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For: van Ruissen F, Ruijter JM, Schaaf GJ, Asgharnegad L, Zwijnenburg DA, Kool M, Baas F. Evaluation of the similarity of gene expression data estimated with SAGE and Affymetrix GeneChips. BMC Genomics 2005;6:91. [PMID: 15955238 DOI: 10.1186/1471-2164-6-91] [Cited by in Crossref: 44] [Cited by in F6Publishing: 44] [Article Influence: 2.6] [Reference Citation Analysis]
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2 Joshi S, Davies H, Sims LP, Levy SE, Dean J. Ovarian gene expression in the absence of FIGLA, an oocyte-specific transcription factor. BMC Dev Biol 2007;7:67. [PMID: 17567914 DOI: 10.1186/1471-213X-7-67] [Cited by in Crossref: 83] [Cited by in F6Publishing: 42] [Article Influence: 5.5] [Reference Citation Analysis]
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6 Dozmorov M, Wu W, Chakrabarty K, Booth JL, Hurst RE, Coggeshall KM, Metcalf JP. Gene expression profiling of human alveolar macrophages infected by B. anthracis spores demonstrates TNF-alpha and NF-kappab are key components of the innate immune response to the pathogen. BMC Infect Dis 2009;9:152. [PMID: 19744333 DOI: 10.1186/1471-2334-9-152] [Cited by in Crossref: 20] [Cited by in F6Publishing: 19] [Article Influence: 1.5] [Reference Citation Analysis]
7 Cookson W, Liang L, Abecasis G, Moffatt M, Lathrop M. Mapping complex disease traits with global gene expression. Nat Rev Genet. 2009;10:184-194. [PMID: 19223927 DOI: 10.1038/nrg2537] [Cited by in Crossref: 607] [Cited by in F6Publishing: 519] [Article Influence: 46.7] [Reference Citation Analysis]
8 Lee CK, Sunkin SM, Kuan C, Thompson CL, Pathak S, Ng L, Lau C, Fischer S, Mortrud M, Slaughterbeck C, Jones A, Lein E, Hawrylycz M. Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data. Genome Biol 2008;9:R23. [PMID: 18234097 DOI: 10.1186/gb-2008-9-1-r23] [Cited by in Crossref: 25] [Cited by in F6Publishing: 22] [Article Influence: 1.8] [Reference Citation Analysis]
9 Dijkmans TF, van Hooijdonk LW, Schouten TG, Kamphorst JT, Vellinga AC, Meerman JH, Fitzsimons CP, de Kloet ER, Vreugdenhil E. Temporal and functional dynamics of the transcriptome during nerve growth factor-induced differentiation. J Neurochem 2008;105:2388-403. [PMID: 18346208 DOI: 10.1111/j.1471-4159.2008.05338.x] [Cited by in Crossref: 27] [Cited by in F6Publishing: 29] [Article Influence: 2.3] [Reference Citation Analysis]
10 Grigoriadis A, Mackay A, Reis-Filho JS, Steele D, Iseli C, Stevenson BJ, Jongeneel CV, Valgeirsson H, Fenwick K, Iravani M. Establishment of the epithelial-specific transcriptome of normal and malignant human breast cells based on MPSS and array expression data. Breast Cancer Res. 2006;8:R56. [PMID: 17014703 DOI: 10.1186/bcr1604] [Cited by in Crossref: 88] [Cited by in F6Publishing: 94] [Article Influence: 5.9] [Reference Citation Analysis]
11 Bainbridge MN, Warren RL, Hirst M, Romanuik T, Zeng T, Go A, Delaney A, Griffith M, Hickenbotham M, Magrini V, Mardis ER, Sadar MD, Siddiqui AS, Marra MA, Jones SJ. Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics 2006;7:246. [PMID: 17010196 DOI: 10.1186/1471-2164-7-246] [Cited by in Crossref: 101] [Cited by in F6Publishing: 104] [Article Influence: 6.3] [Reference Citation Analysis]
12 Porter D, Yao J, Polyak K. SAGE and related approaches for cancer target identification. Drug Discov Today 2006;11:110-8. [PMID: 16533708 DOI: 10.1016/S1359-6446(05)03694-9] [Cited by in Crossref: 18] [Cited by in F6Publishing: 6] [Article Influence: 1.1] [Reference Citation Analysis]
13 Tillett RL, Ergül A, Albion RL, Schlauch KA, Cramer GR, Cushman JC. Identification of tissue-specific, abiotic stress-responsive gene expression patterns in wine grape (Vitis vinifera L.) based on curation and mining of large-scale EST data sets. BMC Plant Biol 2011;11:86. [PMID: 21592389 DOI: 10.1186/1471-2229-11-86] [Cited by in Crossref: 32] [Cited by in F6Publishing: 22] [Article Influence: 2.9] [Reference Citation Analysis]
14 Pizarro F, Vargas FA, Agosin E. A systems biology perspective of wine fermentations. Yeast 2007;24:977-91. [PMID: 17899563 DOI: 10.1002/yea.1545] [Cited by in Crossref: 60] [Cited by in F6Publishing: 40] [Article Influence: 4.3] [Reference Citation Analysis]
15 Weber AP, Weber KL, Carr K, Wilkerson C, Ohlrogge JB. Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiol 2007;144:32-42. [PMID: 17351049 DOI: 10.1104/pp.107.096677] [Cited by in Crossref: 241] [Cited by in F6Publishing: 228] [Article Influence: 16.1] [Reference Citation Analysis]
16 Kwon MJ, Oh E, Lee S, Roh MR, Kim SE, Lee Y, Choi YL, In YH, Park T, Koh SS, Shin YK. Identification of novel reference genes using multiplatform expression data and their validation for quantitative gene expression analysis. PLoS One 2009;4:e6162. [PMID: 19584937 DOI: 10.1371/journal.pone.0006162] [Cited by in Crossref: 75] [Cited by in F6Publishing: 78] [Article Influence: 5.8] [Reference Citation Analysis]
17 Lee TL, Alba D, Baxendale V, Rennert OM, Chan WY. Application of transcriptional and biological network analyses in mouse germ-cell transcriptomes. Genomics 2006;88:18-33. [PMID: 16678385 DOI: 10.1016/j.ygeno.2006.03.008] [Cited by in Crossref: 23] [Cited by in F6Publishing: 18] [Article Influence: 1.4] [Reference Citation Analysis]
18 Zheng W, Wang Z, Collins JE, Andrews RM, Stemple D, Gong Z. Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and mammalian lung. PLoS One 2011;6:e24019. [PMID: 21887364 DOI: 10.1371/journal.pone.0024019] [Cited by in Crossref: 101] [Cited by in F6Publishing: 98] [Article Influence: 9.2] [Reference Citation Analysis]
19 Knoll-Gellida A, André M, Gattegno T, Forgue J, Admon A, Babin PJ. Molecular phenotype of zebrafish ovarian follicle by serial analysis of gene expression and proteomic profiling, and comparison with the transcriptomes of other animals. BMC Genomics 2006;7:46. [PMID: 16526958 DOI: 10.1186/1471-2164-7-46] [Cited by in Crossref: 64] [Cited by in F6Publishing: 62] [Article Influence: 4.0] [Reference Citation Analysis]
20 Depuydt G, Xie F, Petyuk VA, Shanmugam N, Smolders A, Dhondt I, Brewer HM, Camp DG 2nd, Smith RD, Braeckman BP. Reduced insulin/insulin-like growth factor-1 signaling and dietary restriction inhibit translation but preserve muscle mass in Caenorhabditis elegans. Mol Cell Proteomics 2013;12:3624-39. [PMID: 24002365 DOI: 10.1074/mcp.M113.027383] [Cited by in Crossref: 60] [Cited by in F6Publishing: 45] [Article Influence: 6.7] [Reference Citation Analysis]
21 Talantov D, Baden J, Jatkoe T, Hahn K, Yu J, Rajpurohit Y, Jiang Y, Choi C, Ross JS, Atkins D, Wang Y, Mazumder A. A quantitative reverse transcriptase-polymerase chain reaction assay to identify metastatic carcinoma tissue of origin. J Mol Diagn 2006;8:320-9. [PMID: 16825504 DOI: 10.2353/jmoldx.2006.050136] [Cited by in Crossref: 75] [Cited by in F6Publishing: 67] [Article Influence: 4.7] [Reference Citation Analysis]
22 Cerdà J, Bobe J, Babin PJ, Admon A, Lubzens E. Functional Genomics and Proteomic Approaches for the Study of Gamete Formation and Viability in Farmed Finfish. Reviews in Fisheries Science 2008;16:56-72. [DOI: 10.1080/10641260802324685] [Cited by in Crossref: 19] [Cited by in F6Publishing: 9] [Article Influence: 1.4] [Reference Citation Analysis]
23 Emmersen J, Heidenblut AM, Høgh AL, Hahn SA, Welinder KG, Nielsen KL. Discarding duplicate ditags in LongSAGE analysis may introduce significant error. BMC Bioinformatics 2007;8:92. [PMID: 17359537 DOI: 10.1186/1471-2105-8-92] [Cited by in Crossref: 6] [Cited by in F6Publishing: 7] [Article Influence: 0.4] [Reference Citation Analysis]
24 Faulkner GJ, Forrest AR, Chalk AM, Schroder K, Hayashizaki Y, Carninci P, Hume DA, Grimmond SM. A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Genomics 2008;91:281-8. [PMID: 18178374 DOI: 10.1016/j.ygeno.2007.11.003] [Cited by in Crossref: 67] [Cited by in F6Publishing: 63] [Article Influence: 4.8] [Reference Citation Analysis]
25 Elkon R, Agami R. Removal of AU bias from microarray mRNA expression data enhances computational identification of active microRNAs. PLoS Comput Biol 2008;4:e1000189. [PMID: 18833292 DOI: 10.1371/journal.pcbi.1000189] [Cited by in Crossref: 4] [Cited by in F6Publishing: 7] [Article Influence: 0.3] [Reference Citation Analysis]
26 Ruzanov P, Riddle DL, Marra MA, McKay SJ, Jones SM. Genes that may modulate longevity in C. elegans in both dauer larvae and long-lived daf-2 adults. Exp Gerontol 2007;42:825-39. [PMID: 17543485 DOI: 10.1016/j.exger.2007.04.002] [Cited by in Crossref: 21] [Cited by in F6Publishing: 20] [Article Influence: 1.4] [Reference Citation Analysis]
27 Wang SM. Understanding SAGE data. Trends Genet 2007;23:42-50. [PMID: 17109989 DOI: 10.1016/j.tig.2006.11.001] [Cited by in Crossref: 52] [Cited by in F6Publishing: 39] [Article Influence: 3.3] [Reference Citation Analysis]
28 't Hoen PA, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RH, de Menezes RX, Boer JM, van Ommen GJ, den Dunnen JT. Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res. 2008;36:e141. [PMID: 18927111 DOI: 10.1093/nar/gkn705] [Cited by in Crossref: 508] [Cited by in F6Publishing: 525] [Article Influence: 36.3] [Reference Citation Analysis]
29 Hu M, Polyak K. Serial analysis of gene expression. Nat Protoc 2006;1:1743-60. [PMID: 17487157 DOI: 10.1038/nprot.2006.269] [Cited by in Crossref: 25] [Cited by in F6Publishing: 14] [Article Influence: 1.7] [Reference Citation Analysis]
30 Sohal D, Yeatts A, Ye K, Pellagatti A, Zhou L, Pahanish P, Mo Y, Bhagat T, Mariadason J, Boultwood J, Melnick A, Greally J, Verma A. Meta-analysis of microarray studies reveals a novel hematopoietic progenitor cell signature and demonstrates feasibility of inter-platform data integration. PLoS One 2008;3:e2965. [PMID: 18698424 DOI: 10.1371/journal.pone.0002965] [Cited by in Crossref: 17] [Cited by in F6Publishing: 16] [Article Influence: 1.2] [Reference Citation Analysis]
31 Nygaard V, Liu F, Holden M, Kuo WP, Trimarchi J, Ohno-Machado L, Cepko CL, Frigessi A, Glad IK, Wiel MA, Hovig E, Lyng H. Validation of oligoarrays for quantitative exploration of the transcriptome. BMC Genomics 2008;9:258. [PMID: 18513391 DOI: 10.1186/1471-2164-9-258] [Cited by in Crossref: 4] [Cited by in F6Publishing: 3] [Article Influence: 0.3] [Reference Citation Analysis]
32 Nelson PT, Wang WX, Wilfred BR, Tang G. Technical variables in high-throughput miRNA expression profiling: much work remains to be done. Biochim Biophys Acta 2008;1779:758-65. [PMID: 18439437 DOI: 10.1016/j.bbagrm.2008.03.012] [Cited by in Crossref: 65] [Cited by in F6Publishing: 72] [Article Influence: 4.6] [Reference Citation Analysis]
33 Hornshøj H, Bendixen E, Conley LN, Andersen PK, Hedegaard J, Panitz F, Bendixen C. Transcriptomic and proteomic profiling of two porcine tissues using high-throughput technologies. BMC Genomics 2009;10:30. [PMID: 19152685 DOI: 10.1186/1471-2164-10-30] [Cited by in Crossref: 51] [Cited by in F6Publishing: 48] [Article Influence: 3.9] [Reference Citation Analysis]
34 Liu F, Jenssen TK, Trimarchi J, Punzo C, Cepko CL, Ohno-Machado L, Hovig E, Kuo WP. Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates. BMC Genomics 2007;8:153. [PMID: 17555589 DOI: 10.1186/1471-2164-8-153] [Cited by in Crossref: 48] [Cited by in F6Publishing: 49] [Article Influence: 3.2] [Reference Citation Analysis]
35 Jung YC, Hong SJ, Kim YH, Kim SJ, Kang SJ, Choi SW, Rhyu MG. Chromosomal losses are associated with hypomethylation of the gene-control regions in the stomach with a low number of active genes. J Korean Med Sci 2008;23:1068-89. [PMID: 19119454 DOI: 10.3346/jkms.2008.23.6.1068] [Cited by in Crossref: 7] [Cited by in F6Publishing: 6] [Article Influence: 0.5] [Reference Citation Analysis]
36 Thompson FJ, Barker GL, Hughes L, Wilkes CP, Coghill J, Viney ME. A microarray analysis of gene expression in the free-living stages of the parasitic nematode Strongyloides ratti. BMC Genomics 2006;7:157. [PMID: 16784522 DOI: 10.1186/1471-2164-7-157] [Cited by in Crossref: 20] [Cited by in F6Publishing: 19] [Article Influence: 1.3] [Reference Citation Analysis]
37 Li YJ, Xu P, Qin X, Schmechel DE, Hulette CM, Haines JL, Pericak-Vance MA, Gilbert JR. A comparative analysis of the information content in long and short SAGE libraries. BMC Bioinformatics 2006;7:504. [PMID: 17109755 DOI: 10.1186/1471-2105-7-504] [Cited by in Crossref: 6] [Cited by in F6Publishing: 7] [Article Influence: 0.4] [Reference Citation Analysis]
38 Li Z, Zheng W, Wang Z, Zeng Z, Zhan H, Li C, Zhou L, Yan C, Spitsbergen JM, Gong Z. A transgenic zebrafish liver tumor model with inducible Myc expression reveals conserved Myc signatures with mammalian liver tumors. Dis Model Mech. 2013;6:414-423. [PMID: 23038063 DOI: 10.1242/dmm.010462] [Cited by in Crossref: 59] [Cited by in F6Publishing: 53] [Article Influence: 5.9] [Reference Citation Analysis]
39 Li S, Li YH, Wei T, Su EW, Duffin K, Liao B. Too much data, but little inter-changeability: a lesson learned from mining public data on tissue specificity of gene expression. Biol Direct 2006;1:33. [PMID: 17064414 DOI: 10.1186/1745-6150-1-33] [Cited by in Crossref: 6] [Cited by in F6Publishing: 6] [Article Influence: 0.4] [Reference Citation Analysis]
40 van Ruissen F, Schaaf GJ, Kool M, Baas F, Ruijter JM. Scaling of gene expression data allowing the comparison of different gene expression platforms. Methods Mol Biol 2008;387:169-83. [PMID: 18287631 DOI: 10.1007/978-1-59745-454-4_13] [Cited by in Crossref: 3] [Cited by in F6Publishing: 4] [Article Influence: 0.2] [Reference Citation Analysis]
41 Kavak E, Najafov A, Ozturk N, Seker T, Cavusoglu K, Aslan T, Duru AD, Saygili T, Hoxhaj G, Hiz MC, Unal DO, Birgül-iyison N, Ozturk M, Koman A. Analysis of the Wnt/B-catenin/TCF4 pathway using SAGE, genome-wide microarray and promoter analysis: Identification of BRI3 and HSF2 as novel targets. Cellular Signalling 2010;22:1523-35. [DOI: 10.1016/j.cellsig.2010.05.021] [Cited by in Crossref: 8] [Cited by in F6Publishing: 11] [Article Influence: 0.7] [Reference Citation Analysis]
42 Fan J, Peng Z, Zhou C, Qiu G, Tang H, Sun Y, Wang X, Li Q, Le X, Xie K. Gene-expression profiling in Chinese patients with colon cancer by coupling experimental and bioinformatic genomewide gene-expression analyses: identification and validation of IFITM3 as a biomarker of early colon carcinogenesis. Cancer. 2008;113:266-275. [PMID: 18470904 DOI: 10.1002/cncr.23551] [Cited by in Crossref: 29] [Cited by in F6Publishing: 31] [Article Influence: 2.1] [Reference Citation Analysis]
43 Lindlöf A, Bräutigam M, Chawade A, Olsson O, Olsson B. Evaluation of combining several statistical methods with a flexible cutoff for identifying differentially expressed genes in pairwise comparison of EST sets. Bioinform Biol Insights 2008;2:215-37. [PMID: 19812778 DOI: 10.4137/bbi.s431] [Cited by in Crossref: 2] [Cited by in F6Publishing: 1] [Article Influence: 0.1] [Reference Citation Analysis]
44 Castelein N, Hoogewijs D, De Vreese A, Braeckman BP, Vanfleteren JR. Dietary restriction by growth in axenic medium induces discrete changes in the transcriptional output of genes involved in energy metabolism inCaenorhabditis elegans. Biotechnol J 2008;3:803-12. [DOI: 10.1002/biot.200800003] [Cited by in Crossref: 20] [Cited by in F6Publishing: 16] [Article Influence: 1.4] [Reference Citation Analysis]