Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, et al: The sequence of the human genome. Science. 2001, 291 (5507): 1304-1351. 10.1126/science.1058040.
Article
CAS
PubMed
Google Scholar
International Human Genome Sequencing Consortium: Finishing the euchromatic sequence of the human genome. Nature. 2004, 431 (7011): 931-945. 10.1038/nature03001.
Article
Google Scholar
Schena M, Shalon D, Davis RW, Brown PO: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995, 270 (5235): 467-470. 10.1126/science.270.5235.467.
Article
CAS
PubMed
Google Scholar
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B: Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008, 5 (7): 621-628. 10.1038/nmeth.1226.
Article
CAS
PubMed
Google Scholar
Pezzino S, Paratore S, Cavallaro S: Systems biology of apoptosis and survival: implications for drug development. Curr Pharm Des. 2011, 17 (3): 190-203. 10.2174/138161211795049688.
Article
CAS
PubMed
Google Scholar
Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G, et al: Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods. 2008, 5 (7): 613-619. 10.1038/nmeth.1223.
Article
CAS
PubMed
Google Scholar
Slavov N, Dawson KA: Correlation signature of the macroscopic states of the gene regulatory network in cancer. Proc Natl Acad Sci U S A. 2009, 106 (11): 4079-4084. 10.1073/pnas.0810803106.
Article
PubMed Central
CAS
PubMed
Google Scholar
Akutsu T, Kuhara S, Maruyama O, Miyano S: A System for Identifying Genetic Networks from Gene Expression Patterns Produced by Gene Disruptions and Overexpressions. Genome Inform Ser Workshop Genome Inform. 1998, 9: 151-160.
CAS
PubMed
Google Scholar
Butte AJ, Kohane IS: Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac Symp Biocomput. 2000, 418-429.
Google Scholar
Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A: Reverse engineering of regulatory networks in human B cells. Nat Genet. 2005, 37 (4): 382-390. 10.1038/ng1532.
Article
CAS
PubMed
Google Scholar
Hurley D, Araki H, Tamada Y, Dunmore B, Sanders D, Humphreys S, Affara M, Imoto S, Yasuda K, Tomiyasu Y, et al: Gene network inference and visualization tools for biologists: application to new human transcriptome datasets. Nucleic Acids Res. 2011, 40 (6): 2377-2398.
Article
PubMed Central
Google Scholar
Friedman N, Linial M, Nachman I, Pe'er D: Using Bayesian networks to analyze expression data. J Comput Biol. 2000, 7 (3–4): 601-620.
Article
CAS
PubMed
Google Scholar
Hartemink AJ, Gifford DK, Jaakkola TS, Young RA: Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. Pac Symp Biocomput. 2001, 422-433.
Google Scholar
Imoto S, Higuchi T, Goto T, Tashiro K, Kuhara S, Miyano S: Combining microarrays and biological knowledge for estimating gene networks via bayesian networks. J Bioinform Comput Biol. 2004, 2 (1): 77-98. 10.1142/S021972000400048X.
Article
CAS
PubMed
Google Scholar
Brazhnik P, de la Fuente A, Mendes P: Gene networks: how to put the function in genomics. Trends Biotechnol. 2002, 20 (11): 467-472. 10.1016/S0167-7799(02)02053-X.
Article
CAS
PubMed
Google Scholar
Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA: Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol. 2004, 14 (3): 283-291. 10.1016/j.sbi.2004.05.004.
Article
CAS
PubMed
Google Scholar
Duval H, Harris M, Li J, Johnson N, Print C: New insights into the function and regulation of endothelial cell apoptosis. Angiogenesis. 2003, 6 (3): 171-183.
Article
CAS
PubMed
Google Scholar
Affara M, Dunmore B, Savoie C, Imoto S, Tamada Y, Araki H, Charnock-Jones DS, Miyano S, Print C: Understanding endothelial cell apoptosis: what can the transcriptome, glycome and proteome reveal?. Philos Trans R Soc Lond B Biol Sci. 2007, 362 (1484): 1469-1487. 10.1098/rstb.2007.2129.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zhang W, Li D, Mehta JL: Role of AIF in human coronary artery endothelial cell apoptosis. Am J Physiol Heart Circ Physiol. 2004, 286 (1): H354-H358.
Article
CAS
PubMed
Google Scholar
Stefanec T: Endothelial apoptosis: could it have a role in the pathogenesis and treatment of disease?. Chest. 2000, 117 (3): 841-854. 10.1378/chest.117.3.841.
Article
CAS
PubMed
Google Scholar
Xia L, Ding F, Zhu JH, Fu GS: Resveratrol attenuates apoptosis of pulmonary microvascular endothelial cells induced by high shear stress and proinflammatory factors. Hum Cell. 2011, 24 (3): 127-133. 10.1007/s13577-011-0031-2.
Article
CAS
PubMed
Google Scholar
Reed JC: Dysregulation of apoptosis in cancer. J Clin Oncol. 1999, 17 (9): 2941-2953.
CAS
PubMed
Google Scholar
Lunt SJ: Chaudary N. 2008, Hill RP: The tumor microenvironment and metastatic disease. Clin Exp Metastasis
Google Scholar
Palmero EI, de Campos SG, Campos M, de Souza NC, Guerreiro ID, Carvalho AL, Marques MM: Mechanisms and role of microRNA deregulation in cancer onset and progression. Genet Mol Biol. 2011, 34 (3): 363-370. 10.1590/S1415-47572011000300001.
Article
PubMed Central
CAS
PubMed
Google Scholar
Fabregat I: Dysregulation of apoptosis in hepatocellular carcinoma cells. World J Gastroenterol. 2009, 15 (5): 513-520. 10.3748/wjg.15.513.
Article
PubMed Central
CAS
PubMed
Google Scholar
Saraste A, Pulkki K: Morphologic and biochemical hallmarks of apoptosis. Cardiovasc Res. 2000, 45 (3): 528-537. 10.1016/S0008-6363(99)00384-3.
Article
CAS
PubMed
Google Scholar
Kerr JF, Wyllie AH, Currie AR: Apoptosis: a basic biological phenomenon with wide-ranging implications in tissue kinetics. Br J Cancer. 1972, 26 (4): 239-257. 10.1038/bjc.1972.33.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hacker G: The morphology of apoptosis. Cell Tissue Res. 2000, 301 (1): 5-17. 10.1007/s004410000193.
Article
CAS
PubMed
Google Scholar
Johnson NA, Sengupta S, Saidi SA, Lessan K, Charnock-Jones SD, Scott L, Stephens R, Freeman TC, Tom BD, Harris M, et al: Endothelial cells preparing to die by apoptosis initiate a program of transcriptome and glycome regulation. FASEB J. 2004, 18 (1): 188-190.
CAS
PubMed
Google Scholar
Savoie CJ, Aburatani S, Watanabe S, Eguchi Y, Muta S, Imoto S, Miyano S, Kuhara S, Tashiro K: Use of gene networks from full genome microarray libraries to identify functionally relevant drug-affected genes and gene regulation cascades. DNA Res. 2003, 10 (1): 19-25. 10.1093/dnares/10.1.19.
Article
CAS
PubMed
Google Scholar
Jaffe EA, Nachman RL, Becker CG, Minick CR: Culture of human endothelial cells derived from umbilical veins. Identification by morphologic and immunologic criteria. J Clin Invest. 1973, 52 (11): 2745-2756. 10.1172/JCI107470.
Article
PubMed Central
CAS
PubMed
Google Scholar
Schoenfeld J, Lessan K, Johnson NA, Charnock-Jones DS, Evans A, Vourvouhaki E, Scott L, Stephens R, Freeman TC, Saidi SA, et al: Bioinformatic analysis of primary endothelial cell gene array data illustrated by the analysis of transcriptome changes in endothelial cells exposed to VEGF-A and PlGF. Angiogenesis. 2004, 7 (2): 143-156. 10.1007/s10456-004-1677-0.
Article
CAS
PubMed
Google Scholar
Cleveland WS: Robust Locally Weighted Regression and Smoothing Scatterplots. J Am Stat Assoc. 1979, 74 (368): 829-836. 10.1080/01621459.1979.10481038.
Article
Google Scholar
Tai YC, Speed T: A multivariate empirical Bayes statistic for replicated microarray time course data. Ann Stat. 2006, 34 (5): 2387-2412. 10.1214/009053606000000759.
Article
Google Scholar
Al-Shahrour F, Diaz-Uriarte R, Dopazo J: FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics. 2004, 20 (4): 578-580. 10.1093/bioinformatics/btg455.
Article
CAS
PubMed
Google Scholar
Araki H, Knapp C, Tsai P, Print C. GeneSetDB: a comprehensive meta-database, statistical and visualisation framework for gene set analysis. FEBS Open Bio. 2012, 2 (2012): 76-82.
Article
PubMed Central
PubMed
Google Scholar
Imoto S, Tamada Y, Araki H, Yasuda K, Print CG, Charnock-Jones SD, Sanders D, Savoie CJ, Tashiro K, Kuhara S, et al: Computational strategy for discovering druggable gene networks from genome-wide RNA expression profiles. Pac Symp Biocomput. 2006, 559-571.
Google Scholar
Guo RB, Rigolet P, Ren H, Zhang B, Zhang XD, Dou SX, Wang PY, Amor-Gueret M, Xi XG: Structural and functional analyses of disease-causing missense mutations in Bloom syndrome protein. Nucleic Acids Res. 2007, 35 (18): 6297-6310. 10.1093/nar/gkm536.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lan Y, Zhang Y, Wang J, Lin C, Ittmann MM, Wang F: Aberrant expression of Cks1 and Cks2 contributes to prostate tumorigenesis by promoting proliferation and inhibiting programmed cell death. Int J Cancer. 2008, 123 (3): 543-551. 10.1002/ijc.23548.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wang XC, Tian LL, Tian J, Wu HL, Meng AM: Overexpression of Cks1 is associated with poor survival by inhibiting apoptosis in breast cancer. J Cancer Res Clin Oncol. 2009, 135 (10): 1393-1401. 10.1007/s00432-009-0582-8.
Article
CAS
PubMed
Google Scholar
Wang Y, Xing H, Tian Z, Tang K, Wang J, Xu Z, Rao Q, Wang M, Wang J: Overexpression of Midkine promotes the viability of BA/F3 cells. Biochem Biophys Res Commun. 2009, 384 (3): 341-346. 10.1016/j.bbrc.2009.04.119.
Article
CAS
PubMed
Google Scholar
Kerbel RS: Vasohibin: the feedback on a new inhibitor of angiogenesis. J Clin Invest. 2004, 114 (7): 884-886.
Article
PubMed Central
CAS
PubMed
Google Scholar
Watanabe K, Hasegawa Y, Yamashita H, Shimizu K, Ding Y, Abe M, Ohta H, Imagawa K, Hojo K, Maki H, et al: Vasohibin as an endothelium-derived negative feedback regulator of angiogenesis. J Clin Invest. 2004, 114 (7): 898-907.
Article
PubMed Central
CAS
PubMed
Google Scholar
Shimizu K, Watanabe K, Yamashita H, Abe M, Yoshimatsu H, Ohta H, Sonoda H, Sato Y: Gene regulation of a novel angiogenesis inhibitor, vasohibin, in endothelial cells. Biochem Biophys Res Commun. 2005, 327 (3): 700-706. 10.1016/j.bbrc.2004.12.073.
Article
CAS
PubMed
Google Scholar
Chen Y, Zhu J, Lum PY, Yang X, Pinto S, MacNeil DJ, Zhang C, Lamb J, Edwards S, Sieberts SK, et al: Variations in DNA elucidate molecular networks that cause disease. Nature. 2008, 452 (7186): 429-435. 10.1038/nature06757.
Article
PubMed Central
CAS
PubMed
Google Scholar
Emilsson V, Thorleifsson G, Zhang B, Leonardson AS, Zink F, Zhu J, Carlson S, Helgason A, Walters GB, Gunnarsdottir S, et al: Genetics of gene expression and its effect on disease. Nature. 2008, 452 (7186): 423-428. 10.1038/nature06758.
Article
CAS
PubMed
Google Scholar
Lamb J, Crawford ED, Peck D, Modell JW, Blat IC, Wrobel MJ, Lerner J, Brunet JP, Subramanian A, Ross KN, et al: The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science. 2006, 313 (5795): 1929-1935. 10.1126/science.1132939.
Article
CAS
PubMed
Google Scholar
Wang L, Hurley DG, Watkins W, Araki H, Tamada Y, Muthukaruppan A, Ranjard L, Derkac E, Imoto S, Miyano S, et al: Cell cycle gene networks are associated with melanoma prognosis. PLoS One. 2012, 7 (4): e34247-10.1371/journal.pone.0034247.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hurley D, Araki H, Tamada Y, Dunmore B, Sanders D, Humphreys S, Affara M, Imoto S, Yasuda K, Tomiyasu Y, et al: Gene network inference and visualization tools for biologists: application to new human transcriptome datasets. Nucleic Acids Res. 2012, 40 (6): 2377-2398. 10.1093/nar/gkr902.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kern J, Bauer M, Rychli K, Wojta J, Ritsch A, Gastl G, Gunsilius E, Untergasser G: Alternative splicing of vasohibin-1 generates an inhibitor of endothelial cell proliferation, migration, and capillary tube formation. Arterioscler Thromb Vasc Biol. 2008, 28 (3): 478-484. 10.1161/ATVBAHA.107.160432.
Article
CAS
PubMed
Google Scholar
Pearse RN, Swendeman SL, Li Y, Rafii D, Hempstead BL: A neurotrophin axis in myeloma: TrkB and BDNF promote tumor-cell survival. Blood. 2005, 105 (11): 4429-4436. 10.1182/blood-2004-08-3096.
Article
CAS
PubMed
Google Scholar
Kermani P, Hempstead B: Brain-derived neurotrophic factor: a newly described mediator of angiogenesis. Trends Cardiovasc Med. 2007, 17 (4): 140-143. 10.1016/j.tcm.2007.03.002.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kermani P, Rafii D, Jin DK, Whitlock P, Schaffer W, Chiang A, Vincent L, Friedrich M, Shido K, Hackett NR, et al: Neurotrophins promote revascularization by local recruitment of TrkB+ endothelial cells and systemic mobilization of hematopoietic progenitors. J Clin Invest. 2005, 115 (3): 653-663.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kern J, Steurer M, Gastl G, Gunsilius E, Untergasser G: Vasohibin inhibits angiogenic sprouting in vitro and supports vascular maturation processes in vivo. BMC Cancer. 2009, 9: 284-10.1186/1471-2407-9-284.
Article
PubMed Central
PubMed
Google Scholar
Hosaka T, Kimura H, Heishi T, Suzuki Y, Miyashita H, Ohta H, Sonoda H, Moriya T, Suzuki S, Kondo T, et al: Vasohibin-1 expression in endothelium of tumor blood vessels regulates angiogenesis. Am J Pathol. 2009, 175 (1): 430-439. 10.2353/ajpath.2009.080788.
Article
PubMed Central
PubMed
Google Scholar
Sato Y: Is vasohibin-1 for more than angiogenesis inhibition?. J Biochem. 2011, 149 (3): 229-230. 10.1093/jb/mvq152.
Article
CAS
PubMed
Google Scholar
Kimura H, Miyashita H, Suzuki Y, Kobayashi M, Watanabe K, Sonoda H, Ohta H, Fujiwara T, Shimosegawa T, Sato Y: Distinctive localization and opposed roles of vasohibin-1 and vasohibin-2 in the regulation of angiogenesis. Blood. 2009, 113 (19): 4810-4818. 10.1182/blood-2008-07-170316.
Article
CAS
PubMed
Google Scholar
Lu C, Han HD, Mangala LS, Ali-Fehmi R, Newton CS, Ozbun L, Armaiz-Pena GN, Hu W, Stone RL, Munkarah A, et al: Regulation of tumor angiogenesis by EZH2. Cancer Cell. 2010, 18 (2): 185-197. 10.1016/j.ccr.2010.06.016.
Article
PubMed Central
CAS
PubMed
Google Scholar
Aderem A: Systems biology: its practice and challenges. Cell. 2005, 121 (4): 511-513. 10.1016/j.cell.2005.04.020.
Article
CAS
PubMed
Google Scholar