SURF: integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins

Table 1 Overview of the data used by individual modules of SURF

Module	No. of RBPs	Input datasets (sources)
1 – DrSeq	104	104 shRNA-seq with paired control RNA-seq from wild-type condition (ENCODE)
2 – Association	76 ^∗	76 eCLIP-seq with paired control datasets from size-matched input library (ENCODE)
3 – Discovery	54 ^∗∗	173 whole blood RNA-seq (GTEx) and 337 LAML RNA-seq (TCGA)

^*RBPs lacking at least 100 differential ATR events are excluded from the analysis module 2
^**The discovery module studies a subset of RBPs in ^∗ with at least one inferred location feature

ISSN: 1474-760X