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FANTOM5 cell specificity enrichment analysis

MB Mette Boyd
MT Malte Thodberg
MV Morana Vitezic
JB Jette Bornholdt
KV Kristoffer Vitting-Seerup
YC Yun Chen
MC Mehmet Coskun
YL Yuan Li
BL Bobby Zhao Sheng Lo
PK Pia Klausen
PS Pawel Jan Schweiger
AP Anders Gorm Pedersen
NR Nicolas Rapin
KS Kerstin Skovgaard
KD Katja Dahlgaard
RA Robin Andersson
TT Thilde Bagger Terkelsen
BL Berit Lilje
JT Jesper Thorvald Troelsen
AP Andreas Munk Petersen
KJ Kim Bak Jensen
IG Ismail Gögenur
PT Peter Thielsen
JS Jakob Benedict Seidelin
ON Ole Haagen Nielsen
JB Jacob Tveiten Bjerrum
AS Albin Sandelin
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For TSSs that were differentially expressed, we performed enrichment tests for FANTOM5 cell specificity of TSSs. We downloaded the table of cell type specificity of CAGE tag clusters from http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/. For each TSS, we noted whether it was differentially expressed and if it overlapped (based on genomic coordinates) with a FANTOM5 cell-specific tag cluster. We used the table function from base R to create a 2 × 2 contingency table for differential expression statistics and cell specificity, and tested for independence between rows and columns of this table using a Fisher’s Exact test (via R’s fisher.test). P-values for each cell category were corrected for multiple testing using the Benjamini–Hochberg method. The complete table of statistics for all cell type terms can be found in Supplementary Data 8.

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