Author: Timothy A. Dinh; Ramja Sritharan; F. Donelson Smith; Adam B. Francisco; Rosanna K. Ma; Rodica P. Bunaciu; Matt Kanke; Charles G. Danko; Andrew P. Massa; John D. Scott; Praveen Sethupathy
Title: Hotspots of aberrant enhancer activity in fibrolamellar carcinoma reveal molecular mechanisms of oncogenesis and intrinsic drug resistance Document date: 2020_1_18
ID: bf4qpsy7_6
Snippet: In order to identify TREs that are more actively transcribed in FLC relative to NML, we quantified ChRO-seq reads within each TRE across all samples and used the DESeq2 algorithm (Love et al., 2014) to perform differential transcription analysis ( Fig. 2A) . This approach led to the identification of 6824 TREs that are significantly more actively transcribed in FLC (Fig. 2B ,C; FDR < 0.05, log2(fold change) > 0). We refer to these as FLC-specific.....
Document: In order to identify TREs that are more actively transcribed in FLC relative to NML, we quantified ChRO-seq reads within each TRE across all samples and used the DESeq2 algorithm (Love et al., 2014) to perform differential transcription analysis ( Fig. 2A) . This approach led to the identification of 6824 TREs that are significantly more actively transcribed in FLC (Fig. 2B ,C; FDR < 0.05, log2(fold change) > 0). We refer to these as FLC-specific TREs. We also identified 1317 NMLspecific TREs. Most FLC-and NML-specific TREs are located in intronic, intergenic, and TSS regions and do not show major differences in TRE length (Fig S2A,B) .
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