [28], CCSB [29], DIP [30], HPRD [31], IntAct [32], MINT [33], and PINA [34].”
MethodMass Spectrometry-Based Protein Complex Profiling in Time and Space
Zheng, J., Chen, X., Yang, Y., Tan, C. S. H., & Tian, R. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.0c04332 · Cited by 26
Fossati, A., Frommelt, F., Uliana, F., Martelli, C., Vizovišek, M., Gillet, L. C. J., Collins, B. C., Gstaiger, M., & Aebersold, R. H. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1178-4_18 · Cited by 21
Pintacuda, G., Lassen, F. H., Hsu, Y.-H. H., Kim, A., Martín, J. M., Małolepsza, E., Lim, J., Fornelos, N., Eggan, K. C., & Lage, K. (2021) · Nature Communications · doi:10.1038/s41467-021-22648-5 · Cited by 24
“Similar de fi nitions apply to test overlap with InWeb, iRefIndex, BioPlex, gnomAD, GTEx, or HPA data, except in this case the “ population ” ( N ) is the intersection of all genes in the experimental data and in the respective database, while the “ sample ” ( n ) is the subset of N consisting of known interactors for…”
BackgroundInfluentialDisease‐specific interactome alterations via epichaperomics: the case for Alzheimer’s disease
Ginsberg, S. D., Neubert, T. A., Sharma, S., Digwal, C. S., Yan, P., Timbus, C., Wang, T., & Chiosis, G. (2021) · FEBS Journal · doi:10.1111/febs.16031 · Cited by 28
Siepe, D. H., Henneberg, L. T., Wilson, S. C., Hess, G. T., Bassik, M. C., Zinn, K., & García, K. C. (2022) · eLife · doi:10.7554/elife.81398 · Cited by 26
“…screening methods, including affinity purification/mass spectrometry (AP/MS), yeast two-hybrid screening (Y2H), and phage display, are not well suited to analysis of extracellular domain (ECD) interactions (Havugimana et al., 2012; Huttlin et al., 2015; Krogan et al., 2006; Martinez-Martin, 2017).”
MethodVeenma, D. C. M., Cordeiro, D., Sondheimer, N., & Mercimek‐Andrews, S. (2018) · European Journal of Human Genetics · doi:10.1038/s41431-018-0237-9 · Cited by 27
An update on potentials and promises of T cell co‐signaling molecules in transplantation
Mardomi, A., Mohammadi, N., Khosroshahi, H. T., & Abediankenari, S. (2019) · Journal of Cellular Physiology · doi:10.1002/jcp.29369 · Cited by 27
Affinity proteomic dissection of the human nuclear cap-binding complex interactome
Dou, Y., Kalmykova, S., Pashkova, M., Oghbaie, M., Jiang, H. L., Molloy, K. R., Chait, B. T., Rout, M. P., Fenyö, D., Jensen, T. H., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa743 · Cited by 26
“(69,70)) - but the community also understands that there is still a great deal of missing information (54,55).”
BackgroundA reference map of the human protein interactomePreprint
Luck, K., Kim, D., Lambourne, L., Spirohn, K., Begg, B. E., Bian, W., Brignall, R., Cafarelli, T. M., Campos-Laborie, F. J., Charloteaux, B., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/605451 · Cited by 27
Proximity labeling for investigating protein-protein interactions
Pfeiffer, C. T., Paulo, J. A., Gygi, S. P., & Rockman, H. A. (2022) · Methods in cell biology · doi:10.1016/bs.mcb.2021.12.006 · Cited by 28
The Promise of Systems Biology Approaches for Revealing Host Pathogen Interactions in Malaria
Zuck, M., Austin, L. S., Danziger, S. A., Aitchison, J. D., & Kaushansky, A. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.02183 · Cited by 26
“Databases of protein interactions in many organisms, including humans, are becoming highly populated (Hein et al., 2015; Huttlin et al., 2015).”
BackgroundANKRD9 is associated with tumor suppression as a substrate receptor subunit of ubiquitin ligase
Lee, Y., Lim, B., Lee, S., Lee, W. R., Kim, Y., Kim, M., Ju, H., Kim, M. Y., Kang, S., Song, J., et al. (2018) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2018.07.001 · Cited by 26
Su, Y., Yang, L., Li, Z., Wang, W., Xing, M., Fang, Y., Cheng, Y., Lin, G. N., & Cui, D. (2020) · Progress in Neuro-Psychopharmacology and Biological Psychiatry · doi:10.1016/j.pnpbp.2020.110015 · Cited by 27
Lü, J., Jiang, H., Li, D., Chen, T., Wang, Y., Pu, Z., & Xu, G. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.1c00437 · Cited by 26
Co-adaptor driven assembly of a CUL3 E3 ligase complex
Akopian, D., McGourty, C. A., & Rapé, M. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.01.004 · Cited by 26
Receptor clustering by a precise set of extracellular galectins initiates FGFR signaling
Żukowska, D., Gędaj, A., Porębska, N., Poźniak, M., Krzyścik, M., Czyrek, A. A., Krowarsch, D., Zakrzewska, M., Otlewski, J., & Opalinski, L. (2023) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-023-04768-x · Cited by 25
Annexins: Ca2+ Effectors Determining Membrane Trafficking in the Late Endocytic Compartment
Enrich, C., Rentero, C., Meneses‐Salas, E., Tebar, F., & Grewal, T. (2017) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-55858-5_14 · Cited by 26
Zhou, B., Yan, Y., Wang, Y., You, S., Freeman, M. R., & Yang, W. (2019) · Clinical Proteomics · doi:10.1186/s12014-019-9236-2 · Cited by 26
Cholesterol restricts lymphotoxin β receptor-triggered NF-κB signaling
Banach‐Orlowska, M., Wyszyńska, R., Pyrzyńska, B., Maksymowicz, M., Gołąb, J., & Miączyńska, M. (2019) · Cell Communication and Signaling · doi:10.1186/s12964-019-0460-1 · Cited by 26
Raynor, J. L., Collins, N., Shi, H., Guy, C. S., Saravia, J., Lim, S. A., Chapman, N. M., Zhou, P., Wang, Y., Sun, Y., et al. (2024) · Immunity · doi:10.1016/j.immuni.2024.09.013 · Cited by 25
Penterling, C., Drexler, G. A., Böhland, C., Stamp, R., Wilke, C., Braselmann, H., Caldwell, R. B., Reindl, J., Girst, S., Greubel, C., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0156599 · Cited by 25
“These three sites are known targets of HDAC1 and HDAC2 [51,78], with which protein Jarid1A was shown to physically interact [46,79].”
BackgroundProteomic Analysis of the Mediator Complex Interactome in Saccharomyces cerevisiae
Uthe, H., Vanselow, J. T., & Schlösser, A. (2017) · Scientific Reports · doi:10.1038/srep43584 · Cited by 26
Chen, Y., Leng, M., Gao, Y., Zhan, D., Choi, J. M., Song, L., Li, K., Xia, X., Zhang, C., Liu, M., et al. (2019) · Journal of Proteome Research · doi:10.1021/acs.jproteome.9b00427 · Cited by 25
Kavli, B., Iveland, T. S., Buchinger, E., Hagen, L., Liabakk, N., Aas, P. A., Obermann, T., Aachmann, F. L., & Slupphaug, G. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab195 · Cited by 25
Network module‐based drug repositioning for pulmonary arterial hypertension
Wang, R., & Loscalzo, J. (2021) · CPT Pharmacometrics & Systems Pharmacology · doi:10.1002/psp4.12670 · Cited by 24
Matrix Metalloproteinases in Human Decidualized Endometrial Stromal Cells
Hisamatsu, Y., Murata, H., Tsubokura, H., Hashimoto, Y. K., Kitada, M., Tanaka, S., & Okada, H. (2021) · Current Issues in Molecular Biology · doi:10.3390/cimb43030146 · Cited by 26
From Drosophila to Human: Biological Function of E3 Ligase Godzilla and Its Role in Disease
Cabana, V. C., & Lussier, M. P. (2022) · Cells · doi:10.3390/cells11030380 · Cited by 23
“expressed hundreds of FLAG-HA-tagged baits in HEK293T cells and combined immunopurification and mass spectrometry to identify interactors of these bait proteins [54].”
BackgroundLamina Associated Polypeptide 1 (LAP1) Interactome and Its Functional Features
Serrano, J. B., Silva, O. A. B. D. C. E., & Rebelo, S. (2016) · Membranes · doi:10.3390/membranes6010008 · Cited by 25
“PPP1CC Serine/threonine-protein phosphatase PP1-gamma catalytic subunit P36873 Homo sapiens Affinity Capture-WB [47] Two-hybrid [49] PTCH1 Protein patched homolog 1 Q13635 Homo sapiens Affinity Capture-MS [34] RIF1 Telomere-associated protein RIF1 Q5UIP0 Homo sapiens Co-fractionation [38] SCARNA22 ** Small Cajal body-…”
MethodTMEM39A and Human Diseases: A Brief Review
Tran, Q., Park, J., Lee, H., Hong, Y., Hong, S., Park, S., Park, J., & Kim, S.-H. (2017) · Toxicological Research · doi:10.5487/tr.2017.33.3.205 · Cited by 25
“TMEM39A was found to be interacted with several protein baits (28).”
BackgroundAlternate RNA decoding results in stable and abundant proteins in mammals
Tsour, S., Machné, R., Leduc, A., Widmer, S. D., Koo, E., Guez, J., Karczewski, K. J., & Slavov, N. (2026) · Nature · doi:10.1038/s41586-026-10678-2 · Cited by 24
“Immunoprecipitation–MS experiments for 25 proteins with SAAPs detected from human tissue samples were downloaded from the BioPlex project 54 .”
Chaplot, K., Pimpale, L. G., Ramalingam, B., Deivasigamani, S., Kamat, S. S., & Ratnaparkhi, G. S. (2019) · Disease Models & Mechanisms · doi:10.1242/dmm.033803 · Cited by 22
“, 2003; Murphy and Levine, 2016), impairing cellular functions (De Vos et al., 2012; Huttlin et al., 2015; MoustaqimBarrette et al., 2014).”
A network-based deep learning methodology for stratification of tumor mutations
Liu, C., Han, Z. Y., Zhang, Z., Nussinov, R., & Cheng, F. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa1099 · Cited by 23
Thomas, D. M., Kannabiran, C., & Balasubramanian, D. (2021) · Frontiers in Medicine · doi:10.3389/fmed.2021.690594 · Cited by 24
“Based on the evaluations, four genes such as FZD4, LRP5, FZD5, NDP were involved in the process of eye development, retina vasculature development, retinal blood vessel morphogenesis, and the Wnt signaling pathway [Figure 6B; (43, 44)].”
BackgroundOmranian, S., Nikoloski, Z., & Grimm, D. G. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.05.049 · Cited by 28
“the set of protein complexes in a cell) for different species [42,33].”
Liu, L., Kryvokhyzha, D., Rippe, C., Jacob, A. G., Borreguero‐Muñoz, A., Stenkula, K. G., Hansson, O., Smith, C. W. J., Fisher, S. A., & Swärd, K. (2022) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-022-04497-7 · Cited by 22
“Protein levels, determined by western blotting, of MBNL1, RBPMS2, and RBFOX2 did not change after forced expression of MYOCD at 6d (data not shown).”
BackgroundInfluential
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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