A comparative analysis of tissue gene expression data from high-throughput studies

Chinese Science Bulletin

Volumn 57, Issue 22, 2012, Pages 2920-2927

  Ping, Jie ^a   Wang, YaJun ^a   Yu, Yao ^b   Li, YiXue ^a,b   Li, Xuan ^b   Hao, Pei ^b  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

^b Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

Author keywords

comparative analysis; high throughput sequencing; tissue transcriptome

Indexed keywords

EID: 84865489429     PISSN: 10016538     EISSN: 18619541     Source Type: Journal    
DOI: 10.1007/s11434-012-5077-3     Document Type: Article

References (33)

1. Wang Z, Gerstein M, Snyder M. RNA-Seq: A revolutionary tool for transcriptomics. Nat Rev Genet, 2009, 10: 57-63.
2. Attardo G M, Ribeiro J M, Wu Y, et al. Transcriptome analysis of reproductive tissue and intrauterine developmental stages of the tsetse fly (Glossina morsitans morsitans). BMC Genomics, 2010, 11: 160.
3. Lincecum J M, Vieira F G, Wang M Z, et al. From transcriptome analysis to therapeutic anti-CD40L treatment in the SOD1 model of amyotrophic lateral sclerosis. Nat Genet, 2010, 42: 392-399.
4. Velculescu V E, Zhang L, Vogelstein B, et al. Serial analysis of gene expression. Science, 1995, 270: 484-487.
5. Brenner S, Johnson M, Bridgham J, et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol, 2000, 18: 630-634.
6. Sterky F, Regan S, Karlsson J, et al. Gene discovery in the wood-forming tissues of poplar: Analysis of 5, 692 expressed sequence tags. Proc Natl Acad Sci USA, 1998, 95: 13330-13335.
7. Adams M D, Dubnick M, Kerlavage A R, et al. Sequence identification of 2, 375 human brain genes. Nature, 1992, 355: 632-634.
8. Ye S Q, Usher D C, Zhang L Q. Gene expression profiling of human diseases by serial analysis of gene expression. J Biomed Sci, 2002, 9: 384-394.
9. George A J, Gordon L, Beissbarth T, et al. A serial analysis of gene expression profile of the Alzheimer's disease Tg2576 mouse model. Neurotox Res, 2010, 17: 360-379.
10. Reinartz J, Bruyns E, Lin J Z, et al. Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling in all organisms. Brief Funct Genomic Proteomic, 2002, 1: 95-104.
11. Schena M, Shalon D, Davis R W, et al. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 1995, 270: 467-470.
12. Morin R, Bainbridge M, Fejes A, et al. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques, 2008, 45: 81-94.
13. Cloonan N, Forrest A R, Kolle G, et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods, 2008, 5: 613-619.
14. Bertone P, Stolc V, Royce T E, et al. Global identification of human transcribed sequences with genome tiling arrays. Science, 2004, 306: 2242-2246.
15. David L, Huber W, Granovskaia M, et al. A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci USA, 2006, 103: 5320-5325.
16. Sultan M, Schulz M H, Richard H, et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science, 2008, 321: 956-960.
17. Chepelev I, Wei G, Tang Q, et al. Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq. Nucleic Acids Res, 2009, 37: e106.
18. Mortazavi A, Williams B A, McCue K, et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods, 2008, 5: 621-628.
19. Barbazuk W B, Emrich S J, Chen H D, et al. SNP discovery via 454 transcriptome sequencing. Plant J, 2007, 51: 910-918.
20. Marioni J C, Mason C E, Mane S M, et al. RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res, 2008, 18: 1509-1517.
21. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 2009, 25: 1754-1760.
22. He F. Human liver proteome project: Plan, progress, and perspectives. Mol Cell Prot, 2005, 4: 1841-1848.
23. Gautier L, Cope L, Bolstad B M, et al. Affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics, 2004, 20: 307-315.
24. Yu Y, Ping J, Chen H, et al. A comparative analysis of liver transcriptome suggests divergent liver function among human, mouse and rat. Genomics, 2010, 96: 281-289.
25. Uhlen M, Bjorling E, Agaton C, et al. A human protein atlas for normal and cancer tissues based on antibody proteomics. Mol Cell Prot, 2005, 4: 1920-1932.
26. Mortazavi A, Williams A B, McCue K, et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods, 2008, 5: 621-628.
27. Gilliland D G, Griffin J D. The roles of FLT3 in hematopoiesis and leukemia. Blood, 2002, 100: 1532-1542.
28. Péron J M, Esche C, Subbotin V M, et al. FLT3-ligand administration inhibits liver metastases: Role of NK cells. J Immunol, 1998, 161: 6164-6170.
29. Fausther M, Lecka J, Kukulski F, et al. Cloning, purification, and identification of the liver canalicular ecto-ATPase as NTPDase8. Am J Physiol Gastrointest Liver Physiol, 2007, 292: G785-795.
30. Thedieck C, Kuczyk M, Klingel K, et al. Expression of Ksp-cadherin during kidney development and in renal cell carcinoma. Br J Cancer, 2005, 92: 2010-2017.
31. Thedieck C, Kalbacher H, Kratzer U, et al. Alpha B-crystallin is a cytoplasmic interaction partner of the kidney-specific cadherin-16. J Mol Biol, 2008, 378: 145-153.
32. Planelles G. Ammonium homeostasis and human rhesus lycoproteins. Nephron Physiol, 2006, 105: 11-17.
33. Brown A C, Hallouane D, Mawby W J, et al. RhCG is the major putative ammonia transporter expressed in the human kidney, and RhBG is not expressed at detectable levels. Am J Physiol Renal Physiol, 2009, 296: F1279-1290.