A draft network of ligand-receptor-mediated multicellular signalling in human

被引:555
作者
Ramilowski, Jordan A. [1 ]
Goldberg, Tatyana [2 ,3 ]
Harshbarger, Jayson [1 ]
Kloppman, Edda [2 ]
Lizio, Marina [1 ]
Satagopam, Venkata P. [4 ]
Itoh, Masayoshi [1 ,5 ]
Kawaji, Hideya [1 ,5 ]
Carninci, Piero [1 ]
Rost, Burkhard [2 ,3 ]
Forrest, Alistair R. R. [1 ,6 ,7 ]
机构
[1] RIKEN Ctr Life Sci Technol, Div Genom Technol, Tsurumi Ku, Yokohama, Kanagawa 2300045, Japan
[2] TUM, Dept Bioinformat & Computat Biol I12, D-85748 Garching, Germany
[3] Ctr Doctoral Studies Informat & its Applicat CeDo, TUM Grad Sch, D-85748 Garching, Germany
[4] Luxembourg Ctr Syst Biomed, L-4362 Belval, Luxembourg
[5] RIKEN Prevent Med & Diag Innovat Program, Wako, Saitama 3510198, Japan
[6] Univ Western Australia, Harry Perkins Inst Med Res, QEII Med Ctr, Perth, WA 6008, Australia
[7] Univ Western Australia, Med Res Ctr, Perth, WA 6008, Australia
关键词
GENE-EXPRESSION; GROWTH-FACTOR; CELL COMMUNICATION; PROTEIN FAMILIES; T-CELLS; DATABASE; DIFFERENTIATION; IDENTIFICATION; RECRUITMENT; PREDICTION;
D O I
10.1038/ncomms8866
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Cell-to-cell communication across multiple cell types and tissues strictly governs proper functioning of metazoans and extensively relies on interactions between secreted ligands and cell-surface receptors. Herein, we present the first large-scale map of cell-to-cell communication between 144 human primary cell types. We reveal that most cells express tens to hundreds of ligands and receptors to create a highly connected signalling network through multiple ligand-receptor paths. We also observe extensive autocrine signalling with approximately two-thirds of partners possibly interacting on the same cell type. We find that plasma membrane and secreted proteins have the highest cell-type specificity, they are evolutionarily younger than intracellular proteins, and that most receptors had evolved before their ligands. We provide an online tool to interactively query and visualize our networks and demonstrate how this tool can reveal novel cell-to-cell interactions with the prediction that mast cells signal to monoblastic lineages via the CSF1-CSF1R interacting pair.
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页数:11
相关论文
共 61 条
[1]   The InterPro database, an integrated documentation resource for protein families, domains and functional sites [J].
Apweiler, R ;
Attwood, TK ;
Bairoch, A ;
Bateman, A ;
Birney, E ;
Biswas, M ;
Bucher, P ;
Cerutti, T ;
Corpet, F ;
Croning, MDR ;
Durbin, R ;
Falquet, L ;
Fleischmann, W ;
Gouzy, J ;
Hermjakob, H ;
Hulo, N ;
Jonassen, I ;
Kahn, D ;
Kanapin, A ;
Karavidopoulou, Y ;
Lopez, R ;
Marx, B ;
Mulder, NJ ;
Oinn, TM ;
Pagni, M ;
Servant, F ;
Sigrist, CJA ;
Zdobnov, EM .
NUCLEIC ACIDS RESEARCH, 2001, 29 (01) :37-40
[2]   Activities at the Universal Protein Resource (UniProt) [J].
Apweiler, Rolf ;
Bateman, Alex ;
Martin, Maria Jesus ;
O'Donovan, Claire ;
Magrane, Michele ;
Alam-Faruque, Yasmin ;
Alpi, Emanuele ;
Antunes, Ricardo ;
Arganiska, Joanna ;
Casanova, Elisabet Barrera ;
Bely, Benoit ;
Bingley, Mark ;
Bonilla, Carlos ;
Britto, Ramona ;
Bursteinas, Borisas ;
Chan, Wei Mun ;
Chavali, Gayatri ;
Cibrian-Uhalte, Elena ;
Da Silva, Alan ;
De Giorgi, Maurizio ;
Dogan, Tunca ;
Fazzini, Francesco ;
Gane, Paul ;
Castro, Leyla Garcia ;
Garmiri, Penelope ;
Hatton-Ellis, Emma ;
Hieta, Reija ;
Huntley, Rachael ;
Legge, Duncan ;
Liu, Wudong ;
Luo, Jie ;
MacDougall, Alistair ;
Mutowo, Prudence ;
Nightingale, Andrew ;
Orchard, Sandra ;
Pichler, Klemens ;
Poggioli, Diego ;
Pundir, Sangya ;
Pureza, Luis ;
Qi, Guoying ;
Rosanoff, Steven ;
Saidi, Rabie ;
Sawford, Tony ;
Shypitsyna, Aleksandra ;
Turner, Edward ;
Volynkin, Vladimir ;
Wardell, Tony ;
Watkins, Xavier ;
Zellner, Hermann ;
Corbett, Matt .
NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) :D191-D198
[3]   Gene Ontology: tool for the unification of biology [J].
Ashburner, M ;
Ball, CA ;
Blake, JA ;
Botstein, D ;
Butler, H ;
Cherry, JM ;
Davis, AP ;
Dolinski, K ;
Dwight, SS ;
Eppig, JT ;
Harris, MA ;
Hill, DP ;
Issel-Tarver, L ;
Kasarskis, A ;
Lewis, S ;
Matese, JC ;
Richardson, JE ;
Ringwald, M ;
Rubin, GM ;
Sherlock, G .
NATURE GENETICS, 2000, 25 (01) :25-29
[4]   EVIDENCE THAT STIMULATION OF GROWTH-HORMONE RELEASE BY EPINEPHRINE AND VASOACTIVE-INTESTINAL-PEPTIDE IS BASED ON CELL-TO-CELL COMMUNICATION IN THE PITUITARY [J].
BAES, M ;
DENEF, C .
ENDOCRINOLOGY, 1987, 120 (01) :280-290
[5]   Leptin receptor signaling in is required for normal body POW neurons weight homeostasis [J].
Balthasar, N ;
Coppari, R ;
McMinn, J ;
Liu, SM ;
Lee, CE ;
Tang, V ;
Kenny, CD ;
McGovern, RA ;
Chua, SC ;
Elmquist, JK ;
Lowell, BB .
NEURON, 2004, 42 (06) :983-991
[6]   Endoglin is an accessory protein that interacts with the signaling receptor complex of multiple members of the transforming growth factor-β superfamily [J].
Barbara, NP ;
Wrana, JL ;
Letarte, M .
JOURNAL OF BIOLOGICAL CHEMISTRY, 1999, 274 (02) :584-594
[7]  
Bastian M., ICWSM, Vvol 3, ppp 361, DOI [10.1016/B978-0-12-372180-8.50042-1, DOI 10.1609/ICWSM.V3I1.13937]
[8]   GOstat: find statistically overrepresented Gene Ontologies within a group of genes [J].
Beissbarth, T ;
Speed, TP .
BIOINFORMATICS, 2004, 20 (09) :1464-1465
[9]  
Ben-Shlomo Izhar, 2003, Sci STKE, V2003, pRE9, DOI 10.1126/stke.2003.187.re9
[10]   D3: Data-Driven Documents [J].
Bostock, Michael ;
Ogievetsky, Vadim ;
Heer, Jeffrey .
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, 2011, 17 (12) :2301-2309