Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data

BMC Bioinformatics

Volumn 18, Issue 1, 2017, Pages

  Paulson, Joseph N ^a,b,d   Chen, Cho Yi ^a,b   Lopes Ramos, Camila M ^a,b   Kuijjer, Marieke L ^a,b   Platig, John ^a,b   Sonawane, Abhijeet R ^c   Fagny, Maud ^a,b   Glass, Kimberly ^a,b,c   Quackenbush, John ^a,b,c  

^a DANA FARBER CANCER INSTITUTE   (United States)

^b HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^c BRIGHAM AND WOMEN S HOSPITAL   (United States)

^d GENENTECH INC   (United States)

Author keywords

Filtering; GTEx; Normalization; Preprocessing; Quality control; RNA Seq

Indexed keywords

FILTRATION; GENE EXPRESSION; PIPELINES; QUALITY ASSURANCE; RNA; TISSUE; WOOL; YARN;

ANALYTICAL CHALLENGE; COMPLEX DATASETS; GTEX; NORMALIZATION; PREPROCESSING; SOFTWARE PIPELINE; TISSUE EXPRESSION; TRANSCRIPTIONAL PROFILING;

QUALITY CONTROL;

ANTIBODY SPECIFICITY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; HUMAN; MOLECULAR GENETICS; PRINCIPAL COMPONENT ANALYSIS; PROCEDURES; QUALITY CONTROL; SAMPLE SIZE; SEQUENCE ANALYSIS; SOFTWARE; STANDARD; STANDARDS;

DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; MOLECULAR SEQUENCE ANNOTATION; ORGAN SPECIFICITY; PRINCIPAL COMPONENT ANALYSIS; QUALITY CONTROL; REFERENCE STANDARDS; SAMPLE SIZE; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 85030313053     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-017-1847-x     Document Type: Article

References (27)

1. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis. Cell. 2008;133:523-36.
2. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008;5:621-8.
3. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M: The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing. Science (80- ) 2008, 320:1344-1349.
4. Eisenberg E, Levanon EY. Human housekeeping genes, revisited. Trends Genet. 2013:569-74.
5. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002;3:RESEARCH0034.
6. Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003;19:185-93.
7. Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A. A survey of best practices for RNA-seq data analysis. Genome Biol. 2016;17:13.
8. Ardlie KG, Deluca DS, Segre A V., Sullivan TJ, Young TR, Gelfand ET, Trowbridge CA, Maller JB, Tukiainen T, Lek M, Ward LD, Kheradpour P, Iriarte B, Meng Y, Palmer CD, Esko T, Winckler W, Hirschhorn JN, Kellis M, MacArthur DG, Getz G, Shabalin AA, Li G, Zhou Y-H, Nobel AB, Rusyn I, Wright FA, Lappalainen T, Ferreira PG, Ongen H, et al.: The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans. Science (80- ) 2015, 348:648-660.
9. McLendon R, Friedman A, Bigner D, Van Meir EG, Brat DJ, Mastrogianakis MG, Olson JJ, Mikkelsen T, Lehman N, Aldape K, Alfred Yung WK, Bogler O, VandenBerg S, Berger M, Prados M, Muzny D, Morgan M, Scherer S, Sabo A, Nazareth L, Lewis L, Hall O, Zhu Y, Ren Y, Alvi O, Yao J, Hawes A, Jhangiani S, Fowler G, San Lucas A, et al. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008;455:1061-8.
10. Toker L, Feng M, Pavlidis P. Whose sample is it anyway? Widespread misannotation of samples in transcriptomics studies. F1000Research. 2016;5:2103.
11. Glass K, Quackenbush J, Silverman EK, Celli B, Rennard SI, Yuan G-C, DeMeo DL. Sexually-dimorphic targeting of functionally-related genes in COPD. BMC Syst Biol. 2014;8:118.
12. Gower JC. Some Distance Properties of Latent Root and Vector Methods Used in Multivariate Analysis. Biometrika. 1966;53:325-38.
13. Januszyk M, Rennert R, Sorkin M, Maan Z, Wong L, Whittam A, Whitmore A, Duscher D, Gurtner G. Evaluating the Effect of Cell Culture on Gene Expression in Primary Tissue Samples Using Microfluidic-Based Single Cell Transcriptional Analysis. Microarrays. 2015;4:540-50.
14. Lopes-Ramos CM, Paulson JN, Chen C-Y, Kuijjer ML, Fagny M, Platig J, Sonawane AR, DeMeo DL, Quackenbush J, Glass K. Regulatory network changes between cell lines and their tissues of origin. BMC Genomics. 2017;1:723.
15. Fagny M, Paulson JN, Kuijjer ML, Sonawane AR, Chen C-Y, Lopes-Ramos CM, Glass K, Quackenbush J, Platig J. Exploring regulation in tissues with eQTL networks. Proc Natl Acad Sci. 2017;114(37):E7841-50.
16. Schlauch D, Paulson JN, Young A, Glass K, Quackenbush J. Estimating Gene Regulatory Networks withpandaR. Bioinformatics. 2017;33(14):2232-234.
17. Sonawane AR, Paulson JN, Fagny M, Chen C-Y, Lopes-Ramos CM, Platig J, Quackenbush J, Glass K, Kuijjer ML. Understanding tissue-specific gene regulation. Cell Reports. 2017. In press.
18. Chen C-Y, Lopes-Ramos C, Kuijjer M, Paulson JN, Sonawane AR, Fagny M, Platig J, Glass K, Quackenbush J, DeMeo DL. Sexual dimorphism in gene expression and regulatory networks across human tissues. bioRxiv. 2016;82289.
19. Bourgon R, Gentleman R, Huber W. Independent filtering increases detection power for high-throughput experiments. Proc Natl Acad Sci. 2010;107:9546-51.
20. Law CW, Chen Y, Shi W, Smyth GK. Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 2014;15:R29.
21. Hawthorne SK, Goodarzi G, Bagarova J, Gallant KE, Busanelli RR, Olend WJ, Kleene KC. Comparative genomics of the sperm mitochondria-associated cysteine-rich protein gene. Genomics. 2006;87:382-91.
22. Takahashi A, Hirohashi Y, Torigoe T, Tamura Y, Tsukahara T, Kanaseki T, Kochin V, Saijo H, Kubo T, Nakatsugawa M, Asanuma H, Hasegawa T, Kondo T, Sato N. Ectopically Expressed Variant Form of Sperm Mitochondria-Associated Cysteine-Rich Protein Augments Tumorigenicity of the Stem Cell Population of Lung Adenocarcinoma Cells. PLoS One. 2013;8:e69095.
23. Rau A, Gallopin M, Celeux G, Jaffrézic F. Gene expression Data-based filtering for replicated high-throughput transcriptome sequencing experiments. Bioinformatics. 2013;29:2146-52.
24. Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010;11:R25.
25. Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11:R106.
26. Bullard JH, Purdom E, Hansen KD, Dudoit S. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics. 2010;11:94.
27. Hicks SC, Okrah K, Paulson JN, Quackenbush J, Irizarry RA, Bravo C, Bravo HC. Smooth quantile normalization. Biostatistics. 2017;85175:1465-4644.