RT Journal Article
SR Electronic
T1 Human splicing diversity across the Sequence Read Archive
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 038224
DO 10.1101/038224
A1 Abhinav Nellore
A1 Andrew E. Jaffe
A1 Jean-Philippe Fortin
A1 José Alquicira-Hernández
A1 Leonardo Collado-Torres
A1 Siruo Wang
A1 Robert A. Phillips III
A1 Nishika Karbhari
A1 Kasper D. Hansen
A1 Ben Langmead
A1 Jeffrey T. Leek
YR 2016
UL http://biorxiv.org/content/early/2016/01/29/038224.abstract
AB We aligned 21,504 publicly available Illumina-sequenced human RNA-seq samples from the Sequence Read Archive (SRA) to the human genome and compared detected exon-exon junctions with junctions in several recent gene annotations. 56,865 junctions (18.6%) found in at least 1,000 samples were not annotated, and their expression associated with tissue type. Newer samples contributed few novel well-supported junctions, with 96.1% of junctions detected in at least 20 reads across samples present in samples before 2013. Junction data is compiled into a resource called intropolis available at http://intropolis.rail.bio. We discuss an application of this resource to cancer involving a recently validated isoform of the ALK gene.