Title: Gene regulatory networks for 38 human tissues

Type Dataset 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 (2017): Gene regulatory networks for 38 human tissues. Zenodo. Dataset. https://zenodo.org/record/838734

Authors: Sonawane, Abhijeet R (Channing Institute for Network Medicine, Brigham and Women's Hospital, Harvard Medical School) ; Platig, John (Dana-Farber Cancer Institute, Harvard TH Chan School of Public Health) ; Fagny, Maud (Dana-Farber Cancer Institute, Harvard TH Chan School of Public Health) ; Chen, Cho-Yi (Dana-Farber Cancer Institute, Harvard TH Chan School of Public Health) ; Paulson, Joseph N (Dana-Farber Cancer Institute, Harvard TH Chan School of Public Health) ; Lopes-Ramos, Camila M (Dana-Farber Cancer Institute, Harvard TH Chan School of Public Health) ; DeMeo, Dawn L (Channing Institute for Network Medicine, Brigham and Women's Hospital, Harvard Medical School) ; Quackenbush, John (Dana-Farber Cancer Institute, Harvard TH Chan School of Public Health) ; Glass, Kimberly (Channing Institute for Network Medicine, Brigham and Women's Hospital, Harvard Medical School) ; Kuijjer, Marieke Lydia (Dana-Farber Cancer Institute, Harvard TH Chan School of Public Health) ; Kuijjer, Marieke Lydia (Dana-Farber Cancer Institute, Harvard TH Chan School of Public Health) ; Glass, Kimberly (Channing Institute for Network Medicine, Brigham and Women's Hospital, Harvard Medical School) ;

Links

• Item record in Zenodo
• Digital object URL

Summary

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.

More information

• DOI: 10.5281/zenodo.838734

Subjects

• regulatory networks, gene regulation, gene regulatory networks, tissue-specificity, GTEx, gene expression, transcriptome, network biology, transcriptional regulation

Dates

• Publication date: 2017
• Issued: August 03, 2017

Notes

Rights

• https://creativecommons.org/licenses/by-nd/4.0/legalcode Creative Commons Attribution No Derivatives 4.0 International
• info:eu-repo/semantics/openAccess Open Access

Format

electronic resource

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