Dataset Open Access
Sonawane, Abhijeet R; Platig, John; Fagny, Maud; Chen, Cho-Yi; Paulson, Joseph N; Lopes-Ramos, Camila M; DeMeo, Dawn L; Quackenbush, John; Glass, Kimberly; Kuijjer, Marieke Lydia
We reconstructed gene regulatory networks for 38 tissues from the Genotype-Tissue Expression project (GTEx), and used these networks to investigate gene expression and regulation across these tissues. In the RData file, we share the following objects:
- edges: an 19,476,492 by 3 data.frame including three columns: TF (the transcription factor's gene symbol), Gene (Ensembl ID), Prior (whether an edge is canonical (1) or non-canonical (0)).
- exp: a 30,243 by 9,435 matrix including normalized expression data for each sample.
- expTS: a 30,243 by 38 matrix including, for each gene and each tissue, information on whether the gene is expressed in a tissue-specific manner in that tissue (1) or not (0).
- genes: a 30,243 by 4 data.frame that includes annotation information (Symbol) for Ensembl gene IDs (Name). This data.frame also includes information on whether genes are also transcription factors (AlsoTF), with options: no, yes/motif (TF with a known DNA-binding motif) yes/nomotif (TF without a known DNA-binding motif). In addition, the multiplicity of the gene (Multiplicity) is given.
- net: a 19,476,492 by 38 matrix that includes edge weights for each tissue. Edge order corresponds to edge order in the the object "edges".
- netTS: a 19,476,492 by 38 matrix that includes information of whether edges are specific to a tissue (1) or not (0).
- samples: a 9,435 by 2 data.frame that includes sample identifiers (matching the identifiers in "exp") and the tissue to which these samples belong.