title: Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets.
abstract: BACKGROUND
  High throughput parallel sequencing, RNA-Seq, has recently emerged as an appealing alternative to microarray in identifying differentially expressed genes (DEG) between biological groups. However, there still exists considerable discrepancy on gene expression measurements and DEG results between the two platforms. The objective of this study was to compare parallel paired-end RNA-Seq and microarray data generated on 5-azadeoxy-cytidine (5-Aza) treated HT-29 colon cancer cells with an additional simulation study.
  
  
  METHODS
  We first performed general correlation analysis comparing gene expression profiles on both platforms. An Errors-In-Variables (EIV) regression model was subsequently applied to assess proportional and fixed biases between the two technologies. Then several existing algorithms, designed for DEG identification in RNA-Seq and microarray data, were applied to compare the cross-platform overlaps with respect to DEG lists, which were further validated using qRT-PCR assays on selected genes. Functional analyses were subsequently conducted using Ingenuity Pathway Analysis (IPA).
  
  
  RESULTS
  Pearson and Spearman correlation coefficients between the RNA-Seq and microarray data each exceeded 0.80, with 66%~68% overlap of genes on both platforms. The EIV regression model indicated the existence of both fixed and proportional biases between the two platforms. The DESeq and baySeq algorithms (RNA-Seq) and the SAM and eBayes algorithms (microarray) achieved the highest cross-platform overlap rate in DEG results from both experimental and simulated datasets. DESeq method exhibited a better control on the false discovery rate than baySeq on the simulated dataset although it performed slightly inferior to baySeq in the sensitivity test. RNA-Seq and qRT-PCR, but not microarray data, confirmed the expected reversal of SPARC gene suppression after treating HT-29 cells with 5-Aza. Thirty-three IPA canonical pathways were identified by both microarray and RNA-Seq data, 152 pathways by RNA-Seq data only, and none by microarray data only.
  
  
  CONCLUSIONS
  These results suggest that RNA-Seq has advantages over microarray in identification of DEGs with the most consistent results generated from DESeq and SAM methods. The EIV regression model reveals both fixed and proportional biases between RNA-Seq and microarray. This may explain in part the lower cross-platform overlap in DEG lists compared to those in detectable genes.
authors.affiliation: School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA.
authors.forename: Xiao
authors.initials: X
authors.lastname: Xu
authors.forename: Yuanhao
authors.initials: Y
authors.lastname: Zhang
authors.forename: Jennie
authors.initials: J
authors.lastname: Williams
authors.forename: Eric
authors.initials: E
authors.lastname: Antoniou
authors.forename: W Richard
authors.initials: WR
authors.lastname: McCombie
authors.forename: Song
authors.initials: S
authors.lastname: Wu
authors.forename: Wei
authors.initials: W
authors.lastname: Zhu
authors.forename: Nicholas O
authors.initials: NO
authors.lastname: Davidson
authors.forename: Paula
authors.initials: P
authors.lastname: Denoya
authors.forename: Ellen
authors.initials: E
authors.lastname: Li
mesh_terms: D000465:Algorithms; D001374:Azacitidine; D003110:Colonic Neoplasms / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods*; D019073:HT29 Cells; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012334:RNA, Neoplasm / Q000235:genetics; D012044:Regression Analysis; D012680:Sensitivity and Specificity; D017423:Sequence Analysis, RNA / Q000379:methods
chemical_list: D012334:RNA, Neoplasm; D001374:Azacitidine
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