Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

Analysis of TCGA pan-cancer ATAC-seq data

GC Giulia Della Chiara
FG Federica Gervasoni
MF Michaela Fakiola
CG Chiara Godano
CD Claudia D’Oria
LA Luca Azzolin
RB Raoul Jean Pierre Bonnal
GM Giulia Moreni
LD Lorenzo Drufuca
GR Grazisa Rossetti
VR Valeria Ranzani
RB Ramona Bason
MS Marco De Simone
FP Francesco Panariello
IF Ivan Ferrari
TF Tanya Fabbris
FZ Francesca Zanconato
MF Mattia Forcato
OR Oriana Romano
JC Jimmy Caroli
PG Paola Gruarin
MS Maria Lucia Sarnicola
MC Michelangelo Cordenonsi
AB Alberto Bardelli
NZ Nicola Zucchini
AC Andrea Pisani Ceretti
NM Nicolò Maria Mariani
AC Andrea Cassingena
AS Andrea Sartore-Bianchi
GT Giuseppe Testa
LG Luca Gianotti
EO Enrico Opocher
FP Federica Pisati
CT Claudio Tripodo
GM Giuseppe Macino
SS Salvatore Siena
SB Silvio Bicciato
SP Stefano Piccolo
MP Massimiliano Pagani
request Request a Protocol
ask Ask a question
Favorite

To identify potential pan-cancer regulatory regions, pan-cancer ATAC-seq peak sets from the TCGA consortium were used (https://gdc.cancer.gov/about-data/publications/ATACseq-AWG/)17. The pan-cancer peakset was overlapped with the YAP/TAZ-bound gained enhancers conserved in at least eight patients (n = 195). If multiple ATAC-seq peaks were assigned to each enhancer only that with the highest normalized enrichment score was considered. Then, the normalized ATAC-seq insertion counts of the pan-cancer peak sets was downloaded from TCGA site (https://gdc.cancer.gov/about-data/publications/ATACseq-AWG/) and was used to produce a heatmap (pheatmap; clustering_distance_cols = euclidean, clustering_method = complete) of all the TCGA patients and the 195 enhancer regions of interest. To identify pan-cancer accessible regions, we performed hierarchical clustering with cluster_rows = TRUE.

Copyright and License information: The Author(s) ©2021
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

post Post a Question
0 Q&A