Stem cells are capable of self-renewal and differentiation, and the processes regulating these events are among the most comprehensively investigated topics in life sciences. In particular, the molecular mechanisms of the self-renewal, proliferation, and differentiation of stem cells have been extensively examined. Multi-omics integrative analysis, such as transcriptomics combined with proteomics, is one of the most promising approaches to the systemic investigation of stem cell biology. We reviewed the available information on stem cells by examining published results using transcriptomic and proteomic characterization of the different stem cell processes. Comprehensive understanding of these important processes can only be achieved using a systemic methodology, and employing such method will strengthen the study on stem cell biology and promote the clinical applications of stem cells.
Z Wang, M Gerstein, M Snyder. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009; 10(1): 57–63 https://doi.org/10.1038/nrg2484
pmid: 19015660
8
S Efroni, R Duttagupta, J Cheng, H Dehghani, DJ Hoeppner, C Dash, DP Bazett-Jones, S Le Grice, RDG McKay, KH Buetow, TR Gingeras, T Misteli, E Meshorer. Global transcription in pluripotent embryonic stem cells. Cell Stem Cell 2008; 2(5): 437–447 https://doi.org/10.1016/j.stem.2008.03.021
pmid: 18462694
9
MH Chin, MJ Mason, W Xie, S Volinia, M Singer, C Peterson, G Ambartsumyan, O Aimiuwu, L Richter, J Zhang, I Khvorostov, V Ott, M Grunstein, N Lavon, N Benvenisty, CM Croce, AT Clark, T Baxter, AD Pyle, MA Teitell, M Pelegrini, K Plath, WE Lowry. Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell 2009; 5(1): 111–123 https://doi.org/10.1016/j.stem.2009.06.008
pmid: 19570518
10
I Ginis, Y Luo, T Miura, S Thies, R Brandenberger, S Gerecht-Nir, M Amit, A Hoke, MK Carpenter, J Itskovitz-Eldor, MS Rao. Differences between human and mouse embryonic stem cells. Dev Biol 2004; 269(2): 360–380 https://doi.org/10.1016/j.ydbio.2003.12.034
pmid: 15110706
11
B Bhattacharya, T Miura, R Brandenberger, J Mejido, Y Luo, AX Yang, BH Joshi, I Ginis, RS Thies, M Amit, I Lyons, BG Condie, J Itskovitz-Eldor, MS Rao, RK Puri. Gene expression in human embryonic stem cell lines: unique molecular signature. Blood 2004; 103(8): 2956–2964 https://doi.org/10.1182/blood-2003-09-3314
pmid: 15070671
12
R Brandenberger, I Khrebtukova, RS Thies, T Miura, C Jingli, R Puri, T Vasicek, J Lebkowski, M Rao. MPSS profiling of human embryonic stem cells. BMC Dev Biol 2004; 4(1): 10 https://doi.org/10.1186/1471-213X-4-10
pmid: 15304200
13
M Zhan. Genomic studies to explore self-renewal and differentiation properties of embryonic stem cells. Front Biosci 2008; 13(13): 276–283 https://doi.org/10.2741/2678
pmid: 17981546
14
F Djouad, C Bony, F Canovas, O Fromigué, T Rème, C Jorgensen, D Noël. Transcriptomic analysis identifies Foxo3A as a novel transcription factor regulating mesenchymal stem cell chrondrogenic differentiation. Cloning Stem Cells 2009; 11(3): 407–416 https://doi.org/10.1089/clo.2009.0013
pmid: 19751111
15
NB Ivanova, JT Dimos, C Schaniel, JA Hackney, KA Moore, IR Lemischka. A stem cell molecular signature. Science 2002; 298(5593): 601–604 https://doi.org/10.1126/science.1073823
pmid: 12228721
16
M Ramalho-Santos, S Yoon, Y Matsuzaki, RC Mulligan, DA Melton. “Stemness”: transcriptional profiling of embryonic and adult stem cells. Science 2002; 298(5593): 597–600 https://doi.org/10.1126/science.1072530
pmid: 12228720
17
M Suárez-Fariñas, S Noggle, M Heke, A Hemmati-Brivanlou, MO Magnasco. Comparing independent microarray studies: the case of human embryonic stem cells. BMC Genomics 2005; 6(1): 99 https://doi.org/10.1186/1471-2164-6-99
pmid: 16042783
18
Y Yang, H Wang, KH Chang, H Qu, Z Zhang, Q Xiong, H Qi, P Cui, Q Lin, X Ruan, Y Yang, Y Li, C Shu, Q Li, EK Wakeland, J Yan, S Hu, X Fang. Transcriptome dynamics during human erythroid differentiation and development. Genomics 2013; 102(5-6): 431–441 https://doi.org/10.1016/j.ygeno.2013.09.005
pmid: 24121002
19
AA Sigova, AC Mullen, B Molinie, S Gupta, DA Orlando, MG Guenther, AE Almada, C Lin, PA Sharp, CC Giallourakis, RA Young. Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells. Proc Natl Acad Sci USA 2013; 110(8): 2876–2881 https://doi.org/10.1073/pnas.1221904110
pmid: 23382218
20
L Yan, M Yang, H Guo, L Yang, J Wu, R Li, P Liu, Y Lian, X Zheng, J Yan, J Huang, M Li, X Wu, L Wen, K Lao, R Li, J Qiao, F Tang. Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat Struct Mol Biol 2013; 20(9): 1131–1139 https://doi.org/10.1038/nsmb.2660
pmid: 23934149
21
T MacRae, T Sargeant, S Lemieux, J Hébert, E Deneault, G Sauvageau. RNA-Seq reveals spliceosome and proteasome genes as most consistent transcripts in human cancer cells. PLoS ONE 2013; 8(9): e72884 https://doi.org/10.1371/journal.pone.0072884
pmid: 24069164
22
K Jääger, S Islam, P Zajac, S Linnarsson, T Neuman. RNA-seq analysis reveals different dynamics of differentiation of human dermis- and adipose-derived stromal stem cells. PLoS ONE 2012; 7(6): e38833 https://doi.org/10.1371/journal.pone.0038833
pmid: 22723894
23
G Gargiulo, M Cesaroni, M Serresi, N de Vries, D Hulsman, SW Bruggeman, C Lancini, M van Lohuizen.In vivo RNAi screen for BMI1 targets identifies TGF-β/BMP-ER stress pathways as key regulators of neural- and malignant glioma-stem cell homeostasis. Cancer Cell 2013; 23(5): 660–676 https://doi.org/10.1016/j.ccr.2013.03.030
pmid: 23680149
24
N Salomonis, CR Schlieve, L Pereira, C Wahlquist, A Colas, AC Zambon, K Vranizan, MJ Spindler, AR Pico, MS Cline, TA Clark, A Williams, JE Blume, E Samal, M Mercola, BJ Merrill, BR Conklin. Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation. Proc Natl Acad Sci USA 2010; 107(23): 10514–10519 https://doi.org/10.1073/pnas.0912260107
pmid: 20498046
25
JQ Wu, L Habegger, P Noisa, A Szekely, C Qiu, S Hutchison, D Raha, M Egholm, H Lin, S Weissman, W Cui, M Gerstein, M Snyder. Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proc Natl Acad Sci USA 2010; 107(11): 5254–5259 https://doi.org/10.1073/pnas.0914114107
pmid: 20194744
26
R Brandenberger, H Wei, S Zhang, S Lei, J Murage, GJ Fisk, Y Li, C Xu, R Fang, K Guegler, MS Rao, R Mandalam, J Lebkowski, LW Stanton. Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation. Nat Biotechnol 2004; 22(6): 707–716 https://doi.org/10.1038/nbt971
pmid: 15146197
27
SV Anisimov, KV Tarasov, D Tweedie, MD Stern, AM Wobus, KR Boheler. SAGE identification of gene transcripts with profiles unique to pluripotent mouse R1 embryonic stem cells. Genomics 2002; 79(2): 169–176 https://doi.org/10.1006/geno.2002.6687
pmid: 11829487
MR Suh, Y Lee, JY Kim, SK Kim, SH Moon, JY Lee, KY Cha, HM Chung, HS Yoon, SY Moon, VN Kim, KS Kim. Human embryonic stem cells express a unique set of microRNAs. Dev Biol 2004; 270(2): 488–498 https://doi.org/10.1016/j.ydbio.2004.02.019
pmid: 15183728
30
A Jouneau, C Ciaudo, O Sismeiro, V Brochard, L Jouneau, S Vandormael-Pournin, JY Coppée, Q Zhou, E Heard, C Antoniewski, M Cohen-Tannoudji. Naive and primed murine pluripotent stem cells have distinct miRNA expression profiles. RNA 2012; 18(2): 253–264 https://doi.org/10.1261/rna.028878.111
pmid: 22201644
31
FF Kirigin, K Lindstedt, M Sellars, M Ciofani, SL Low, L Jones, F Bell, F Pauli, R Bonneau, RM Myers, DR Littman, MMW Chong. Dynamic microRNA gene transcription and processing during T cell development. J Immunol 2012; 188(7): 3257–3267 https://doi.org/10.4049/jimmunol.1103175
pmid: 22379031
32
A Marson, SS Levine, MF Cole, GM Frampton, T Brambrink, S Johnstone, MG Guenther, WK Johnston, M Wernig, J Newman, JM Calabrese, LM Dennis, TL Volkert, S Gupta, J Love, N Hannett, PA Sharp, DP Bartel, R Jaenisch, RA Young. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 2008; 134(3): 521–533 https://doi.org/10.1016/j.cell.2008.07.020
pmid: 18692474
J Sheik Mohamed, PM Gaughwin, B Lim, P Robson, L Lipovich. Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells. RNA 2010; 16(2): 324–337 https://doi.org/10.1261/rna.1441510
pmid: 20026622
35
ME Dinger, PP Amaral, TR Mercer, KC Pang, SJ Bruce, BB Gardiner, ME Askarian-Amiri, K Ru, G Soldà, C Simons, SM Sunkin, ML Crowe, SM Grimmond, AC Perkins, JS Mattick. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 2008; 18(9): 1433–1445 https://doi.org/10.1101/gr.078378.108
pmid: 18562676
36
AD Ramos, A Diaz, A Nellore, RN Delgado, KY Park, G Gonzales-Roybal, MC Oldham, JS Song, DA Lim. Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo. Cell Stem Cell 2013; 12(5): 616–628 https://doi.org/10.1016/j.stem.2013.03.003
pmid: 23583100
K Nagano, M Taoka, Y Yamauchi, C Itagaki, T Shinkawa, K Nunomura, N Okamura, N Takahashi, T Izumi, T Isobe. Large-scale identification of proteins expressed in mouse embryonic stem cells. Proteomics 2005; 5(5): 1346–1361 https://doi.org/10.1002/pmic.200400990
pmid: 15742316
40
D Nasrabadi, M Rezaei Larijani, L Pirhaji, H Gourabi, A Shahverdi, H Baharvand, GH Salekdeh. Proteomic analysis of monkey embryonic stem cell during differentiation. J Proteome Res 2009; 8(3): 1527–1539 https://doi.org/10.1021/pr800880v
pmid: 19226164
41
A Böser, HCA Drexler, H Reuter, H Schmitz, G Wu, HR Schöler, L Gentile, K Bartscherer. SILAC proteomics of planarians identifies Ncoa5 as a conserved component of pluripotent stem cells. Cell Reports 2013; 5(4): 1142–1155 https://doi.org/10.1016/j.celrep.2013.10.035
pmid: 24268775
42
Y Sun, Y Yang, S Zeng, Y Tan, G Lu, G Lin. Identification of proteins related to epigenetic regulation in the malignant transformation of aberrant karyotypic human embryonic stem cells by quantitative proteomics. PLoS ONE 2014; 9(1): e85823 https://doi.org/10.1371/journal.pone.0085823
pmid: 24465727
43
S D’Aguanno, D Barcaroli, C Rossi, M Zucchelli, D Ciavardelli, C Cortese, A De Cola, S Volpe, D D’Agostino, M Todaro, G Stassi, C Di Ilio, A Urbani, V De Laurenzi. p63 Isoforms Regulate Metabolism of Cancer Stem Cells. J Proteome Res 2014; 13(4): 2120–2136 https://doi.org/10.1021/pr4012574
pmid: 24597989
44
H Lin, E Lee, K Hestir, C Leo, M Huang, E Bosch, R Halenbeck, G Wu, A Zhou, D Behrens, D Hollenbaugh, T Linnemann, M Qin, J Wong, K Chu, SK Doberstein, LT Williams. Discovery of a cytokine and its receptor by functional screening of the extracellular proteome. Science 2008; 320(5877): 807–811 https://doi.org/10.1126/science.1154370
pmid: 18467591
45
R Gonzalez, LL Jennings, M Knuth, AP Orth, HE Klock, W Ou, J Feuerhelm, MV Hull, E Koesema, Y Wang, J Zhang, C Wu, CY Cho, AI Su, S Batalov, H Chen, K Johnson, B Laffitte, DG Nguyen, EY Snyder, PG Schultz, JL Harris, SA Lesley. Screening the mammalian extracellular proteome for regulators of embryonic human stem cell pluripotency. Proc Natl Acad Sci USA 2010; 107(8): 3552–3557 https://doi.org/10.1073/pnas.0914019107
pmid: 20133595
46
M Gemei, C Corbo, F D’Alessio, R Di Noto, R Vento, L Del Vecchio. Surface proteomic analysis of differentiated versus stem-like osteosarcoma human cells. Proteomics 2013; 13(22): 3293–3297 https://doi.org/10.1002/pmic.201300170
pmid: 24106197
47
D Van Hoof, J Muñoz, SR Braam, MWH Pinkse, R Linding, AJR Heck, CL Mummery, J Krijgsveld. Phosphorylation dynamics during early differentiation of human embryonic stem cells. Cell Stem Cell 2009; 5(2): 214–226 https://doi.org/10.1016/j.stem.2009.05.021
pmid: 19664995
48
LM Brill, W Xiong, KB Lee, SB Ficarro, A Crain, Y Xu, A Terskikh, EY Snyder, S Ding. Phosphoproteomic analysis of human embryonic stem cells. Cell Stem Cell 2009; 5(2): 204–213 https://doi.org/10.1016/j.stem.2009.06.002
pmid: 19664994
49
DL Swaney, CD Wenger, JA Thomson, JJ Coon. Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry. Proc Natl Acad Sci USA 2009; 106(4): 995–1000 https://doi.org/10.1073/pnas.0811964106
pmid: 19144917
50
KT Rigbolt, TA Prokhorova, V Akimov, J Henningsen, PT Johansen, I Kratchmarova, M Kassem, M Mann, JV Olsen, B Blagoev. System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. Sci Signal 2011; 4(164): rs3 https://doi.org/10.1126/scisignal.2001570
pmid: 21406692
51
H Xu, C Baroukh, R Dannenfelser, EY Chen, CM Tan, Y Kou, YE Kim, IR Lemischka, A Ma’ayan. ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells. Database (Oxford) 2013; 2013: bat045 https://doi.org/10.1093/database/bat045
pmid: 23794736
52
MH Chin, MJ Mason, W Xie, S Volinia, M Singer, C Peterson, G Ambartsumyan, O Aimiuwu, L Richter, J Zhang, I Khvorostov, V Ott, M Grunstein, N Lavon, N Benvenisty, CM Croce, AT Clark, T Baxter, AD Pyle, MA Teitell, M Pelegrini, K Plath, WE Lowry. Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell 2009; 5(1): 111–123 https://doi.org/10.1016/j.stem.2009.06.008
pmid: 19570518
53
J Yu, K Hu, K Smuga-Otto, S Tian, R Stewart, II Slukvin, JA Thomson. Human induced pluripotent stem cells free of vector and transgene sequences. Science 2009; 324(5928): 797–801 https://doi.org/10.1126/science.1172482
pmid: 19325077
54
D Van Hoof, J Muñoz, SR Braam, MWH Pinkse, R Linding, AJR Heck, CL Mummery, J Krijgsveld. Phosphorylation dynamics during early differentiation of human embryonic stem cells. Cell Stem Cell 2009; 5(2): 214–226 https://doi.org/10.1016/j.stem.2009.05.021
pmid: 19664995
55
J Munoz, TY Low, YJ Kok, A Chin, CK Frese, V Ding, A Choo, AJR Heck. The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells. Mol Syst Biol 2011; 7: 550 https://doi.org/10.1038/msb.2011.84
pmid: 22108792
56
R Sridharan, M Gonzales-Cope, C Chronis, G Bonora, R McKee, C Huang, S Patel, D Lopez, N Mishra, M Pellegrini, M Carey, BA Garcia, K Plath. Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency. Nat Cell Biol 2013; 15(7): 872–882 https://doi.org/10.1038/ncb2768
pmid: 23748610
57
DH Phanstiel, J Brumbaugh, CD Wenger, S Tian, MD Probasco, DJ Bailey, DL Swaney, MA Tervo, JM Bolin, V Ruotti, R Stewart, JA Thomson, JJ Coon. Proteomic and phosphoproteomic comparison of human ES and iPS cells. Nat Methods 2011; 8(10): 821–827 https://doi.org/10.1038/nmeth.1699
pmid: 21983960
58
C Perez-Iratxeta, G Palidwor, CJ Porter, NA Sanche, MR Huska, BP Suomela, EM Muro, PM Krzyzanowski, E Hughes, PA Campbell, MA Rudnicki, MA Andrade. Study of stem cell function using microarray experiments. FEBS Lett 2005; 579(8): 1795–1801 https://doi.org/10.1016/j.febslet.2005.02.020
pmid: 15763554
59
SA Sansone, P Rocca-Serra, D Field, E Maguire, C Taylor, O Hofmann, H Fang, S Neumann, W Tong, L Amaral-Zettler, K Begley, T Booth, L Bougueleret, G Burns, B Chapman, T Clark, LA Coleman, J Copeland, S Das, A de Daruvar, P de Matos, I Dix, S Edmunds, CT Evelo, MJ Forster, P Gaudet, J Gilbert, C Goble, JL Griffin, D Jacob, J Kleinjans, L Harland, K Haug, H Hermjakob, SJ Ho Sui, A Laederach, S Liang, S Marshall, A McGrath, E Merrill, D Reilly, M Roux, CE Shamu, CA Shang, C Steinbeck, A Trefethen, B Williams-Jones, K Wolstencroft, I Xenarios, W Hide. Toward interoperable bioscience data. Nat Genet 2012; 44(2): 121–126 https://doi.org/10.1038/ng.1054
pmid: 22281772
60
SJ Ho Sui, K Begley, D Reilly, B Chapman, R McGovern, P Rocca-Sera, E Maguire, GM Altschuler, TAA Hansen, R Sompallae, A Krivtsov, RA Shivdasani, SA Armstrong, AC Culhane, M Correll, SA Sansone, O Hofmann, W Hide. The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons. Nucleic Acids Res 2012; 40(Database issue): D984–D991 https://doi.org/10.1093/nar/gkr1051
pmid: 22121217
61
M Jung, H Peterson, L Chavez, P Kahlem, H Lehrach, J Vilo, J Adjaye. A data integration approach to mapping OCT4 gene regulatory networks operative in embryonic stem cells and embryonal carcinoma cells. PLoS ONE 2010; 5(5): e10709 https://doi.org/10.1371/journal.pone.0010709
pmid: 20505756
62
BS Mallon, JG Chenoweth, KR Johnson, RS Hamilton, PJ Tesar, AS Yavatkar, LJ Tyson, K Park, KG Chen, YC Fann, RDG McKay. StemCellDB: the human pluripotent stem cell database at the National Institutes of Health. Stem Cell Res (Amst) 2013; 10(1): 57–66 https://doi.org/10.1016/j.scr.2012.09.002
pmid: 23117585
63
V Costa, C Angelini, I De Feis, A Ciccodicola. Uncovering the complexity of transcriptomes with RNA-Seq. J Biomed Biotechnol 2010; 2010: 853916.
SH Nagaraj, RB Gasser, S Ranganathan. A hitchhiker’s guide to expressed sequence tag (EST) analysis. Brief Bioinform 2007; 8(1): 6–21 https://doi.org/10.1093/bib/bbl015
pmid: 16772268
B Langmead, C Trapnell, M Pop, SL Salzberg. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009; 10(3): R25 https://doi.org/10.1186/gb-2009-10-3-r25
pmid: 19261174
70
G Jean, A Kahles, VT Sreedharan, F De Bona, G Ratsch. RNA-Seq read alignments with PALMapper. Curr Protoc Bioinformatics 2010; Chapter 11: Unit 11 6
K Wang, D Singh, Z Zeng, SJ Coleman, Y Huang, GL Savich, X He, P Mieczkowski, SA Grimm, CM Perou, JN MacLeod, DY Chiang, JF Prins, J Liu. MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res 2010; 38(18): e178 https://doi.org/10.1093/nar/gkq622
pmid: 20802226
M Guttman, M Garber, JZ Levin, J Donaghey, J Robinson, X Adiconis, L Fan, MJ Koziol, A Gnirke, C Nusbaum, JL Rinn, ES Lander, A Regev. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol 2010; 28(5): 503–510 https://doi.org/10.1038/nbt.1633
pmid: 20436462
75
KF Au, H Jiang, L Lin, Y Xing, WH Wong. Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res 2010; 38(14): 4570–4578 https://doi.org/10.1093/nar/gkq211
pmid: 20371516
76
A Roberts, C Trapnell, J Donaghey, JL Rinn, L Pachter. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol 2011; 12(3): R22 https://doi.org/10.1186/gb-2011-12-3-r22
pmid: 21410973
77
MR Friedländer, W Chen, C Adamidi, J Maaskola, R Einspanier, S Knespel, N Rajewsky. Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 2008; 26(4): 407–415 https://doi.org/10.1038/nbt1394
pmid: 18392026
78
R Ronen, I Gan, S Modai, A Sukacheov, G Dror, E Halperin, N Shomron. miRNAkey: a software for microRNA deep sequencing analysis. Bioinformatics 2010; 26(20): 2615–2616 https://doi.org/10.1093/bioinformatics/btq493
pmid: 20801911
79
M Hackenberg, N Rodríguez-Ezpeleta, AM Aransay. miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments. Nucleic Acids Res 2011; 39(Web Server issue): W132–138
pmid: 21515631
80
PJ Huang, YC Liu, CC Lee, WC Lin, RRC Gan, PC Lyu, P Tang. DSAP: deep-sequencing small RNA analysis pipeline. Nucleic Acids Res 2010; 38(Web Server issue): W385–391
pmid: 20478825
81
BP Lewis, CB Burge, DP Bartel. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005; 120(1): 15–20 https://doi.org/10.1016/j.cell.2004.12.035
pmid: 15652477
82
A Krek, D Grün, MN Poy, R Wolf, L Rosenberg, EJ Epstein, P MacMenamin, I da Piedade, KC Gunsalus, M Stoffel, N Rajewsky. Combinatorial microRNA target predictions. Nat Genet 2005; 37(5): 495–500 https://doi.org/10.1038/ng1536
pmid: 15806104
83
D Betel, M Wilson, A Gabow, DS Marks, C Sander. The microRNA.org resource: targets and expression. Nucleic Acids Res 2008; 36(Database issue): D149–D153
pmid: 18158296
84
M Maragkakis, M Reczko, VA Simossis, P Alexiou, GL Papadopoulos, T Dalamagas, G Giannopoulos, G Goumas, E Koukis, K Kourtis, T Vergoulis, N Koziris, T Sellis, P Tsanakas, AG Hatzigeorgiou. DIANA-microT web server: elucidating microRNA functions through target prediction. Nucleic Acids Res 2009; 37(Web Server issue): W273-276
pmid: 19406924
85
T Rabilloud, M Chevallet, S Luche, C Lelong. Two-dimensional gel electrophoresis in proteomics: Past, present and future. J Proteomics 2010; 73(11): 2064–2077 https://doi.org/10.1016/j.jprot.2010.05.016
pmid: 20685252
O Stoevesandt, MJ Taussig, M He. Protein microarrays: high-throughput tools for proteomics. Expert Rev Proteomics 2009; 6(2): 145–157 https://doi.org/10.1586/epr.09.2
pmid: 19385942
89
A Novak, M Amit, T Ziv, H Segev, B Fishman, A Admon, J Itskovitz-Eldor. Proteomics profiling of human embryonic stem cells in the early differentiation stage. Stem Cell Rev 2012; 8(1): 137–149 https://doi.org/10.1007/s12015-011-9286-y
pmid: 21732092
PG Pedrioli, JK Eng, R Hubley, M Vogelzang, EW Deutsch, B Raught, B Pratt, E Nilsson, RH Angeletti, R Apweiler, K Cheung, CE Costello, H Hermjakob, S Huang, RK Julian, E Kapp, ME McComb, SG Oliver, G Omenn, NW Paton, R Simpson, R Smith, CF Taylor, W Zhu, R Aebersold. A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol 2004; 22(11): 1459–1466 https://doi.org/10.1038/nbt1031
pmid: 15529173
92
LN Mueller, MY Brusniak, DR Mani, R Aebersold. An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J Proteome Res 2008; 7(1): 51–61 https://doi.org/10.1021/pr700758r
pmid: 18173218
93
J Cox, M Mann. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 2008; 26(12): 1367–1372 https://doi.org/10.1038/nbt.1511
pmid: 19029910
94
Z Khan, JS Bloom, BA Garcia, M Singh, L Kruglyak. Protein quantification across hundreds of experimental conditions. Proc Natl Acad Sci USA 2009; 106(37): 15544–15548 https://doi.org/10.1073/pnas.0904100106
pmid: 19717460
95
WT Lin, WN Hung, YH Yian, KP Wu, CL Han, YR Chen, YJ Chen, TY Sung, WL Hsu. Multi-Q: a fully automated tool for multiplexed protein quantitation. J Proteome Res 2006; 5(9): 2328–2338 https://doi.org/10.1021/pr060132c
pmid: 16944945
MO Arntzen, CJ Koehler, H Barsnes, FS Berven, A Treumann, B Thiede. IsobariQ: software for isobaric quantitative proteomics using IPTL, iTRAQ, and TMT. J Proteome Res 2011; 10(2): 913–920 https://doi.org/10.1021/pr1009977
pmid: 21067241
98
A Keller, J Eng, N Zhang, XJ Li, R Aebersold. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol Syst Biol 2005; 1: 2005.0017
pmid: 16729052
99
MY Brusniak, B Bodenmiller, D Campbell, K Cooke, J Eddes, A Garbutt, H Lau, S Letarte, LN Mueller, V Sharma, O Vitek, N Zhang, R Aebersold, JD Watts. Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics. BMC Bioinformatics 2008; 9(1): 542 https://doi.org/10.1186/1471-2105-9-542
pmid: 19087345
100
CC Tsou, CF Tsai, YH Tsui, PR Sudhir, YT Wang, YJ Chen, JY Chen, TY Sung, WL Hsu. IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation. Mol Cell Proteomics 2010; 9(1): 131–144 https://doi.org/10.1074/mcp.M900177-MCP200
pmid: 19752006
101
P Mortensen, JW Gouw, JV Olsen, SE Ong, KTG Rigbolt, J Bunkenborg, J Cox, LJ Foster, AJR Heck, B Blagoev, JS Andersen, M Mann. MSQuant, an open source platform for mass spectrometry-based quantitative proteomics. J Proteome Res 2010; 9(1): 393–403 https://doi.org/10.1021/pr900721e
pmid: 19888749
102
CH Hokke, JM Fitzpatrick, KF Hoffmann. Integrating transcriptome, proteome and glycome analyses of Schistosoma biology. Trends Parasitol 2007; 23(4): 165–174 https://doi.org/10.1016/j.pt.2007.02.007
pmid: 17336161
103
JA Nielsen, P Lau, D Maric, JL Barker, LD Hudson. Integrating microRNA and mRNA expression profiles of neuronal progenitors to identify regulatory networks underlying the onset of cortical neurogenesis. BMC Neurosci 2009; 10(1): 98 https://doi.org/10.1186/1471-2202-10-98
pmid: 19689821
104
F Liu, J Lu, W Hu, SY Wang, SJ Cui, M Chi, Q Yan, XR Wang, HD Song, XN Xu, JJ Wang, XL Zhang, X Zhang, ZQ Wang, CL Xue, PJ Brindley, DP McManus, PY Yang, Z Feng, Z Chen, ZG Han. New perspectives on host-parasite interplay by comparative transcriptomic and proteomic analyses of Schistosoma japonicum. PLoS Pathog 2006; 2(4): e29 https://doi.org/10.1371/journal.ppat.0020029
pmid: 16617374
105
AS Tarun, X Peng, RF Dumpit, Y Ogata, H Silva-Rivera, N Camargo, TM Daly, LW Bergman, SHI Kappe. A combined transcriptome and proteome survey of malaria parasite liver stages. Proc Natl Acad Sci USA 2008; 105(1): 305–310 https://doi.org/10.1073/pnas.0710780104
pmid: 18172196
106
RD Unwin, AD Whetton. Systematic proteome and transcriptome analysis of stem cell populations. Cell Cycle 2006; 5(15): 1587–1591 https://doi.org/10.4161/cc.5.15.3101
pmid: 16861929
107
H Xu, IR Lemischka, A Ma’ayan. SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells. BMC Syst Biol 2010; 4(1): 173 https://doi.org/10.1186/1752-0509-4-173
pmid: 21176149
108
SJ Ho Sui, K Begley, D Reilly, B Chapman, R McGovern, P Rocca-Sera, E Maguire, GM Altschuler, TA Hansen, R Sompallae, A Krivtsov, RA Shivdasani, SA Armstrong, AC Culhane, M Correll, SA Sansone, O Hofmann, W Hide. The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons. Nucleic Acids Res 2012; 40(Database issue): D984–D991 https://doi.org/10.1093/nar/gkr1051
pmid: 22121217