10.6084/m9.figshare.c.3878266_D5.v1
Camila Lopes-Ramos
Camila
Lopes-Ramos
Joseph Paulson
Joseph
Paulson
Cho-Yi Chen
Cho-Yi
Chen
Marieke Kuijjer
Marieke
Kuijjer
Maud Fagny
Maud
Fagny
John Platig
John
Platig
Abhijeet Sonawane
Abhijeet
Sonawane
Dawn DeMeo
Dawn
DeMeo
John Quackenbush
John
Quackenbush
Kimberly Glass
Kimberly
Glass
Additional file 1: of Regulatory network changes between cell lines and their tissues of origin
Springer Nature
2017
Regulatory networks
Transcriptome
GTEx
Lymphoblastoid cell lines
Fibroblast cell lines
2017-09-12 05:00:00
Journal contribution
https://springernature.figshare.com/articles/journal_contribution/Additional_file_1_of_Regulatory_network_changes_between_cell_lines_and_their_tissues_of_origin/5401291
Similarity between cell lines and their tissues of origin based on gene expression. (A) Principal component analysis (PCA) was performed to evaluate possible batch effects in the gene expression data. Samples are labeled based on the year the sample was analyzed by the GTEx project, and the plots show the sample separation for the first 7 PCs. (B) Number of genes expressed in each group (LCL, whole blood, fibroblast, skin). Genes were separated into biological classes using the definitions from GENCODE release 19 (GRCh37.p13). (C) PCA of paired samples between the two tissues and cell lines (total of 89 subjects with all four samples) based on the normalized expression of all genes. The primary axis separates samples by tissue; the secondary axis separates primary tissue from cell lines. (D) To access whether the PCA results were dependent on the 89 samples chosen because they were present in all four groups, we repeated the analysis 100 times using 89 randomly selected samples in each group. The left panel shows the projection of the first 2 PCs for one random analysis, and right panel shows the distribution of PC1 and PC2 for each of the 100 analyses. (PDF 267Â kb)