Densely interconnected transcriptional circuits control cell states in human hematopoiesis

Cell

Volumn 144, Issue 2, 2011, Pages 296-309

  Novershtern, Noa ^a,b,c   Subramanian, Aravind ^a   Lawton, Lee N ^d   Mak, Raymond H ^a   Haining, W Nicholas ^e   McConkey, Marie E ^f   Habib, Naomi ^c   Yosef, Nir ^a   Chang, Cindy Y ^a,f   Shay, Tal ^a   Frampton, Garrett M ^b,d   Drake, Adam C B ^b   Leskov, Ilya ^b   Nilsson, Bjorn ^a,f   Preffer, Fred ^g   Dombkowski, David ^g   Evans, John W ^e   Liefeld, Ted ^a   Smutko, John S ^h   Chen, Jianzhu ^b   Friedman, Nir ^c   Young, Richard A ^b,d   Golub, Todd R ^a,e,i   Regev, Aviv ^a,b,i   Ebert, Benjamin L ^a,e,f   more..

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c HEBREW UNIVERSITY OF JERUSALEM   (Israel)

^d WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^e DANA FARBER CANCER INSTITUTE   (United States)

^f BRIGHAM AND WOMEN S HOSPITAL   (United States)

^g MASSACHUSETTS GENERAL HOSPITAL   (United States)

^h NuGEN Technologies   (United States)

ⁱ HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; TRANSCRIPTION FACTOR;

ARTICLE; CELL DIFFERENTIATION; GENE EXPRESSION; GENE MAPPING; GENE SEQUENCE; GENETIC TRANSCRIPTION; HEMATOPOIESIS; HEMATOPOIETIC STEM CELL; HUMAN; PRIORITY JOURNAL; PROMOTER REGION;

EID: 78651486442     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cell.2011.01.004     Document Type: Article

References (107)

1. K. Akashi Lineage promiscuity and plasticity in hematopoietic development Ann. N Y Acad. Sci. 1044 2005 125 131
2. I. Amit, M. Garber, N. Chevrier, A.P. Leite, Y. Donner, T. Eisenhaure, M. Guttman, J.K. Grenier, W. Li, and O. Zuk Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses Science 326 2009 257 263
3. P.D. Aplan, K. Nakahara, S.H. Orkin, and I.R. Kirsch The SCL gene product: a positive regulator of erythroid differentiation EMBO J. 11 1992 4073 4081
4. J. Aramburu, L. Azzoni, A. Rao, and B. Perussia Activation and expression of the nuclear factors of activated T cells, NFATp and NFATc, in human natural killer cells: regulation upon CD16 ligand binding J. Exp. Med. 182 1995 801 810
5. B. Argiropoulos, E. Yung, and R.K. Humphries Unraveling the crucial roles of Meis1 in leukemogenesis and normal hematopoiesis Genes Dev. 21 2007 2845 2849
6. W.J. Bakker, T.B. van Dijk, M. Parren-van Amelsvoort, A. Kolbus, K. Yamamoto, P. Steinlein, R.G. Verhaak, T.W. Mak, H. Beug, B. Löwenberg, and M. von Lindern Differential regulation of Foxo3a target genes in erythropoiesis Mol. Cell. Biol. 27 2007 3839 3854
7. A. Bhattacharjee, W.G. Richards, J. Staunton, C. Li, S. Monti, P. Vasa, C. Ladd, J. Beheshti, R. Bueno, and M. Gillette Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses Proc. Natl. Acad. Sci. USA 98 2001 13790 13795
8. L.A. Boyer, T.I. Lee, M.F. Cole, S.E. Johnstone, S.S. Levine, J.P. Zucker, M.G. Guenther, R.M. Kumar, H.L. Murray, and R.G. Jenner Core transcriptional regulatory circuitry in human embryonic stem cells Cell 122 2005 947 956
9. J.-P. Brunet, P. Tamayo, T.R. Golub, and J.P. Mesirov Metagenes and molecular pattern discovery using matrix factorization Proc. Natl. Acad. Sci. USA 101 2004 4164 4169
10. L. Bullinger, K. Döhner, E. Bair, S. Fröhling, R.F. Schlenk, R. Tibshirani, H. Döhner, and J.R. Pollack Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemia N. Engl. J. Med. 350 2004 1605 1616
11. A.B. Cantor, and S.H. Orkin Transcriptional regulation of erythropoiesis: an affair involving multiple partners Oncogene 21 2002 3368 3376
12. M.L. Chen, T.D. Logan, M.L. Hochberg, S.G. Shelat, X. Yu, G.E. Wilding, W. Tan, G.C. Kujoth, T.A. Prolla, and M.A. Selak Erythroid dysplasia, megaloblastic anemia, and impaired lymphopoiesis arising from mitochondrial dysfunction Blood 114 2009 4045 4053
13. K. Chin, S. DeVries, J. Fridlyand, P.T. Spellman, R. Roydasgupta, W.L. Kuo, A. Lapuk, R.M. Neve, Z. Qian, and T. Ryder Genomic and transcriptional aberrations linked to breast cancer pathophysiologies Cancer Cell 10 2006 529 541
14. E.H. Davidson Genomic Regulatory Systems: In Development and Evolution 2001 Academic Press Burlington, MA
15. B.L. Ebert, and T.R. Golub Genomic approaches to hematologic malignancies Blood 104 2004 923 932
16. M. Fontenay, S. Cathelin, M. Amiot, E. Gyan, and E. Solary Mitochondria in hematopoiesis and hematological diseases Oncogene 25 2006 4757 4767
17. A.P. Funnell, C.A. Maloney, L.J. Thompson, J. Keys, M. Tallack, A.C. Perkins, and M. Crossley Erythroid Krüppel-like factor directly activates the basic Krüppel-like factor gene in erythroid cells Mol. Cell. Biol. 27 2007 2777 2790
18. K. Hahm, B.S. Cobb, A.S. McCarty, K.E. Brown, C.A. Klug, R. Lee, K. Akashi, I.L. Weissman, A.G. Fisher, and S.T. Smale Helios, a T cell-restricted Ikaros family member that quantitatively associates with Ikaros at centromeric heterochromatin Genes Dev. 12 1998 782 796
19. W.N. Haining, B.L. Ebert, A. Subrmanian, E.J. Wherry, Q. Eichbaum, J.W. Evans, R. Mak, S. Rivoli, J. Pretz, and J. Angelosanto Identification of an evolutionarily conserved transcriptional signature of CD8 memory differentiation that is shared by T and B cells J. Immunol. 181 2008 1859 1868
20. H. Hirai, P. Zhang, T. Dayaram, C.J. Hetherington, S. Mizuno, J. Imanishi, K. Akashi, and D.G. Tenen C/EBPbeta is required for 'emergency' granulopoiesis Nat. Immunol. 7 2006 732 739
21. H. Iwasaki, and K. Akashi Hematopoietic developmental pathways: on cellular basis Oncogene 26 2007 6687 6696
22. H.D. Kim, T. Shay, E.K. O'Shea, and A. Regev Transcriptional regulatory circuits: predicting numbers from alphabets Science 325 2009 429 432
23. T. Kino, H. Takatori, I. Manoli, Y. Wang, A. Tiulpakov, M.R. Blackman, Y.A. Su, G.P. Chrousos, A.H. DeCherney, and J.H. Segars Brx mediates the response of lymphocytes to osmotic stress through the activation of NFAT5 Sci. Signal. 2 2009 ra5
24. A.V. Krivtsov, D. Twomey, Z. Feng, M.C. Stubbs, Y. Wang, J. Faber, J.E. Levine, J. Wang, W.C. Hahn, and D.G. Gilliland Transformation from committed progenitor to leukaemia stem cell initiated by MLL-AF9 Nature 442 2006 818 822
25. E. Lécuyer, and T. Hoang SCL: from the origin of hematopoiesis to stem cells and leukemia Exp. Hematol. 32 2004 11 24
26. H.M. Lee, H. Zhang, V. Schulz, D.P. Tuck, and B.G. Forget Downstream targets of HOXB4 in a cell line model of primitive hematopoietic progenitor cells Blood 116 2010 720 730
27. Q. Li, J.L. Frestedt, and J.H. Kersey AF4 encodes a ubiquitous protein that in both native and MLL-AF4 fusion types localizes to subnuclear compartments Blood 92 1998 3841 3847
28. M. Liu, M.H. Lee, M. Cohen, M. Bommakanti, and L.P. Freedman Transcriptional activation of the Cdk inhibitor p21 by vitamin D3 leads to the induced differentiation of the myelomonocytic cell line U937 Genes Dev. 10 1996 142 153
29. A.T. Look Oncogenic transcription factors in the human acute leukemias Science 278 1997 1059 1064
30. R. Lu, F. Markowetz, R.D. Unwin, J.T. Leek, E.M. Airoldi, B.D. MacArthur, A. Lachmann, R. Rozov, A. Ma'ayan, and L.A. Boyer Systems-level dynamic analyses of fate change in murine embryonic stem cells Nature 462 2009 358 362
31. C.Y. McLean, D. Bristor, M. Hiller, S.L. Clarke, B.T. Schaar, C.B. Lowe, A.M. Wenger, and G. Bejerano GREAT improves functional interpretation of cis-regulatory regions Nat. Biotechnol. 28 2010 495 501
32. Mitelman, F., Johansson, B., and Mertens, F. (2010). Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer (http://cgap.nci.nih.gov/ Chromosomes/Mitelman).
33. S. Monti, K.J. Savage, J.L. Kutok, F. Feuerhake, P. Kurtin, M. Mihm, B. Wu, L. Pasqualucci, D. Neuberg, and R.C. Aguiar Molecular profiling of diffuse large B-cell lymphoma identifies robust subtypes including one characterized by host inflammatory response Blood 105 2005 1851 1861
34. F.J. Müller, L.C. Laurent, D. Kostka, I. Ulitsky, R. Williams, C. Lu, I.H. Park, M.S. Rao, R. Shamir, and P.H. Schwartz Regulatory networks define phenotypic classes of human stem cell lines Nature 455 2008 401 405
35. S.Y. Ng, T. Yoshida, and K. Georgopoulos Ikaros and chromatin regulation in early hematopoiesis Curr. Opin. Immunol. 19 2007 116 122
36. S.H. Orkin, and L.I. Zon Hematopoiesis: an evolving paradigm for stem cell biology Cell 132 2008 631 644
37. D. Peck, E.D. Crawford, K.N. Ross, K. Stegmaier, T.R. Golub, and J. Lamb A method for high-throughput gene expression signature analysis Genome Biol. 7 2006 R61
38. L. Pevny, M.C. Simon, E. Robertson, W.H. Klein, S.F. Tsai, V. D'Agati, S.H. Orkin, and F. Costantini Erythroid differentiation in chimaeric mice blocked by a targeted mutation in the gene for transcription factor GATA-1 Nature 349 1991 257 260
39. P.J. Quesenberry, and G.A. Colvin Hematopoietic Stem Cells, Progenitor Cells, and Cytokines E. Beutler, M.A. Lichtman, B.S. Coller, T.J. Kipps, U. Seligsohn, Williams Hematology 2005 McGraw-Hill New York 153 174
40. H. Rincón-Arano, V. Valadez-Graham, G. Guerrero, M. Escamilla-Del-Arenal, and F. Recillas-Targa YY1 and GATA-1 interaction modulate the chicken 3′-side alpha-globin enhancer activity J. Mol. Biol. 349 2005 961 975
41. F. Rosenbauer, and D.G. Tenen Transcription factors in myeloid development: balancing differentiation with transformation Nat. Rev. Immunol. 7 2007 105 117
42. A. Sandelin, W. Alkema, P. Engström, W.W. Wasserman, and B. Lenhard JASPAR: an open-access database for eukaryotic transcription factor binding profiles Nucleic Acids Res. 32 Database issue 2004 D91 D94
43. E.W. Scott, M.C. Simon, J. Anastasi, and H. Singh Requirement of transcription factor PU.1 in the development of multiple hematopoietic lineages Science 265 1994 1573 1577
44. E. Segal, M. Shapira, A. Regev, D. Pe'er, D. Botstein, D. Koller, and N. Friedman Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data Nat. Genet. 34 2003 166 176
45. E. Segal, D. Pe'er, A. Regev, D. Koller, and N. Friedman Learning module networks J. Mach. Learn. Res. 6 2005 557 588
46. H. Singh, R.P. DeKoter, and J.C. Walsh PU.1, a shared transcriptional regulator of lymphoid and myeloid cell fates Cold Spring Harb. Symp. Quant. Biol. 64 1999 13 20
47. A.I. Su, T. Wiltshire, S. Batalov, H. Lapp, K.A. Ching, D. Block, J. Zhang, R. Soden, M. Hayakawa, and G. Kreiman A gene atlas of the mouse and human protein-encoding transcriptomes Proc. Natl. Acad. Sci. USA 101 2004 6062 6067
48. A. Subramanian, P. Tamayo, V.K. Mootha, S. Mukherjee, B.L. Ebert, M.A. Gillette, A. Paulovich, S.L. Pomeroy, T.R. Golub, E.S. Lander, and J.P. Mesirov Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles Proc. Natl. Acad. Sci. USA 102 2005 15545 15550
49. H. Suzuki, A.R. Forrest, E. van Nimwegen, C.O. Daub, P.J. Balwierz, K.M. Irvine, T. Lassmann, T. Ravasi, Y. Hasegawa, M.J. de Hoon FANTOM Consortium Riken Omics Science Center The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line Nat. Genet. 41 2009 553 562
50. P. Tamayo, D. Scanfeld, B.L. Ebert, M.A. Gillette, C.W. Roberts, and J.P. Mesirov Metagene projection for cross-platform, cross-species characterization of global transcriptional states Proc. Natl. Acad. Sci. USA 104 2007 5959 5964
51. R. Tibshirani, and T. Hastie Outlier sums for differential gene expression analysis Biostatistics 8 2007 2 8
52. S.A. Tomlins, D.R. Rhodes, S. Perner, S.M. Dhanasekaran, R. Mehra, X.W. Sun, S. Varambally, X. Cao, J. Tchinda, and R. Kuefer Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer Science 310 2005 644 648
53. P.J. Valk, R.G. Verhaak, M.A. Beijen, C.A. Erpelinck, S. Barjesteh van Waalwijk van Doorn-Khosrovani, J.M. Boer, H.B. Beverloo, M.J. Moorhouse, P.J. van der Spek, B. Löwenberg, and R. Delwel Prognostically useful gene-expression profiles in acute myeloid leukemia N. Engl. J. Med. 350 2004 1617 1628
54. A. Valouev, D.S. Johnson, A. Sundquist, C. Medina, E. Anton, S. Batzoglou, R.M. Myers, and A. Sidow Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data Nat. Methods 5 2008 829 834
55. R.H. Xu, T.L. Sampsell-Barron, F. Gu, S. Root, R.M. Peck, G. Pan, J. Yu, J. Antosiewicz-Bourget, S. Tian, R. Stewart, and J.A. Thomson NANOG is a direct target of TGFbeta/activin-mediated SMAD signaling in human ESCs Cell Stem Cell 3 2008 196 206
56. Y. Zhang, T. Liu, C.A. Meyer, J. Eeckhoute, D.S. Johnson, B.E. Bernstein, C. Nusbaum, R.M. Myers, M. Brown, W. Li, and X.S. Liu Model-based analysis of ChIP-Seq (MACS) Genome Biol. 9 2008 R137
57. Astier, A.L., Xu, R., Svoboda, M., Hinds, E., Munoz, O., de Beaumont, R., Crean, C.D., Gabig, T., and Freedman, A.S. (2003). Temporal gene expression profile of human precursor B leukemia cells induced by adhesion receptor: identification of pathways regulating B-cell survival. Blood 101, 1118-1127.
58. Badis, G., Berger, M.F., Philippakis, A.A., Talukder, S., Gehrke, A.R., Jaeger, S.A., Chan, E.T., Metzler, G., Vedenko, A., Chen, X., et al. (2009). Diversity and complexity in DNA recognition by transcription factors. Science 324, 1720-1723.
59. Bailey, T.L., and Elkan, C. (1995). The value of prior knowledge in discovering motifs with MEME. Proc. Int. Conf. Intell. Syst. Mol. Biol. 3, 21-29.
60. Barash, Y., Bejerano, G., and Friedman, N. (2002). A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites. In Algorithms in Bioinformatics, pp. 278-293.
61. Benjamini, Y., and Yoseph, H. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc., B 57, 289-300.
62. Berger, M.F., Badis, G., Gehrke, A.R., Talukder, S., Philippakis, A.A., Peña-Castillo, L., Alleyne, T.M., Mnaimneh, S., Botvinnik, O.B., Chan, E.T., et al. (2008). Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 133, 1266-1276.
63. Bhattacharjee, A., Richards, W.G., Staunton, J., Li, C., Monti, S., Vasa, P., Ladd, C., Beheshti, J., Bueno, R., Gillette, M., et al. (2001). Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc. Natl. Acad. Sci. USA 98, 13790-13795.
64. Bonferroni, C.E. (1936). Teoria statistica delle classi e calcolo delle probabilita. Pubblicazioni del R Istituto Superiore di Scienze Economiche e Commerciali di Firenze 8, 3-62.
65. Boyer, L.A., Lee, T.I., Cole, M.F., Johnstone, S.E., Levine, S.S., Zucker, J.P., Guenther, M.G., Kumar, R.M., Murray, H.L., Jenner, R.G., et al. (2005). Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947-956.
66. Brunet, J.-P., Tamayo, P., Golub, T.R., and Mesirov, J.P. (2004). Metagenes and molecular pattern discovery using matrix factorization. Proc. Natl. Acad. Sci. USA 101, 4164-4169.
67. Bult, C.J., Kadin, J.A., Richardson, J.E., Blake, J.A., and Eppig, J.T.; Mouse Genome Database Group. (2010). The Mouse Genome Database: enhancements and updates. Nucleic Acids Res. 38 (Database issue), D586-D592.
68. Cam, H., Balciunaite, E., Blais, A., Spektor, A., Scarpulla, R.C., Young, R., Kluger, Y., and Dynlacht, B.D. (2004). A common set of gene regulatory networks links metabolism and growth inhibition. Mol. Cell 16, 399-411.
69. Chang, L.W., Payton, J.E., Yuan, W., Ley, T.J., Nagarajan, R., and Stormo, G.D. (2008). Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia. Genome Biol. 9, R38.
70. Chen, J., and Sadowski, I. (2005). Identification of the mismatch repair genes PMS2 and MLH1 as p53 target genes by using serial analysis of binding elements. Proc. Natl. Acad. Sci. USA 102, 4813-4818.
71. Chin, K., DeVries, S., Fridlyand, J., Spellman, P.T., Roydasgupta, R., Kuo, W.L., Lapuk, A., Neve, R.M., Qian, Z., Ryder, T., et al. (2006). Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 10, 529-541.
72. Ebert, B.L., Lee, M.M., Pretz, J.L., Subramanian, A., Mak, R., Golub, T.R., and Sieff, C.A. (2005). An RNA interference model of RPS19 deficiency in Diamond-Blackfan anemia recapitulates defective hematopoiesis and rescue by dexamethasone: identification of dexamethasone-responsive genes by microarray. Blood 105, 4620-4626.
73. Elemento, O., Slonim, N., and Tavazoie, S. (2007). A universal framework for regulatory element discovery across all genomes and data types. Mol. Cell 28, 337-350.
74. Fisher, R.A. (1954). Statistical Methods for Research Workers (Edinburgh, UK: Oliver and Boyd).
75. Gentleman, R.C., Carey, V.J., Bates, D.M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., et al. (2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80.
76. Georgantas, R.W., III, Tanadve, V., Malehorn, M., Heimfeld, S., Chen, C., Carr, L., Martinez-Murillo, F., Riggins, G., Kowalski, J., and Civin, C.I. (2004). Microarray and serial analysis of gene expression analyses identify known and novel transcripts overexpressed in hematopoietic stem cells. Cancer Res. 64, 4434-4441.
77. Gordon, D.B., Nekludova, L., McCallum, S., and Fraenkel, E. (2005). TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs. Bioinformatics 21, 3164-3165.
78. Habib, N., Kaplan, T., Margalit, H., and Friedman, N. (2008). A novel Bayesian DNA motif comparison method for clustering and retrieval. PLoS Comput. Biol. 4, e1000010.
79. Hughes, J.D., Estep, P.W., Tavazoie, S., and Church, G.M. (2000). Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol. 296, 1205-1214.
80. Irizarry, R.A., Hobbs, B., Collin, F., Beazer-Barclay, Y.D., Antonellis, K.J., Scherf, U., and Speed, T.P. (2003). Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4, 249-264.
81. Ivanova, N.B., Dimos, J.T., Schaniel, C., Hackney, J.A., Moore, K.A., and Lemischka, I.R. (2002). A stem cell molecular signature. Science 298, 601-604.
82. Jeffrey, K.L., Brummer, T., Rolph, M.S., Liu, S.M., Callejas, N.A., Grumont, R.J., Gillieron, C., Mackay, F., Grey, S., Camps, M., et al. (2006). Positive regulation of immune cell function and inflammatory responses by phosphatase PAC-1. Nat. Immunol. 7, 274-283.
83. Johnson, W.E.L., Li, C., and Rabinovic, A. (2007). Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8, 118-127.
84. Langmead, B., Trapnell, C., Pop, M., and Salzberg, S.L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25.
85. Lee, M.S., Hanspers, K., Barker, C.S., Korn, A.P., and McCune, J.M. (2004). Gene expression profiles during human CD4+ T cell differentiation. Int. Immunol. 16, 1109-1124.
86. Lee, T.I., Johnstone, S.E., and Young, R.A. (2006). Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat. Protoc. 1, 729-748.
87. Linhart, C., Halperin, Y., and Shamir, R. (2008). Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets. Genome Res. 18, 1180-1189.
88. Liu, X.S., Brutlag, D.L., and Liu, J.S. (2002). An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat. Biotechnol. 20, 835-839.
89. Macaulay, I.C., Tijssen, M.R., Thijssen-Timmer, D.C., Gusnanto, A., Steward, M., Burns, P., Langford, C.F., Ellis, P.D., Dudbridge, F., Zwaginga, J.J., et al. (2007). Comparative gene expression profiling of in vitro differentiated megakaryocytes and erythroblasts identifies novel activatory and inhibitory platelet membrane proteins. Blood 109, 3260-3269.
90. Matys, V., Fricke, E., Geffers, R., Gössling, E., Haubrock, M., Hehl, R., Hornischer, K., Karas, D., Kel, A.E., Kel-Margoulis, O.V., et al. (2003). TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 31, 374-378.
91. McLean, C.Y., Bristor, D., Hiller, M., Clarke, S.L., Schaar, B.T., Lowe, C.B., Wenger, A.M., and Bejerano, G. (2010). GREAT improves functional interpretation of cis-regulatory regions. Nat. Biotechnol. 28, 495-501.
92. Mitelman, F., Johansson, B., and Mertens, F. (2010). Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer (http://cgap.nci.nih.gov/ Chromosomes/Mitelman).
93. Moffat, J., Grueneberg, D.A., Yang, X., Kim, S.Y., Kloepfer, A.M., Hinkle, G., Piqani, B., Eisenhaure, T.M., Luo, B., Grenier, J.K., et al. (2006). A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell 124, 1283-1298.
94. Monti, S., Savage, K.J., Kutok, J.L., Feuerhake, F., Kurtin, P., Mihm, M., Wu, B., Pasqualucci, L., Neuberg, D., Aguiar, R.C., et al. (2005). Molecular profiling of diffuse large B-cell lymphoma identifies robust subtypes including one characterized by host inflammatory response. Blood 105, 1851-1861.
95. Monti, S., Tamayo, P., Mesirov, J., and Golub, T. (2003). Consensus clustering: a resampling-based method for class discovery and visualization of gene expression microarray data. Mach. Learn. 52, 91-118.
96. Peck, D., Crawford, E.D., Ross, K.N., Stegmaier, K., Golub, T.R., and Lamb, J. (2006). A method for high-throughput gene expression signature analysis. Genome Biol. 7, R61.
97. Reich, M., Liefeld, T., Gould, J., Lerner, J., Tamayo, P., and Mesirov, J.P. (2006). GenePattern 2.0. Nat. Genet. 38, 500-501.
98. Sandelin, A., Alkema, W., Engström, P., Wasserman, W.W., and Lenhard, B. (2004). JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 32 (Database issue), D91-D94.
99. Su, A.I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K.A., Block, D., Zhang, J., Soden, R., Hayakawa, M., Kreiman, G., et al. (2004). A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. USA 101, 6062-6067.
100. Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, M.A., Paulovich, A., Pomeroy, S.L., Golub, T.R., Lander, E.S., and Mesirov, J.P. (2005). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545-15550.
101. Tamayo, P., Scanfeld, D., Ebert, B.L., Gillette, M.A., Roberts, C.W., and Mesirov, J.P. (2007). Metagene projection for cross-platform, cross-species characterization of global transcriptional states. Proc. Natl. Acad. Sci. USA 104, 5959-5964.
102. Tanay, A., Steinfeld, I., Kupiec, M., and Shamir, R. (2005). Integrative analysis of genome-wide experiments in the context of a large high-throughput data compendium. Mol. Syst. Biol. 1, 2005.0002.
103. Tarte, K., Zhan, F., De Vos, J., Klein, B., and Shaughnessy, J., Jr. (2003). Gene expression profiling of plasma cells and plasmablasts: toward a better understanding of the late stages of B-cell differentiation. Blood 102, 592-600.
104. Valouev, A., Johnson, D.S., Sundquist, A., Medina, C., Anton, E., Batzoglou, S., Myers, R.M., and Sidow, A. (2008). Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat. Methods 5, 829-834.
105. Welch, J.J., Watts, J.A., Vakoc, C.R., Yao, Y., Wang, H., Hardison, R.C., Blobel, G.A., Chodosh, L.A., and Weiss, M.J. (2004). Global regulation of erythroid gene expression by transcription factor GATA-1. Blood 104, 3136-3147.
106. Wilson, N.K., Foster, S.D., Wang, X., Knezevic, K., Schütte, J., Kaimakis, P., Chilarska, P.M., Kinston, S., Ouwehand, W.H., Dzierzak, E., et al. (2010). Combinatorial transcriptional control in blood stem/progenitor cells: genome-wide analysis of ten major transcriptional regulators. Cell Stem Cell 7, 532-544.
107. Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B.E., Nusbaum, C., Myers, R.M., Brown, M., Li, W., and Liu, X.S. (2008). Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137.